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class="external-links-container"><ul class="profile-links new-profile js-UserInfo-social"><li class="profile-profiles js-social-profiles-container"><i class="fa fa-spin fa-spinner"></i></li></ul></div></div></div><div class="right-panel-container"><div class="user-content-wrapper"><div class="uploads-container" id="social-redesign-work-container"><div class="upload-header"><h2 class="ds2-5-heading-sans-serif-xs">Uploads</h2></div><div class="documents-container backbone-social-profile-documents" style="width: 100%;"><div class="u-taCenter"></div><div class="profile--tab_content_container js-tab-pane tab-pane active" id="all"><div class="profile--tab_heading_container js-section-heading" data-section="Papers" id="Papers"><h3 class="profile--tab_heading_container">Papers by James Cotton</h3></div><div class="js-work-strip profile--work_container" data-work-id="8008454"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008454/Phylogenomic_analyses_elucidate_the_evolutionary_relationships_of_bats"><img alt="Research paper thumbnail of Phylogenomic analyses elucidate the evolutionary relationships of bats" class="work-thumbnail" src="https://attachments.academia-assets.com/48255232/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008454/Phylogenomic_analyses_elucidate_the_evolutionary_relationships_of_bats">Phylogenomic analyses elucidate the evolutionary relationships of bats</a></div><div class="wp-workCard_item"><span>Current biology : CB</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal g...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups , yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) . Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic [7-9] or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes , we show that-contrary to recent suggestions-bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="ebbac085c20dc090cd4b5172be74ab9b" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255232,"asset_id":8008454,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255232/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008454"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008454"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008454; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008454]").text(description); $(".js-view-count[data-work-id=8008454]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008454; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008454']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "ebbac085c20dc090cd4b5172be74ab9b" } } $('.js-work-strip[data-work-id=8008454]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008454,"title":"Phylogenomic analyses elucidate the evolutionary relationships of bats","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","ai_title_tag":"Bats' Evolutionary Relationships Revealed","grobid_abstract":"Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups , yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) . Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic [7-9] or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes , we show that-contrary to recent suggestions-bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. 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We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255232,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255232/thumbnails/1.jpg","file_name":"00463528bf07e3d93d000000.pdf","download_url":"https://www.academia.edu/attachments/48255232/download_file","bulk_download_file_name":"Phylogenomic_analyses_elucidate_the_evol.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255232/00463528bf07e3d93d000000-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DPhylogenomic_analyses_elucidate_the_evol.pdf\u0026Expires=1743265560\u0026Signature=FoE26hfm9AQ1~3WOWDoLKFKH-YC1t11xlOX0AOqdLvxshtXfFGNkIrHqqEsQ6JIw0z4NizhAIbPry-mqYLrG85AFIW0LEolZ94gA89tAQfQ5P14FT1bVJBum3U7Fyi-cwv0iL4FIFj4uArPtzOPsqHbJwQZiZ0HxYsQ1jQmCm8aqcT3rQ9ARytR18PFOXKuEWeblAB8mQMTxv9npQgqBt-KhO593vN9~TAx1Ik~oqYHgJMtFMwNznd91p~WZpmHMKoh2qMqjxLg71OvL2RaUsbmK0sh3OJfi-TujrbFetD8YPocPZRKRMQnjvA--e9zT5EtdEvrXw1o3LU4PzgKdWQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":4207,"name":"Phylogenetics","url":"https://www.academia.edu/Documents/in/Phylogenetics"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":4967,"name":"Molecular Evolution","url":"https://www.academia.edu/Documents/in/Molecular_Evolution"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"},{"id":11186,"name":"Mammalogy","url":"https://www.academia.edu/Documents/in/Mammalogy"},{"id":18075,"name":"Bats (Mammalogy)","url":"https://www.academia.edu/Documents/in/Bats_Mammalogy_"},{"id":27230,"name":"Chiroptera","url":"https://www.academia.edu/Documents/in/Chiroptera"},{"id":34912,"name":"Phylogenomics","url":"https://www.academia.edu/Documents/in/Phylogenomics"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":170896,"name":"Echolocation","url":"https://www.academia.edu/Documents/in/Echolocation"},{"id":176486,"name":"Genome","url":"https://www.academia.edu/Documents/in/Genome"},{"id":191815,"name":"Biological evolution","url":"https://www.academia.edu/Documents/in/Biological_evolution"}],"urls":[{"id":3350935,"url":"http://dx.doi.org/10.1016/j.cub.2013.09.014"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008454-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008453"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008453/The_evolution_of_bat_vestibular_systems_in_the_face_of_potential_antagonistic_selection_pressures_for_flight_and_echolocation"><img alt="Research paper thumbnail of The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation" class="work-thumbnail" src="https://attachments.academia-assets.com/48255277/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008453/The_evolution_of_bat_vestibular_systems_in_the_face_of_potential_antagonistic_selection_pressures_for_flight_and_echolocation">The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation</a></div><div class="wp-workCard_item"><span>PloS one</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The vestibular system maintains the body's sense of balance and, therefore, was probably subject ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The vestibular system maintains the body's sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged semicircular canals. Second, many bats have enlarged cochleae associated with echolocation, and both cochleae and semicircular canals share a space within the petrosal bone. To determine how bat vestibular systems have evolved in the face of these pressures, we used micro-CT scans to compare canal morphology across species with contrasting flight and echolocation capabilities. We found no increase in canal radius in bats associated with the acquisition of powered flight, but canal radius did correlate with body mass in bat species from the suborder Yangochiroptera, and also in non-echolocating Old World fruit bats from the suborder Yinpterochiroptera. No such trend was seen in members of the Yinpterochiroptera that use laryngeal echolocation, although canal radius was associated with wing-tip roundedness in this group. We also found that the vestibular system scaled with cochlea size, although the relationship differed in species that use constant frequency echolocation. Across all bats, the shape of the anterior and lateral canals was associated with large cochlea size and small body size respectively, suggesting differential spatial constraints on each canal depending on its orientation within the skull. Thus in many echolocating bats, it seems that the combination of small body size and enlarged cochlea together act as a principal force on the vestibular system. The two main groups of echolocating bats displayed different canal morphologies, in terms of size and shape in relation to body mass and cochlear size, thus suggesting independent evolutionary pathways and offering tentative support for multiple acquisitions of echolocation.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8759fe958ed961cefadc27da0e8ee52a" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255277,"asset_id":8008453,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255277/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008453"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008453"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008453; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008453]").text(description); $(".js-view-count[data-work-id=8008453]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008453; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008453']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "8759fe958ed961cefadc27da0e8ee52a" } } $('.js-work-strip[data-work-id=8008453]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008453,"title":"The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"The vestibular system maintains the body's sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged semicircular canals. Second, many bats have enlarged cochleae associated with echolocation, and both cochleae and semicircular canals share a space within the petrosal bone. To determine how bat vestibular systems have evolved in the face of these pressures, we used micro-CT scans to compare canal morphology across species with contrasting flight and echolocation capabilities. We found no increase in canal radius in bats associated with the acquisition of powered flight, but canal radius did correlate with body mass in bat species from the suborder Yangochiroptera, and also in non-echolocating Old World fruit bats from the suborder Yinpterochiroptera. No such trend was seen in members of the Yinpterochiroptera that use laryngeal echolocation, although canal radius was associated with wing-tip roundedness in this group. We also found that the vestibular system scaled with cochlea size, although the relationship differed in species that use constant frequency echolocation. Across all bats, the shape of the anterior and lateral canals was associated with large cochlea size and small body size respectively, suggesting differential spatial constraints on each canal depending on its orientation within the skull. Thus in many echolocating bats, it seems that the combination of small body size and enlarged cochlea together act as a principal force on the vestibular system. The two main groups of echolocating bats displayed different canal morphologies, in terms of size and shape in relation to body mass and cochlear size, thus suggesting independent evolutionary pathways and offering tentative support for multiple acquisitions of echolocation.","publication_date":{"day":null,"month":null,"year":2013,"errors":{}},"publication_name":"PloS one","grobid_abstract_attachment_id":48255277},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008453/The_evolution_of_bat_vestibular_systems_in_the_face_of_potential_antagonistic_selection_pressures_for_flight_and_echolocation","translated_internal_url":"","created_at":"2014-08-18T01:12:16.404-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255277,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255277/thumbnails/1.jpg","file_name":"The_Evolution_of_Bat_Vestibular_Systems_20160823-28130-dptk1r.pdf","download_url":"https://www.academia.edu/attachments/48255277/download_file","bulk_download_file_name":"The_evolution_of_bat_vestibular_systems.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255277/The_Evolution_of_Bat_Vestibular_Systems_20160823-28130-dptk1r-libre.pdf?1471956956=\u0026response-content-disposition=attachment%3B+filename%3DThe_evolution_of_bat_vestibular_systems.pdf\u0026Expires=1743265560\u0026Signature=RTmqyH~YdjIUkztXGO8zv7iJjXtWrDF40w0As2K7Wu~dh1QbxiDDp9SDI0Q12LdAOvIjERwKINHDjZK3MJZ7fFeMDqr3UzcdS9RbRlWHbe~rQdLtbLfQWr09TvQvfAB3pwOLyzkAI-nKMR3zoogke1c7x~tTc20Y2L-ez0MbrpVxsMUpU5eQzLkV25SZEIdeJCO39GuuGgmreMkuUqI7bniEGZKzt83cnhSDxyp6FzCJTWaeFmbgz~o7hO-brFis2HMjRSLsFx7dzcs2h7Z-eUsOmzP-OUASfv8hfSMkH3gPmn82NxO2Z22kCRUeAVBdunmxDrp5VCuwxL0gTKZG2Q__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"The_evolution_of_bat_vestibular_systems_in_the_face_of_potential_antagonistic_selection_pressures_for_flight_and_echolocation","translated_slug":"","page_count":13,"language":"en","content_type":"Work","summary":"The vestibular system maintains the body's sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged semicircular canals. Second, many bats have enlarged cochleae associated with echolocation, and both cochleae and semicircular canals share a space within the petrosal bone. To determine how bat vestibular systems have evolved in the face of these pressures, we used micro-CT scans to compare canal morphology across species with contrasting flight and echolocation capabilities. We found no increase in canal radius in bats associated with the acquisition of powered flight, but canal radius did correlate with body mass in bat species from the suborder Yangochiroptera, and also in non-echolocating Old World fruit bats from the suborder Yinpterochiroptera. No such trend was seen in members of the Yinpterochiroptera that use laryngeal echolocation, although canal radius was associated with wing-tip roundedness in this group. We also found that the vestibular system scaled with cochlea size, although the relationship differed in species that use constant frequency echolocation. Across all bats, the shape of the anterior and lateral canals was associated with large cochlea size and small body size respectively, suggesting differential spatial constraints on each canal depending on its orientation within the skull. Thus in many echolocating bats, it seems that the combination of small body size and enlarged cochlea together act as a principal force on the vestibular system. The two main groups of echolocating bats displayed different canal morphologies, in terms of size and shape in relation to body mass and cochlear size, thus suggesting independent evolutionary pathways and offering tentative support for multiple acquisitions of echolocation.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255277,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255277/thumbnails/1.jpg","file_name":"The_Evolution_of_Bat_Vestibular_Systems_20160823-28130-dptk1r.pdf","download_url":"https://www.academia.edu/attachments/48255277/download_file","bulk_download_file_name":"The_evolution_of_bat_vestibular_systems.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255277/The_Evolution_of_Bat_Vestibular_Systems_20160823-28130-dptk1r-libre.pdf?1471956956=\u0026response-content-disposition=attachment%3B+filename%3DThe_evolution_of_bat_vestibular_systems.pdf\u0026Expires=1743265560\u0026Signature=RTmqyH~YdjIUkztXGO8zv7iJjXtWrDF40w0As2K7Wu~dh1QbxiDDp9SDI0Q12LdAOvIjERwKINHDjZK3MJZ7fFeMDqr3UzcdS9RbRlWHbe~rQdLtbLfQWr09TvQvfAB3pwOLyzkAI-nKMR3zoogke1c7x~tTc20Y2L-ez0MbrpVxsMUpU5eQzLkV25SZEIdeJCO39GuuGgmreMkuUqI7bniEGZKzt83cnhSDxyp6FzCJTWaeFmbgz~o7hO-brFis2HMjRSLsFx7dzcs2h7Z-eUsOmzP-OUASfv8hfSMkH3gPmn82NxO2Z22kCRUeAVBdunmxDrp5VCuwxL0gTKZG2Q__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":27230,"name":"Chiroptera","url":"https://www.academia.edu/Documents/in/Chiroptera"},{"id":28235,"name":"Multidisciplinary","url":"https://www.academia.edu/Documents/in/Multidisciplinary"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":170896,"name":"Echolocation","url":"https://www.academia.edu/Documents/in/Echolocation"},{"id":191815,"name":"Biological evolution","url":"https://www.academia.edu/Documents/in/Biological_evolution"},{"id":197299,"name":"Inner Ear","url":"https://www.academia.edu/Documents/in/Inner_Ear"},{"id":220780,"name":"PLoS one","url":"https://www.academia.edu/Documents/in/PLoS_one"},{"id":1151963,"name":"Cochlea","url":"https://www.academia.edu/Documents/in/Cochlea"},{"id":2253257,"name":"Wing","url":"https://www.academia.edu/Documents/in/Wing"}],"urls":[{"id":3350934,"url":"http://dx.doi.org/10.1371/journal.pone.0061998"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008453-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008452"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008452/New_approaches_for_unravelling_reassortment_pathways"><img alt="Research paper thumbnail of New approaches for unravelling reassortment pathways" class="work-thumbnail" src="https://attachments.academia-assets.com/48255288/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008452/New_approaches_for_unravelling_reassortment_pathways">New approaches for unravelling reassortment pathways</a></div><div class="wp-workCard_item"><span>BMC evolutionary biology</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: Every year the human population encounters epidemic outbreaks of influenza, and histo...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="b011408280dee1e815807bf70d0d632d" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255288,"asset_id":8008452,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255288/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008452"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008452"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008452; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008452]").text(description); $(".js-view-count[data-work-id=8008452]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008452; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008452']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "b011408280dee1e815807bf70d0d632d" } } $('.js-work-strip[data-work-id=8008452]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008452,"title":"New approaches for unravelling reassortment pathways","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","ai_title_tag":"Identifying Reassortant Influenza Strains","grobid_abstract":"Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.","publication_date":{"day":null,"month":null,"year":2013,"errors":{}},"publication_name":"BMC evolutionary biology","grobid_abstract_attachment_id":48255288},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008452/New_approaches_for_unravelling_reassortment_pathways","translated_internal_url":"","created_at":"2014-08-18T01:12:15.820-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255288,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255288/thumbnails/1.jpg","file_name":"1471-2148-13-1.pdf","download_url":"https://www.academia.edu/attachments/48255288/download_file","bulk_download_file_name":"New_approaches_for_unravelling_reassortm.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255288/1471-2148-13-1-libre.pdf?1471956956=\u0026response-content-disposition=attachment%3B+filename%3DNew_approaches_for_unravelling_reassortm.pdf\u0026Expires=1743265560\u0026Signature=dE53b9WVEbvWB8Mu51VKbIlkLITDTlVsAr~D6NW~~0jARLqTgbm5AGedkEUppHUEDa-Jto62eFk-Kiv~G4Rkk~zBAbryYdejBIFzPg2Navqmqvvd4nuthMeQfch68pkrLyIQCdEWxpZdT-6RMabFZKjVXRQFTKGkTnqJuJK88e~IYtWbiTygvOKll-t60~BulenfR-8nepu1xec2ceHUw4OUbJHqhx0~oHt6ZaEJ25-cc6sNe6b4ZOE697GCgrDdapOJXwZ248CW3w9GRMOXeLa6-efIGkrJelVUhiYMME~qe2I5ZGAFgjqGlikkLoGj3nlkpo6hc-24WstVgJWoow__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"New_approaches_for_unravelling_reassortment_pathways","translated_slug":"","page_count":14,"language":"en","content_type":"Work","summary":"Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255288,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255288/thumbnails/1.jpg","file_name":"1471-2148-13-1.pdf","download_url":"https://www.academia.edu/attachments/48255288/download_file","bulk_download_file_name":"New_approaches_for_unravelling_reassortm.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255288/1471-2148-13-1-libre.pdf?1471956956=\u0026response-content-disposition=attachment%3B+filename%3DNew_approaches_for_unravelling_reassortm.pdf\u0026Expires=1743265560\u0026Signature=dE53b9WVEbvWB8Mu51VKbIlkLITDTlVsAr~D6NW~~0jARLqTgbm5AGedkEUppHUEDa-Jto62eFk-Kiv~G4Rkk~zBAbryYdejBIFzPg2Navqmqvvd4nuthMeQfch68pkrLyIQCdEWxpZdT-6RMabFZKjVXRQFTKGkTnqJuJK88e~IYtWbiTygvOKll-t60~BulenfR-8nepu1xec2ceHUw4OUbJHqhx0~oHt6ZaEJ25-cc6sNe6b4ZOE697GCgrDdapOJXwZ248CW3w9GRMOXeLa6-efIGkrJelVUhiYMME~qe2I5ZGAFgjqGlikkLoGj3nlkpo6hc-24WstVgJWoow__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":428,"name":"Algorithms","url":"https://www.academia.edu/Documents/in/Algorithms"},{"id":2513,"name":"Molecular Biology","url":"https://www.academia.edu/Documents/in/Molecular_Biology"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"},{"id":25021,"name":"Hong Kong","url":"https://www.academia.edu/Documents/in/Hong_Kong"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":561000,"name":"influenza A virus","url":"https://www.academia.edu/Documents/in/influenza_A_virus"},{"id":880279,"name":"Bayes Theorem","url":"https://www.academia.edu/Documents/in/Bayes_Theorem-1"},{"id":1191613,"name":"Likelihood Functions","url":"https://www.academia.edu/Documents/in/Likelihood_Functions"}],"urls":[{"id":3350933,"url":"http://dx.doi.org/10.1186/1471-2148-13-1"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008452-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008450"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008450/The_genome_and_life_stage_specific_transcriptomes_of_Globodera_pallida_elucidate_key_aspects_of_plant_parasitism_by_a_cyst_nematode"><img alt="Research paper thumbnail of The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode" class="work-thumbnail" src="https://attachments.academia-assets.com/48255291/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008450/The_genome_and_life_stage_specific_transcriptomes_of_Globodera_pallida_elucidate_key_aspects_of_plant_parasitism_by_a_cyst_nematode">The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode</a></div><div class="wp-workCard_item"><span>Genome biology</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Globodera pallida is a devastating pathogen of potato crops, making it one of the most economical...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="e5e56efd61321808d5dac44bb94eced2" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255291,"asset_id":8008450,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255291/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008450"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008450"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008450; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008450]").text(description); $(".js-view-count[data-work-id=8008450]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008450; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008450']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "e5e56efd61321808d5dac44bb94eced2" } } $('.js-work-strip[data-work-id=8008450]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008450,"title":"The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. 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Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="1f615450f4c17016f546d12e8074d118" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255297,"asset_id":8008449,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255297/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008449"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008449"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008449; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008449]").text(description); $(".js-view-count[data-work-id=8008449]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008449; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008449']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "1f615450f4c17016f546d12e8074d118" } } $('.js-work-strip[data-work-id=8008449]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008449,"title":"Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.","publication_date":{"day":null,"month":null,"year":2012,"errors":{}},"publication_name":"PLoS pathogens","grobid_abstract_attachment_id":48255297},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008449/Comparative_genomics_of_the_apicomplexan_parasites_Toxoplasma_gondii_and_Neospora_caninum_Coccidia_differing_in_host_range_and_transmission_strategy","translated_internal_url":"","created_at":"2014-08-18T01:11:55.607-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255297,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255297/thumbnails/1.jpg","file_name":"journal.ppat.1002567.pdf","download_url":"https://www.academia.edu/attachments/48255297/download_file","bulk_download_file_name":"Comparative_genomics_of_the_apicomplexan.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255297/journal.ppat.1002567-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DComparative_genomics_of_the_apicomplexan.pdf\u0026Expires=1743265560\u0026Signature=bxUXUnxIyE8T7uXu4Wb57RYwlRLbU7bZ4CzH3vmSJ5JoK8N6bS8NrowtdpKDxReEMslpte9vfZncp7LNFyy4MHViY4FupBIA1wC8cNLsJwjlUxQHMiXhw~LHA~NX6i2Dyi8ATXSVHO0GeDWNbhvb35SH2hG9pH~wofDQaK7myKhb1AqEKSXqrYueA7ASRJEIYoFa8MKomsupJQUB7Xqg~XnpUgd2GpZpQNONb2G1mfiqyqebHAnUOJuX8EiFaNQFH4X6VqZkoQ9ccPTGA7iKoXtiRAGuAUABwxo0fLah7NtM9CjIJpRg7CPBtP2CxuHTq9oXEown0w7HnmVTMHxryQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Comparative_genomics_of_the_apicomplexan_parasites_Toxoplasma_gondii_and_Neospora_caninum_Coccidia_differing_in_host_range_and_transmission_strategy","translated_slug":"","page_count":15,"language":"en","content_type":"Work","summary":"Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255297,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255297/thumbnails/1.jpg","file_name":"journal.ppat.1002567.pdf","download_url":"https://www.academia.edu/attachments/48255297/download_file","bulk_download_file_name":"Comparative_genomics_of_the_apicomplexan.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255297/journal.ppat.1002567-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DComparative_genomics_of_the_apicomplexan.pdf\u0026Expires=1743265560\u0026Signature=bxUXUnxIyE8T7uXu4Wb57RYwlRLbU7bZ4CzH3vmSJ5JoK8N6bS8NrowtdpKDxReEMslpte9vfZncp7LNFyy4MHViY4FupBIA1wC8cNLsJwjlUxQHMiXhw~LHA~NX6i2Dyi8ATXSVHO0GeDWNbhvb35SH2hG9pH~wofDQaK7myKhb1AqEKSXqrYueA7ASRJEIYoFa8MKomsupJQUB7Xqg~XnpUgd2GpZpQNONb2G1mfiqyqebHAnUOJuX8EiFaNQFH4X6VqZkoQ9ccPTGA7iKoXtiRAGuAUABwxo0fLah7NtM9CjIJpRg7CPBtP2CxuHTq9oXEown0w7HnmVTMHxryQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":159,"name":"Microbiology","url":"https://www.academia.edu/Documents/in/Microbiology"},{"id":1290,"name":"Immunology","url":"https://www.academia.edu/Documents/in/Immunology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":5504,"name":"Comparative Genomics","url":"https://www.academia.edu/Documents/in/Comparative_Genomics"},{"id":6947,"name":"Medical Microbiology","url":"https://www.academia.edu/Documents/in/Medical_Microbiology"},{"id":13345,"name":"Apicomplexans","url":"https://www.academia.edu/Documents/in/Apicomplexans"},{"id":13346,"name":"Toxoplasma","url":"https://www.academia.edu/Documents/in/Toxoplasma"},{"id":19080,"name":"Zoonoses","url":"https://www.academia.edu/Documents/in/Zoonoses"},{"id":19652,"name":"Ecological Niche Modeling","url":"https://www.academia.edu/Documents/in/Ecological_Niche_Modeling"},{"id":27784,"name":"Gene expression","url":"https://www.academia.edu/Documents/in/Gene_expression"},{"id":37798,"name":"Toxoplasmosis","url":"https://www.academia.edu/Documents/in/Toxoplasmosis"},{"id":37801,"name":"Toxoplasma gondii","url":"https://www.academia.edu/Documents/in/Toxoplasma_gondii"},{"id":52873,"name":"Virulence","url":"https://www.academia.edu/Documents/in/Virulence"},{"id":74253,"name":"Neospora","url":"https://www.academia.edu/Documents/in/Neospora"},{"id":142138,"name":"Host-parasite interactions","url":"https://www.academia.edu/Documents/in/Host-parasite_interactions"},{"id":587939,"name":"Virulence factor","url":"https://www.academia.edu/Documents/in/Virulence_factor"},{"id":589504,"name":"Coccidiosis","url":"https://www.academia.edu/Documents/in/Coccidiosis"},{"id":750576,"name":"Host Range","url":"https://www.academia.edu/Documents/in/Host_Range"},{"id":906078,"name":"Neospora Caninum","url":"https://www.academia.edu/Documents/in/Neospora_Caninum"},{"id":965375,"name":"Vertical Transmission","url":"https://www.academia.edu/Documents/in/Vertical_Transmission"},{"id":999803,"name":"Gene Family","url":"https://www.academia.edu/Documents/in/Gene_Family"},{"id":1557716,"name":"Comparative Genomic Hybridization","url":"https://www.academia.edu/Documents/in/Comparative_Genomic_Hybridization"},{"id":1763968,"name":"Gene Expression Regulation","url":"https://www.academia.edu/Documents/in/Gene_Expression_Regulation"}],"urls":[{"id":3350930,"url":"http://dx.doi.org/10.1371/journal.ppat.1002567"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008449-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008447"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008447/Experimental_design_in_phylogenetics_testing_predictions_from_expected_information"><img alt="Research paper thumbnail of Experimental design in phylogenetics: testing predictions from expected information" class="work-thumbnail" src="https://attachments.academia-assets.com/48255271/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008447/Experimental_design_in_phylogenetics_testing_predictions_from_expected_information">Experimental design in phylogenetics: testing predictions from expected information</a></div><div class="wp-workCard_item"><span>Systematic biology</span><span>, 2012</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Taxon and character sampling are central to phylogenetic experimental design; yet, we lack genera...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species and studied how information (both expected and observed) and bootstrap support vary as each new taxon is individually added to our previous data set. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the 4th (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: Information is related to the ability to estimate branch length accurately and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well chosen) taxon may increase phylogenetic resolution and support in weakly supported parts of the tree without adding more characters/genes. Altogether our results corroborate that, although still underexplored, Goldman's method offers a powerful tool for experimental design in molecular phylogenetic studies. However, there are still several drawbacks to overcome, and further assessment of the method is needed in order to make it better understood, more accessible, and able to assess the addition of multiple taxa. [Bootstrap support; branch lengths; caecilians; experimental design; Gymnophiona; mitochondrial genome; phylogenetic information; rag1; taxon sampling.]</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="c0ec63aa8b3c9b59436159c81716f641" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255271,"asset_id":8008447,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255271/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008447"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008447"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008447; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008447]").text(description); $(".js-view-count[data-work-id=8008447]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008447; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008447']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "c0ec63aa8b3c9b59436159c81716f641" } } $('.js-work-strip[data-work-id=8008447]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008447,"title":"Experimental design in phylogenetics: testing predictions from expected information","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","ai_title_tag":"Enhancing Phylogenetic Design via Taxon Sampling","grobid_abstract":"Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species and studied how information (both expected and observed) and bootstrap support vary as each new taxon is individually added to our previous data set. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the 4th (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: Information is related to the ability to estimate branch length accurately and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well chosen) taxon may increase phylogenetic resolution and support in weakly supported parts of the tree without adding more characters/genes. Altogether our results corroborate that, although still underexplored, Goldman's method offers a powerful tool for experimental design in molecular phylogenetic studies. However, there are still several drawbacks to overcome, and further assessment of the method is needed in order to make it better understood, more accessible, and able to assess the addition of multiple taxa. [Bootstrap support; branch lengths; caecilians; experimental design; Gymnophiona; mitochondrial genome; phylogenetic information; rag1; taxon sampling.]","publication_date":{"day":null,"month":null,"year":2012,"errors":{}},"publication_name":"Systematic biology","grobid_abstract_attachment_id":48255271},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008447/Experimental_design_in_phylogenetics_testing_predictions_from_expected_information","translated_internal_url":"","created_at":"2014-08-18T01:11:54.880-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255271,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255271/thumbnails/1.jpg","file_name":"Experimental_Design_in_Phylogenetics_Tes20160823-20824-u8bxc5.pdf","download_url":"https://www.academia.edu/attachments/48255271/download_file","bulk_download_file_name":"Experimental_design_in_phylogenetics_tes.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255271/Experimental_Design_in_Phylogenetics_Tes20160823-20824-u8bxc5-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DExperimental_design_in_phylogenetics_tes.pdf\u0026Expires=1743265560\u0026Signature=JJiZC3QXPqBLPZjuBqKYuXVfuBGFikfTphW0WZ-LZ1WLKehZUW5lr0y8NWR8IDmFuSpZ3BEwxCB7US~HzxL2WOVEZP5Pua-frx~4uYDlKBjKwE~eFGcroetsoyePMmdamKDX1UeR~FC6ykOvwgFmJ-ff6PZqEhKAVCTX4fGNQHOQ8YZLP8A4uomzEe6DbUgn9hN6IX9HczIgtlbkZtlZSKwDL~65VLzcyUovmUzkdckrhA4jkQyY4osTiuziWrgb1LSVAWcg3dZAKV1nr7KmvHjQFwmrru7wzkOPhf~OT8dbrO0jCHNAxN5~yLwY88yCqXfIuTm-l97o3jhpEErUTw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Experimental_design_in_phylogenetics_testing_predictions_from_expected_information","translated_slug":"","page_count":14,"language":"en","content_type":"Work","summary":"Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. 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Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the 4th (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: Information is related to the ability to estimate branch length accurately and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well chosen) taxon may increase phylogenetic resolution and support in weakly supported parts of the tree without adding more characters/genes. Altogether our results corroborate that, although still underexplored, Goldman's method offers a powerful tool for experimental design in molecular phylogenetic studies. However, there are still several drawbacks to overcome, and further assessment of the method is needed in order to make it better understood, more accessible, and able to assess the addition of multiple taxa. [Bootstrap support; branch lengths; caecilians; experimental design; Gymnophiona; mitochondrial genome; phylogenetic information; rag1; taxon sampling.]","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255271,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255271/thumbnails/1.jpg","file_name":"Experimental_Design_in_Phylogenetics_Tes20160823-20824-u8bxc5.pdf","download_url":"https://www.academia.edu/attachments/48255271/download_file","bulk_download_file_name":"Experimental_design_in_phylogenetics_tes.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255271/Experimental_Design_in_Phylogenetics_Tes20160823-20824-u8bxc5-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DExperimental_design_in_phylogenetics_tes.pdf\u0026Expires=1743265560\u0026Signature=JJiZC3QXPqBLPZjuBqKYuXVfuBGFikfTphW0WZ-LZ1WLKehZUW5lr0y8NWR8IDmFuSpZ3BEwxCB7US~HzxL2WOVEZP5Pua-frx~4uYDlKBjKwE~eFGcroetsoyePMmdamKDX1UeR~FC6ykOvwgFmJ-ff6PZqEhKAVCTX4fGNQHOQ8YZLP8A4uomzEe6DbUgn9hN6IX9HczIgtlbkZtlZSKwDL~65VLzcyUovmUzkdckrhA4jkQyY4osTiuziWrgb1LSVAWcg3dZAKV1nr7KmvHjQFwmrru7wzkOPhf~OT8dbrO0jCHNAxN5~yLwY88yCqXfIuTm-l97o3jhpEErUTw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":3363,"name":"Systematic Biology","url":"https://www.academia.edu/Documents/in/Systematic_Biology"},{"id":4967,"name":"Molecular Evolution","url":"https://www.academia.edu/Documents/in/Molecular_Evolution"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":170540,"name":"Amphibians","url":"https://www.academia.edu/Documents/in/Amphibians"},{"id":222708,"name":"Mitochondrial Genome","url":"https://www.academia.edu/Documents/in/Mitochondrial_Genome"},{"id":2467566,"name":"Molecular Sequence Data","url":"https://www.academia.edu/Documents/in/Molecular_Sequence_Data"}],"urls":[{"id":3350928,"url":"http://dx.doi.org/10.1093/sysbio/sys028"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008447-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008445"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008445/Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals"><img alt="Research paper thumbnail of Genome-wide signatures of convergent evolution in echolocating mammals" class="work-thumbnail" src="https://attachments.academia-assets.com/48255259/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008445/Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals">Genome-wide signatures of convergent evolution in echolocating mammals</a></div><div class="wp-workCard_item"><span>Nature</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Evolution is typically thought to proceed through divergence of genes, proteins and ultimately ph...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="27022e1e29a12d29a112514c45b560bc" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255259,"asset_id":8008445,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255259/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008445"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008445"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008445; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008445]").text(description); $(".js-view-count[data-work-id=8008445]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008445; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008445']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "27022e1e29a12d29a112514c45b560bc" } } $('.js-work-strip[data-work-id=8008445]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008445,"title":"Genome-wide signatures of convergent evolution in echolocating mammals","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.","publication_date":{"day":null,"month":null,"year":2013,"errors":{}},"publication_name":"Nature","grobid_abstract_attachment_id":48255259},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008445/Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals","translated_internal_url":"","created_at":"2014-08-18T01:11:52.526-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255259,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255259/thumbnails/1.jpg","file_name":"0c9605227ba4cedeb1000000.pdf","download_url":"https://www.academia.edu/attachments/48255259/download_file","bulk_download_file_name":"Genome_wide_signatures_of_convergent_evo.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255259/0c9605227ba4cedeb1000000-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DGenome_wide_signatures_of_convergent_evo.pdf\u0026Expires=1743265560\u0026Signature=R-~xx9ATcy5dBTm4wbgDlraIqt9WkEk~UShC4XYxGdhh9TgH71My7Za-SFnVD9BBuY3X3PcMz5MiAUtS7p5~I0RVFo9If8YXNRaVvXZKaAU0W4pkWGIYyg~7bHPnuyHP~igdtlAGdsYecQ6XcyyfL5~8EbvFo8AvqJHSprV9Q5b9ezp7WQ6XIynZ0CHmPHbZhdXJ-cj7NpoeXVy0qZ9S6SmEJfrIzUgZXAe4ql5XvW0ZzH0La5ND-2dL571iemOAu70rl0aw8Wy8N0yi~Uo1ZUTTnSNU5-KQkVsEmjyxrRf7R9nQe5Ltw2HoH05xPcKrxJVmpZ4to87fXcrrSI0MYg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals","translated_slug":"","page_count":9,"language":"en","content_type":"Work","summary":"Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255259,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255259/thumbnails/1.jpg","file_name":"0c9605227ba4cedeb1000000.pdf","download_url":"https://www.academia.edu/attachments/48255259/download_file","bulk_download_file_name":"Genome_wide_signatures_of_convergent_evo.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255259/0c9605227ba4cedeb1000000-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DGenome_wide_signatures_of_convergent_evo.pdf\u0026Expires=1743265560\u0026Signature=R-~xx9ATcy5dBTm4wbgDlraIqt9WkEk~UShC4XYxGdhh9TgH71My7Za-SFnVD9BBuY3X3PcMz5MiAUtS7p5~I0RVFo9If8YXNRaVvXZKaAU0W4pkWGIYyg~7bHPnuyHP~igdtlAGdsYecQ6XcyyfL5~8EbvFo8AvqJHSprV9Q5b9ezp7WQ6XIynZ0CHmPHbZhdXJ-cj7NpoeXVy0qZ9S6SmEJfrIzUgZXAe4ql5XvW0ZzH0La5ND-2dL571iemOAu70rl0aw8Wy8N0yi~Uo1ZUTTnSNU5-KQkVsEmjyxrRf7R9nQe5Ltw2HoH05xPcKrxJVmpZ4to87fXcrrSI0MYg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":2513,"name":"Molecular Biology","url":"https://www.academia.edu/Documents/in/Molecular_Biology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":4207,"name":"Phylogenetics","url":"https://www.academia.edu/Documents/in/Phylogenetics"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":4481,"name":"Evolutionary genetics","url":"https://www.academia.edu/Documents/in/Evolutionary_genetics"},{"id":4967,"name":"Molecular Evolution","url":"https://www.academia.edu/Documents/in/Molecular_Evolution"},{"id":5504,"name":"Comparative Genomics","url":"https://www.academia.edu/Documents/in/Comparative_Genomics"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"},{"id":13797,"name":"Marine Mammals","url":"https://www.academia.edu/Documents/in/Marine_Mammals"},{"id":15124,"name":"Convergence","url":"https://www.academia.edu/Documents/in/Convergence"},{"id":18075,"name":"Bats (Mammalogy)","url":"https://www.academia.edu/Documents/in/Bats_Mammalogy_"},{"id":27230,"name":"Chiroptera","url":"https://www.academia.edu/Documents/in/Chiroptera"},{"id":28235,"name":"Multidisciplinary","url":"https://www.academia.edu/Documents/in/Multidisciplinary"},{"id":33319,"name":"Nature","url":"https://www.academia.edu/Documents/in/Nature"},{"id":34912,"name":"Phylogenomics","url":"https://www.academia.edu/Documents/in/Phylogenomics"},{"id":41779,"name":"Mammals","url":"https://www.academia.edu/Documents/in/Mammals"},{"id":54065,"name":"Cetaceans","url":"https://www.academia.edu/Documents/in/Cetaceans"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":59693,"name":"Hearing","url":"https://www.academia.edu/Documents/in/Hearing"},{"id":75055,"name":"Dolphins","url":"https://www.academia.edu/Documents/in/Dolphins"},{"id":170896,"name":"Echolocation","url":"https://www.academia.edu/Documents/in/Echolocation"},{"id":176486,"name":"Genome","url":"https://www.academia.edu/Documents/in/Genome"},{"id":191815,"name":"Biological evolution","url":"https://www.academia.edu/Documents/in/Biological_evolution"}],"urls":[{"id":3350926,"url":"http://dx.doi.org/10.1038/nature12511"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008445-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008444"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008444/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery"><img alt="Research paper thumbnail of The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery" class="work-thumbnail" src="https://attachments.academia-assets.com/48255275/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008444/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery">The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery</a></div><div class="wp-workCard_item"><span>Genome biology</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic ne...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. Conclusions: The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="6060be248b46fbbebede47c7d422476e" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255275,"asset_id":8008444,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255275/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008444"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008444"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008444; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008444]").text(description); $(".js-view-count[data-work-id=8008444]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008444; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008444']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "6060be248b46fbbebede47c7d422476e" } } $('.js-work-strip[data-work-id=8008444]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008444,"title":"The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","ai_title_tag":"Genome and Transcriptome Analysis of Haemonchus contortus","grobid_abstract":"Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. 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Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008444-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008442"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008442/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_%CE%B2_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes"><img alt="Research paper thumbnail of Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes" class="work-thumbnail" src="https://attachments.academia-assets.com/48255280/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008442/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_%CE%B2_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes">Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes</a></div><div class="wp-workCard_item"><span>International journal for parasitology</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: High-molecular-weight glutenin subunits (HMW-GSs) have been considered as most import...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: High-molecular-weight glutenin subunits (HMW-GSs) have been considered as most important seed storage proteins for wheat flour quality. 1Ay subunits are of great interest because they are always silent in common wheat. The presence of expressed 1Ay subunits in diploid and tetraploid wheat genotypes makes it possible to investigate molecular information of active 1Ay genes.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8bf23c2c86302553333ba64718cd1ff3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255280,"asset_id":8008442,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255280/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008442"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008442"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008442; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008442]").text(description); $(".js-view-count[data-work-id=8008442]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008442; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008442']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "8bf23c2c86302553333ba64718cd1ff3" } } $('.js-work-strip[data-work-id=8008442]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008442,"title":"Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Background: High-molecular-weight glutenin subunits (HMW-GSs) have been considered as most important seed storage proteins for wheat flour quality. 1Ay subunits are of great interest because they are always silent in common wheat. 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class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938645/New_approaches_for_unravelling_reassortment_pathways"><img alt="Research paper thumbnail of New approaches for unravelling reassortment pathways" class="work-thumbnail" src="https://attachments.academia-assets.com/32910590/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938645/New_approaches_for_unravelling_reassortment_pathways">New approaches for unravelling reassortment pathways</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: Every year the human population encounters epidemic outbreaks of influenza, and histo...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.</span></div><div class="wp-workCard_item"><div class="carousel-container carousel-container--sm" id="profile-work-5938645-figures"><div class="prev-slide-container js-prev-button-container"><button aria-label="Previous" class="carousel-navigation-button js-profile-work-5938645-figures-prev"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">arrow_back_ios</span></button></div><div class="slides-container js-slides-container"><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044207/figure-3-trees-ns-and-na-confidence-intervals-and-spr"><img alt="Figure 3 Trees NS and NA, confidence intervals and SPR modifications. Subtree pruning and regrafting (SPR) modifications that the NA tree proposes on the NS tree, and the confidence interval around each tree (coloured shapes). Three paths are possible. The labels on the arrows refer to nodes involved in a move: m1 - move outgroup to cluster with hk1774, m2 — move hk1073 to cluster with hk1774, m2r — reverse of m2, m3 -— move hk1073 to cluster with outgroup, m4 — move env99 to cluster with quail99/sh39/hk1073 group. t1 - t6 are trees resulting from applying these SPR modifications to the NS tree. Arrows between two trees in the same confidence interval (Cl) reflect trivial differences (e.g. m1, black arrow), whereas ones between trees from different Cls are considered significant (e.g. m2, red arrow). We consider m2 as significant as we're interested in the minimum amount of significant branch moves between NS and NA. " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_003.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044209/figure-4-new-approaches-for-unravelling-reassortment"><img alt="" class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_004.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044203/figure-1-simulated-data-with-manually-introduced-spr"><img alt="Figure 1 Simulated data with manually introduced SPR modifications. The HA data was simulated on a tree modified by moving taxon ‘G’ to group with taxon ‘B’. (A) Output from the ML analysis for seven segments: MP, NA, NP, NS, PA, PB1 and PB2. A significant SPR was detected that would require moving taxon ‘G' to group with taxon 'B’, as suggested by the HA segment (direction of arc from empty to filled circle). Colours of arcs correspond to specific SPR operations. (B) HA tree: seven segments propose a significant SPR modification on the HA tree that would require moving taxon ‘G’ to group with taxon ‘F’. (C) Frequency network from Bayesian results. Edges point from segment proposing an SPR, to the segment whose tree needs to be modified (filled circle). Legend shows SPRs corresponding to the coloured edges. HA proposes moving taxon ‘G’ to group with taxon ‘B’ for the other seven segments. Conversely, the rest of the segments suggest that ‘G’ should move to cluster with ‘F’ on the HA tree. (D), (E) Overlap between MLreassort and Breassort. The x-axis represents the segments that propose the SPR move whereas the y-axis represents the segments whose trees need to be modified according to that SPR. The name of a tree segment is greyed out in the case where the SPR move is irrelevant, i.e. when the taxa involved in the move are sister-taxa. " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_001.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044205/figure-2-peqmps-avmitisvuipt-uum-ulstahiles-moeuweeh-lees-ui"><img alt="PEQMPS 2 AVMITISVUIPT UUM UlStaHILes MOEUWEEH Lees UI Le PIU Kong dataset. The intensity of the squares corresponds to the degree of distance. Distances range from 0 to 6, representing the number of bipartitions present in one tree but not in the other. Some trees have the same topology (NP and PB1, NS and PB2) whereas the NA tree seems to be most distant to the other trees (distance of 6). AU p values). We have corrected these p values using the Benjamini and Hochberg [37] test (BH test) and note that the correction has little impact on the resulting confidence intervals (data not shown). This means that for these 24 tree pairs, the topological differences can be accounted for by stochastic errors; 46% (26/56) of cases with non-overlapping confidence regions remained. Sig- nificant edits (SPR operations that result in a significant change in likelihood score) between trees with non- overlapping confidence regions were determined and depicted on each ML tree (shown in Additional file 1: Figure $1). In the cases where the arcs are bidirectional, " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_002.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044211/figure-5-network-of-the-most-frequent-sprs-from-breassort"><img alt="Figure 5 Network of the most frequent SPRs from Breassort. Each node represents the set of trees for the corresponding segment. Edge colours correspond to different types of SPR operations, as shown. Edges point from a segment that proposes the branch swap, to the one that needs to be modified (ending in filled circle). For example, the orange edge going from NA to NS depicts the following operation: cutting the branch leading to A/HongKong/1073/99 H9N2 and reconnecting it to the branch ending in A/HongKong/1774/99 H3N2. The NS tree is the one being modified, and the NA tree proposes this modification. " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_005.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044212/figure-6-combined-sprs-from-mlreassort-and-breassort-each"><img alt="Figure 6 Combined SPRs from MLreassort and Breassort. Each plot depicts an SPR move, with symbols indicating the cases when this move is significant. Circles represent results from the maximum likelihood-based approach, while crosses represent results from applying the algorithm based on a Bayesian framework. The x-axis shows the segments that propose the specified SPR, while the y-axis shows the segments whose trees need to be modified. The name of a tree segment is greyed out in the case where the SPR move is irrelevant, i.e. when the taxa involved in the move are sister-taxa. For example, moving hk1073 to group with hk1774 in the NA tree is irrelevant, as the NA tree already has these grouping together. " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_006.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044214/table-1-alignments-and-models-for-hong-kong-dataset-the"><img alt="Table 1 Alignments and models for Hong Kong 1999 dataset the source and recipient taxa cannot be determined with certainty. Bayesian phylogenetics (Breassort) was also used to infer the evolutionary histories of each segment, by car- rying out 28 pairwise comparisons of sets of trees using 95% confidence intervals (as described in methods). In 57% (16 out of 28) of cases the two sets of trees do not overlap, which indicates that the trees in one set cannot be used to explain the data from which the trees in the other set are derived. The analysis was repeated using dif- ferent thresholds (90%, 95%, 99%, 99.9%, 3 replicates each) for determining confidence intervals (Additional file 1: Figure $3). Small variations in the networks are expected to occur due to the reduction of multi-dimensional space to 2D, and the arbitrary choice of trees to compare from each convex hull. However, consistent signals were identi- fied irrespective of the analyses, and variations between different CI thresholds are not greater than those observed when repeating the analysis with the same parameters. The findings from both algorithms are discussed below, starting with the example of a specific pair of segments: NS (non-structural) and NA (neuraminidase). " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/table_001.jpg" /></a></figure></div><div class="next-slide-container js-next-button-container"><button aria-label="Next" class="carousel-navigation-button js-profile-work-5938645-figures-next"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">arrow_forward_ios</span></button></div></div></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="cade0040df109ee8d5913ee03d76b2d2" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910590,"asset_id":5938645,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910590/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938645"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938645"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938645; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938645]").text(description); $(".js-view-count[data-work-id=5938645]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938645; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938645']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "cade0040df109ee8d5913ee03d76b2d2" } } $('.js-work-strip[data-work-id=5938645]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938645,"title":"New approaches for unravelling reassortment pathways","translated_title":"","metadata":{"ai_title_tag":"Detecting Reassortment Pathways in Influenza Strains","grobid_abstract":"Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.","grobid_abstract_attachment_id":32910590},"translated_abstract":null,"internal_url":"https://www.academia.edu/5938645/New_approaches_for_unravelling_reassortment_pathways","translated_internal_url":"","created_at":"2014-02-03T18:21:40.622-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":32910590,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910590/thumbnails/1.jpg","file_name":"SvintiCottonMcInerney_2013_NewApproachesToUnravellingReassortmentPathways_BMCEvolutionaryBiology.pdf","download_url":"https://www.academia.edu/attachments/32910590/download_file","bulk_download_file_name":"New_approaches_for_unravelling_reassortm.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910590/SvintiCottonMcInerney_2013_NewApproachesToUnravellingReassortmentPathways_BMCEvolutionaryBiology-libre.pdf?1392028819=\u0026response-content-disposition=attachment%3B+filename%3DNew_approaches_for_unravelling_reassortm.pdf\u0026Expires=1743265560\u0026Signature=O0aPHe~UmxeTs5Xf1km04km1rDg5cYVnOnqOO0qR62uEtHerZDCqpqtKuhy5WouRjF2FG2uX0ULb-zKtZ7nQq3pG7wgEgUbtwHVeSrwJjWVBo9kiiJZhXZiv1nPYJVfXEDSQzZJm7t3AoZ-h6K2RKFciSFYIPka7qTHamU-NR69vIyO7U9w6uVCUNFTIPjrm2hiKyVuaXepghAduG~KGhwBuedA7~wY9h0hWg~DoH9jL3PCH7vuUeDC4EZJfIXuxx7UFoCLfSaWqoEX9X-FPsgwez7TsJ34lu9iZh6~opH82Za36B6julQeGn9KBYc3YrzLevCEO4ueQtfF2qAM59g__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"New_approaches_for_unravelling_reassortment_pathways","translated_slug":"","page_count":14,"language":"en","content_type":"Work","summary":"Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":32910590,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910590/thumbnails/1.jpg","file_name":"SvintiCottonMcInerney_2013_NewApproachesToUnravellingReassortmentPathways_BMCEvolutionaryBiology.pdf","download_url":"https://www.academia.edu/attachments/32910590/download_file","bulk_download_file_name":"New_approaches_for_unravelling_reassortm.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910590/SvintiCottonMcInerney_2013_NewApproachesToUnravellingReassortmentPathways_BMCEvolutionaryBiology-libre.pdf?1392028819=\u0026response-content-disposition=attachment%3B+filename%3DNew_approaches_for_unravelling_reassortm.pdf\u0026Expires=1743265560\u0026Signature=O0aPHe~UmxeTs5Xf1km04km1rDg5cYVnOnqOO0qR62uEtHerZDCqpqtKuhy5WouRjF2FG2uX0ULb-zKtZ7nQq3pG7wgEgUbtwHVeSrwJjWVBo9kiiJZhXZiv1nPYJVfXEDSQzZJm7t3AoZ-h6K2RKFciSFYIPka7qTHamU-NR69vIyO7U9w6uVCUNFTIPjrm2hiKyVuaXepghAduG~KGhwBuedA7~wY9h0hWg~DoH9jL3PCH7vuUeDC4EZJfIXuxx7UFoCLfSaWqoEX9X-FPsgwez7TsJ34lu9iZh6~opH82Za36B6julQeGn9KBYc3YrzLevCEO4ueQtfF2qAM59g__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":2513,"name":"Molecular Biology","url":"https://www.academia.edu/Documents/in/Molecular_Biology"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (true) { Aedu.setUpFigureCarousel('profile-work-5938645-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938644"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938644/Phylogenomic_Analyses_Elucidate_the_Evolutionary_Relationships_of_Bats"><img alt="Research paper thumbnail of Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats" class="work-thumbnail" src="https://attachments.academia-assets.com/32910587/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938644/Phylogenomic_Analyses_Elucidate_the_Evolutionary_Relationships_of_Bats">Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal g...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups , yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) . Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes , we show that-contrary to recent suggestions-bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="2c22df9feaa393268430880b972cd5d0" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910587,"asset_id":5938644,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910587/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938644"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938644"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938644; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938644]").text(description); $(".js-view-count[data-work-id=5938644]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938644; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938644']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "2c22df9feaa393268430880b972cd5d0" } } $('.js-work-strip[data-work-id=5938644]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938644,"title":"Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats","translated_title":"","metadata":{"grobid_abstract":"Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups , yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) . 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We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. 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Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes , we show that-contrary to recent suggestions-bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. 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However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="4b25fc31009394f2d6f91afc1970d858" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910586,"asset_id":5938643,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910586/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938643"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938643"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938643; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938643]").text(description); $(".js-view-count[data-work-id=5938643]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938643; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938643']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "4b25fc31009394f2d6f91afc1970d858" } } $('.js-work-strip[data-work-id=5938643]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938643,"title":"Genome-wide signatures of convergent evolution in echolocating mammals","translated_title":"","metadata":{"grobid_abstract":"Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.","grobid_abstract_attachment_id":32910586},"translated_abstract":null,"internal_url":"https://www.academia.edu/5938643/Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals","translated_internal_url":"","created_at":"2014-02-03T18:21:40.309-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":32910586,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910586/thumbnails/1.jpg","file_name":"ParkerTsagkogeogaCottonLiuProveroStupkaRossiter_2013_GenomeWideSignaturesOfConvergentEvolutionInEcholocatingMammals_Nature.pdf","download_url":"https://www.academia.edu/attachments/32910586/download_file","bulk_download_file_name":"Genome_wide_signatures_of_convergent_evo.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910586/ParkerTsagkogeogaCottonLiuProveroStupkaRossiter_2013_GenomeWideSignaturesOfConvergentEvolutionInEcholocatingMammals_Nature-libre.pdf?1392038841=\u0026response-content-disposition=attachment%3B+filename%3DGenome_wide_signatures_of_convergent_evo.pdf\u0026Expires=1743265560\u0026Signature=ONnargV~-f8p~8rElJA3hQ94KYfWSijslkrkcGi6k4gWHIVeEViv6ZLY-sgYbGI~O6j-Vn1F8hhlNZhoLGoE4GBO2~e7YwI7ok9OA3yp0QpCac6QCe1-FHE8cKwtZokXoRE7WWxe45ZtILy4g1jkbVA6dbQhRPKfWo11oj3lA6VrlgVK1V302pqhdjaieUPjLf4bsSbYPtuLgD8VZ8~E32~7S4eigNkSZt-orVHXDsGlChZ2TaccA8Ao4JLz5rMyUHWPm9eMwUqm2TiuMUJnFL4QkzOhWFvvS3aa1~jPDPk9uvbYEAxsz6oi3d2BN3UEiVHY6sI0oCkL6WYA~8GAvQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals","translated_slug":"","page_count":9,"language":"en","content_type":"Work","summary":"Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":32910586,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910586/thumbnails/1.jpg","file_name":"ParkerTsagkogeogaCottonLiuProveroStupkaRossiter_2013_GenomeWideSignaturesOfConvergentEvolutionInEcholocatingMammals_Nature.pdf","download_url":"https://www.academia.edu/attachments/32910586/download_file","bulk_download_file_name":"Genome_wide_signatures_of_convergent_evo.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910586/ParkerTsagkogeogaCottonLiuProveroStupkaRossiter_2013_GenomeWideSignaturesOfConvergentEvolutionInEcholocatingMammals_Nature-libre.pdf?1392038841=\u0026response-content-disposition=attachment%3B+filename%3DGenome_wide_signatures_of_convergent_evo.pdf\u0026Expires=1743265560\u0026Signature=ONnargV~-f8p~8rElJA3hQ94KYfWSijslkrkcGi6k4gWHIVeEViv6ZLY-sgYbGI~O6j-Vn1F8hhlNZhoLGoE4GBO2~e7YwI7ok9OA3yp0QpCac6QCe1-FHE8cKwtZokXoRE7WWxe45ZtILy4g1jkbVA6dbQhRPKfWo11oj3lA6VrlgVK1V302pqhdjaieUPjLf4bsSbYPtuLgD8VZ8~E32~7S4eigNkSZt-orVHXDsGlChZ2TaccA8Ao4JLz5rMyUHWPm9eMwUqm2TiuMUJnFL4QkzOhWFvvS3aa1~jPDPk9uvbYEAxsz6oi3d2BN3UEiVHY6sI0oCkL6WYA~8GAvQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":2513,"name":"Molecular Biology","url":"https://www.academia.edu/Documents/in/Molecular_Biology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-5938643-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938566"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938566/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_b_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes"><img alt="Research paper thumbnail of Characterization and comparative analysis of the complete Haemonchus contortus b-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes" class="work-thumbnail" src="https://attachments.academia-assets.com/32910545/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938566/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_b_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes">Characterization and comparative analysis of the complete Haemonchus contortus b-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Parasitic nematode β-tubulin genes are of particular interest because they are the targets of ben...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Parasitic nematode β-tubulin genes are of particular interest because they are the targets of benzimidazole drugs. However, in spite of this, the full β-tubulin gene family has not been characterized for any parasitic nematode to date. Haemonchus contortus is the parasite species for which we understand benzimidazole resistance the best and its close phylogenetic relationship with Caenorhabditis elegans potentially allows inferences of gene function by comparative analysis. Consequently, we have characterized the full β-tubulin gene family in H. contortus. Further to the previously identified Hco-tbb-iso-1 and Hco-tbb-iso-2 genes, we have characterized two additional family members designated Hco-tbb-iso-3 and Hco-tbb-iso-4. We show that Hco-tbb-iso-1 is not a one-to-one orthologue with Cel-ben-1, the only β-tubulin gene in C. elegans that is a benzimidazole drug target. Instead, both Hco-tbb-iso-1 and Hco-tbb-iso-2 have a complex evolutionary relationship with three C. elegans β-tubulin genes: Cel-ben-1, Cel-tbb-1 and Cel-tbb-2. Furthermore, we show that both Hco-tbb-iso-1 and Hco-tbb-iso-2 are highly expressed in adult worms; in contrast, Hco-tbb-iso-3 and Hco-tbb-iso-4 are expressed only at very low levels and are orthologous to the Cel-mec-7 and Cel-tbb-4 genes, respectively, suggesting that they have specialized functional roles. Indeed, we have found that the expression pattern of Hco-tbb-iso-3 in H. contortus is identical to that of Cel-mec-7 in C. elegans, being expressed in just six "touch receptor" mechano-sensory neurons. These results suggest that further investigation is warranted into the potential involvement of strongylid isotype-2 β-tubulin genes in mechanisms of benzimidazole resistance.Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="218c9bfc9c698cdb1476e293fa5e604d" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910545,"asset_id":5938566,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910545/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938566"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938566"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938566; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938566]").text(description); $(".js-view-count[data-work-id=5938566]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938566; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938566']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "218c9bfc9c698cdb1476e293fa5e604d" } } $('.js-work-strip[data-work-id=5938566]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938566,"title":"Characterization and comparative analysis of the complete Haemonchus contortus b-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes","translated_title":"","metadata":{"abstract":"Parasitic nematode β-tubulin genes are of particular interest because they are the targets of benzimidazole drugs. However, in spite of this, the full β-tubulin gene family has not been characterized for any parasitic nematode to date. Haemonchus contortus is the parasite species for which we understand benzimidazole resistance the best and its close phylogenetic relationship with Caenorhabditis elegans potentially allows inferences of gene function by comparative analysis. Consequently, we have characterized the full β-tubulin gene family in H. contortus. Further to the previously identified Hco-tbb-iso-1 and Hco-tbb-iso-2 genes, we have characterized two additional family members designated Hco-tbb-iso-3 and Hco-tbb-iso-4. We show that Hco-tbb-iso-1 is not a one-to-one orthologue with Cel-ben-1, the only β-tubulin gene in C. elegans that is a benzimidazole drug target. Instead, both Hco-tbb-iso-1 and Hco-tbb-iso-2 have a complex evolutionary relationship with three C. elegans β-tubulin genes: Cel-ben-1, Cel-tbb-1 and Cel-tbb-2. Furthermore, we show that both Hco-tbb-iso-1 and Hco-tbb-iso-2 are highly expressed in adult worms; in contrast, Hco-tbb-iso-3 and Hco-tbb-iso-4 are expressed only at very low levels and are orthologous to the Cel-mec-7 and Cel-tbb-4 genes, respectively, suggesting that they have specialized functional roles. Indeed, we have found that the expression pattern of Hco-tbb-iso-3 in H. contortus is identical to that of Cel-mec-7 in C. elegans, being expressed in just six \"touch receptor\" mechano-sensory neurons. These results suggest that further investigation is warranted into the potential involvement of strongylid isotype-2 β-tubulin genes in mechanisms of benzimidazole resistance.Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.","ai_title_tag":"H. contortus β-Tubulin Gene Family and Resistance"},"translated_abstract":"Parasitic nematode β-tubulin genes are of particular interest because they are the targets of benzimidazole drugs. However, in spite of this, the full β-tubulin gene family has not been characterized for any parasitic nematode to date. Haemonchus contortus is the parasite species for which we understand benzimidazole resistance the best and its close phylogenetic relationship with Caenorhabditis elegans potentially allows inferences of gene function by comparative analysis. Consequently, we have characterized the full β-tubulin gene family in H. contortus. Further to the previously identified Hco-tbb-iso-1 and Hco-tbb-iso-2 genes, we have characterized two additional family members designated Hco-tbb-iso-3 and Hco-tbb-iso-4. We show that Hco-tbb-iso-1 is not a one-to-one orthologue with Cel-ben-1, the only β-tubulin gene in C. elegans that is a benzimidazole drug target. Instead, both Hco-tbb-iso-1 and Hco-tbb-iso-2 have a complex evolutionary relationship with three C. elegans β-tubulin genes: Cel-ben-1, Cel-tbb-1 and Cel-tbb-2. Furthermore, we show that both Hco-tbb-iso-1 and Hco-tbb-iso-2 are highly expressed in adult worms; in contrast, Hco-tbb-iso-3 and Hco-tbb-iso-4 are expressed only at very low levels and are orthologous to the Cel-mec-7 and Cel-tbb-4 genes, respectively, suggesting that they have specialized functional roles. Indeed, we have found that the expression pattern of Hco-tbb-iso-3 in H. contortus is identical to that of Cel-mec-7 in C. elegans, being expressed in just six \"touch receptor\" mechano-sensory neurons. These results suggest that further investigation is warranted into the potential involvement of strongylid isotype-2 β-tubulin genes in mechanisms of benzimidazole resistance.Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.","internal_url":"https://www.academia.edu/5938566/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_b_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes","translated_internal_url":"","created_at":"2014-02-03T18:16:03.738-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":32910545,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910545/thumbnails/1.jpg","file_name":"SaundersWasmuthBeechLaingHuntNaghraCottonBerrimanBrittonGilleard_2013_CharacterizationAndComparativeAnalysisOfTheCompleteHaemonchusConto.pdf","download_url":"https://www.academia.edu/attachments/32910545/download_file","bulk_download_file_name":"Characterization_and_comparative_analysi.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910545/SaundersWasmuthBeechLaingHuntNaghraCottonBerrimanBrittonGilleard_2013_CharacterizationAndComparativeAnalysisOfTheCompleteHaemonchusConto-libre.pdf?1392033993=\u0026response-content-disposition=attachment%3B+filename%3DCharacterization_and_comparative_analysi.pdf\u0026Expires=1743265560\u0026Signature=MIxtdqLB0jf1Q6Voh7qdD0W61RVA7OreJEAwW~RRAVEf6UNCmccy2Pk~QxLZDas23jV-hmc4hrfOFGW2fvAWpu2B0~NiqhRkHfMhHF2-H-sYVdZRFQYwDNqGabPxgkAsMX-ly8rDf-Te93bwbeTQ~2zojVEw93VdSKGImo5KCb7Qu2LwGgFL-nlRBxxD4hQPPLKEPOTHeK4Qd1Nuh8v2Z93ffUzo8ISwooCcW0eVx4gz6mqT2vBx-V-BdI4YAcu5A8hGjE4CvVev2ZFJdlUVU4TMko4g7znHBDqDVK~QTR8-f2IzgPmurhraNJ~CA7f-ybMzNRGOxfixS~1u~dyvCw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_b_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes","translated_slug":"","page_count":11,"language":"en","content_type":"Work","summary":"Parasitic nematode β-tubulin genes are of particular interest because they are the targets of benzimidazole drugs. However, in spite of this, the full β-tubulin gene family has not been characterized for any parasitic nematode to date. Haemonchus contortus is the parasite species for which we understand benzimidazole resistance the best and its close phylogenetic relationship with Caenorhabditis elegans potentially allows inferences of gene function by comparative analysis. Consequently, we have characterized the full β-tubulin gene family in H. contortus. Further to the previously identified Hco-tbb-iso-1 and Hco-tbb-iso-2 genes, we have characterized two additional family members designated Hco-tbb-iso-3 and Hco-tbb-iso-4. We show that Hco-tbb-iso-1 is not a one-to-one orthologue with Cel-ben-1, the only β-tubulin gene in C. elegans that is a benzimidazole drug target. Instead, both Hco-tbb-iso-1 and Hco-tbb-iso-2 have a complex evolutionary relationship with three C. elegans β-tubulin genes: Cel-ben-1, Cel-tbb-1 and Cel-tbb-2. Furthermore, we show that both Hco-tbb-iso-1 and Hco-tbb-iso-2 are highly expressed in adult worms; in contrast, Hco-tbb-iso-3 and Hco-tbb-iso-4 are expressed only at very low levels and are orthologous to the Cel-mec-7 and Cel-tbb-4 genes, respectively, suggesting that they have specialized functional roles. Indeed, we have found that the expression pattern of Hco-tbb-iso-3 in H. contortus is identical to that of Cel-mec-7 in C. elegans, being expressed in just six \"touch receptor\" mechano-sensory neurons. These results suggest that further investigation is warranted into the potential involvement of strongylid isotype-2 β-tubulin genes in mechanisms of benzimidazole resistance.Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":32910545,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910545/thumbnails/1.jpg","file_name":"SaundersWasmuthBeechLaingHuntNaghraCottonBerrimanBrittonGilleard_2013_CharacterizationAndComparativeAnalysisOfTheCompleteHaemonchusConto.pdf","download_url":"https://www.academia.edu/attachments/32910545/download_file","bulk_download_file_name":"Characterization_and_comparative_analysi.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910545/SaundersWasmuthBeechLaingHuntNaghraCottonBerrimanBrittonGilleard_2013_CharacterizationAndComparativeAnalysisOfTheCompleteHaemonchusConto-libre.pdf?1392033993=\u0026response-content-disposition=attachment%3B+filename%3DCharacterization_and_comparative_analysi.pdf\u0026Expires=1743265560\u0026Signature=MIxtdqLB0jf1Q6Voh7qdD0W61RVA7OreJEAwW~RRAVEf6UNCmccy2Pk~QxLZDas23jV-hmc4hrfOFGW2fvAWpu2B0~NiqhRkHfMhHF2-H-sYVdZRFQYwDNqGabPxgkAsMX-ly8rDf-Te93bwbeTQ~2zojVEw93VdSKGImo5KCb7Qu2LwGgFL-nlRBxxD4hQPPLKEPOTHeK4Qd1Nuh8v2Z93ffUzo8ISwooCcW0eVx4gz6mqT2vBx-V-BdI4YAcu5A8hGjE4CvVev2ZFJdlUVU4TMko4g7znHBDqDVK~QTR8-f2IzgPmurhraNJ~CA7f-ybMzNRGOxfixS~1u~dyvCw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[],"urls":[{"id":2348733,"url":"http://www.ncbi.nlm.nih.gov/pubmed/23416426"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-5938566-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938512"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938512/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery"><img alt="Research paper thumbnail of The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery" class="work-thumbnail" src="https://attachments.academia-assets.com/32910513/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938512/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery">The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic ne...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. Conclusions: The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="7d2b813d818d6ad0e3066bc5c6d6c599" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910513,"asset_id":5938512,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910513/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938512"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938512"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938512; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938512]").text(description); $(".js-view-count[data-work-id=5938512]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938512; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938512']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "7d2b813d818d6ad0e3066bc5c6d6c599" } } $('.js-work-strip[data-work-id=5938512]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938512,"title":"The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery","translated_title":"","metadata":{"ai_title_tag":"Genome and Transcriptome of Haemonchus contortus","grobid_abstract":"Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. Conclusions: The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.","grobid_abstract_attachment_id":32910513},"translated_abstract":null,"internal_url":"https://www.academia.edu/5938512/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery","translated_internal_url":"","created_at":"2014-02-03T18:12:26.360-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":32910513,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910513/thumbnails/1.jpg","file_name":"LaingEtAl_2013_TheGenomeAndTranscriptomeOfHaemonchusContortusAKeyModelParasiteForDrugAndVaccineDiscovery_GenomeBiology.pdf","download_url":"https://www.academia.edu/attachments/32910513/download_file","bulk_download_file_name":"The_genome_and_transcriptome_of_Haemonch.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910513/LaingEtAl_2013_TheGenomeAndTranscriptomeOfHaemonchusContortusAKeyModelParasiteForDrugAndVaccineDiscovery_GenomeBiology-libre.pdf?1392033125=\u0026response-content-disposition=attachment%3B+filename%3DThe_genome_and_transcriptome_of_Haemonch.pdf\u0026Expires=1743265560\u0026Signature=PvXWAfFVIHLPXmHc5Qu0nLbdHxNbF--Uq9LxZzeyx7z~8pqYbrTpgu6vemv~XGBaFf6xxqYE4YzAXnUHThKT29AXc6LTzz5dAA3WkjE2JP2Zds4qNaJKxYUAp2y7W4leIIYfDWpnvA15Rp3ePai~IrDy0rcYykZnAgXL3aRWDi4wlQH5bYr-auavwEnNZuQ3KYYB~496yF3AbuJOQ3xhJlcVIwStXnvwSL827E4wAiA7PR8cgS44XlMaMlO~V2fAfOwQ2CKbyu7nFYrnGnc6qm1KRaO-JLuH6v18qRuJAv0ZnUhnbsaIaWU0vaRl7sKNbBHObNJeliRMyM3bjeSRkA__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery","translated_slug":"","page_count":16,"language":"en","content_type":"Work","summary":"Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. Conclusions: The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":32910513,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910513/thumbnails/1.jpg","file_name":"LaingEtAl_2013_TheGenomeAndTranscriptomeOfHaemonchusContortusAKeyModelParasiteForDrugAndVaccineDiscovery_GenomeBiology.pdf","download_url":"https://www.academia.edu/attachments/32910513/download_file","bulk_download_file_name":"The_genome_and_transcriptome_of_Haemonch.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910513/LaingEtAl_2013_TheGenomeAndTranscriptomeOfHaemonchusContortusAKeyModelParasiteForDrugAndVaccineDiscovery_GenomeBiology-libre.pdf?1392033125=\u0026response-content-disposition=attachment%3B+filename%3DThe_genome_and_transcriptome_of_Haemonch.pdf\u0026Expires=1743265560\u0026Signature=PvXWAfFVIHLPXmHc5Qu0nLbdHxNbF--Uq9LxZzeyx7z~8pqYbrTpgu6vemv~XGBaFf6xxqYE4YzAXnUHThKT29AXc6LTzz5dAA3WkjE2JP2Zds4qNaJKxYUAp2y7W4leIIYfDWpnvA15Rp3ePai~IrDy0rcYykZnAgXL3aRWDi4wlQH5bYr-auavwEnNZuQ3KYYB~496yF3AbuJOQ3xhJlcVIwStXnvwSL827E4wAiA7PR8cgS44XlMaMlO~V2fAfOwQ2CKbyu7nFYrnGnc6qm1KRaO-JLuH6v18qRuJAv0ZnUhnbsaIaWU0vaRl7sKNbBHObNJeliRMyM3bjeSRkA__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-5938512-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938482"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938482/The_peculiar_epidemiology_of_dracunculiasis_in_chad"><img alt="Research paper thumbnail of The peculiar epidemiology of dracunculiasis in chad" class="work-thumbnail" src="https://attachments.academia-assets.com/49083292/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938482/The_peculiar_epidemiology_of_dracunculiasis_in_chad">The peculiar epidemiology of dracunculiasis in chad</a></div><div class="wp-workCard_item"><span>The American journal of tropical medicine and hygiene</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Dracunculiasis was rediscovered in Chad in 2010 after an apparent absence of 10 years. In April 2...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Dracunculiasis was rediscovered in Chad in 2010 after an apparent absence of 10 years. In April 2012 active village-based surveillance was initiated to determine where, when, and how transmission of the disease was occurring, and to implement interventions to interrupt it. The current epidemiologic pattern of the disease in Chad is unlike that seen previously in Chad or other endemic countries, i.e., no clustering of cases by village or association with a common water source, the average number of worms per person was small, and a large number of dogs were found to be infected. Molecular sequencing suggests these infections were all caused by Dracunculus medinensis. It appears that the infection in dogs is serving as the major driving force sustaining transmission in Chad, that an aberrant life cycle involving a paratenic host common to people and dogs is occurring, and that the cases in humans are sporadic and incidental.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="4c1966b079000edb75b9e356a61922f3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":49083292,"asset_id":5938482,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/49083292/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938482"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938482"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938482; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938482]").text(description); $(".js-view-count[data-work-id=5938482]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938482; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938482']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "4c1966b079000edb75b9e356a61922f3" } } $('.js-work-strip[data-work-id=5938482]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938482,"title":"The peculiar epidemiology of dracunculiasis in chad","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Dracunculiasis was rediscovered in Chad in 2010 after an apparent absence of 10 years. In April 2012 active village-based surveillance was initiated to determine where, when, and how transmission of the disease was occurring, and to implement interventions to interrupt it. The current epidemiologic pattern of the disease in Chad is unlike that seen previously in Chad or other endemic countries, i.e., no clustering of cases by village or association with a common water source, the average number of worms per person was small, and a large number of dogs were found to be infected. Molecular sequencing suggests these infections were all caused by Dracunculus medinensis. It appears that the infection in dogs is serving as the major driving force sustaining transmission in Chad, that an aberrant life cycle involving a paratenic host common to people and dogs is occurring, and that the cases in humans are sporadic and incidental.","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The American journal of tropical medicine and hygiene","grobid_abstract_attachment_id":49083292},"translated_abstract":null,"internal_url":"https://www.academia.edu/5938482/The_peculiar_epidemiology_of_dracunculiasis_in_chad","translated_internal_url":"","created_at":"2014-02-03T18:10:14.083-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":49083292,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/49083292/thumbnails/1.jpg","file_name":"The_Peculiar_Epidemiology_of_Dracunculia20160924-14558-yubiwf.pdf","download_url":"https://www.academia.edu/attachments/49083292/download_file","bulk_download_file_name":"The_peculiar_epidemiology_of_dracunculia.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/49083292/The_Peculiar_Epidemiology_of_Dracunculia20160924-14558-yubiwf-libre.pdf?1474720240=\u0026response-content-disposition=attachment%3B+filename%3DThe_peculiar_epidemiology_of_dracunculia.pdf\u0026Expires=1743265561\u0026Signature=MMH2aK5Ywpbp~wj~THxH1uxeKGK-Rimaw5lP70AEBj0ncLjwCCyOE3CTD1cY3tyZDC51bDJYbtAgyU9bKW6SBXbiqnJbI6of7H~x8w35AWNOs~7n8Uc7s8FlCJAE5RY-e-dSLbNVJTfOrWC9lV1~UQ7FQuCRf4mKksSpqKwAhweVb-JniET1qmBF1NHyya~Dlmm9N9v1M3nqfGFmSTD0cudYSjFGl1X5M-ZDmIa7zJGr2rDEENiHK1d83uWwno7jlCR5SJH13ZaqO0-qZ4etyofWIF-zNU5L4xIVp3TPq9D18b4DqWP~VUDc3idO7UsgiQ96JnXV1Rnk4eZBCwNxQg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"The_peculiar_epidemiology_of_dracunculiasis_in_chad","translated_slug":"","page_count":10,"language":"en","content_type":"Work","summary":"Dracunculiasis was rediscovered in Chad in 2010 after an apparent absence of 10 years. In April 2012 active village-based surveillance was initiated to determine where, when, and how transmission of the disease was occurring, and to implement interventions to interrupt it. The current epidemiologic pattern of the disease in Chad is unlike that seen previously in Chad or other endemic countries, i.e., no clustering of cases by village or association with a common water source, the average number of worms per person was small, and a large number of dogs were found to be infected. Molecular sequencing suggests these infections were all caused by Dracunculus medinensis. It appears that the infection in dogs is serving as the major driving force sustaining transmission in Chad, that an aberrant life cycle involving a paratenic host common to people and dogs is occurring, and that the cases in humans are sporadic and incidental.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":49083292,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/49083292/thumbnails/1.jpg","file_name":"The_Peculiar_Epidemiology_of_Dracunculia20160924-14558-yubiwf.pdf","download_url":"https://www.academia.edu/attachments/49083292/download_file","bulk_download_file_name":"The_peculiar_epidemiology_of_dracunculia.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/49083292/The_Peculiar_Epidemiology_of_Dracunculia20160924-14558-yubiwf-libre.pdf?1474720240=\u0026response-content-disposition=attachment%3B+filename%3DThe_peculiar_epidemiology_of_dracunculia.pdf\u0026Expires=1743265561\u0026Signature=MMH2aK5Ywpbp~wj~THxH1uxeKGK-Rimaw5lP70AEBj0ncLjwCCyOE3CTD1cY3tyZDC51bDJYbtAgyU9bKW6SBXbiqnJbI6of7H~x8w35AWNOs~7n8Uc7s8FlCJAE5RY-e-dSLbNVJTfOrWC9lV1~UQ7FQuCRf4mKksSpqKwAhweVb-JniET1qmBF1NHyya~Dlmm9N9v1M3nqfGFmSTD0cudYSjFGl1X5M-ZDmIa7zJGr2rDEENiHK1d83uWwno7jlCR5SJH13ZaqO0-qZ4etyofWIF-zNU5L4xIVp3TPq9D18b4DqWP~VUDc3idO7UsgiQ96JnXV1Rnk4eZBCwNxQg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":29570,"name":"Chad","url":"https://www.academia.edu/Documents/in/Chad"},{"id":52438,"name":"Dogs","url":"https://www.academia.edu/Documents/in/Dogs"},{"id":1739635,"name":"Dracunculiasis","url":"https://www.academia.edu/Documents/in/Dracunculiasis"}],"urls":[{"id":2348706,"url":"http://dx.doi.org/10.4269/ajtmh.13-0554"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-5938482-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938481"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938481/Genomic_confirmation_of_hybridisation_and_recent_inbreeding_in_a_vector_isolated_leishmania_population"><img alt="Research paper thumbnail of Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated leishmania population" class="work-thumbnail" src="https://attachments.academia-assets.com/49083291/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938481/Genomic_confirmation_of_hybridisation_and_recent_inbreeding_in_a_vector_isolated_leishmania_population">Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated leishmania population</a></div><div class="wp-workCard_item"><span>PLoS genetics</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Although asexual reproduction via clonal propagation has been proposed as the principal reproduct...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Although asexual reproduction via clonal propagation has been proposed as the principal reproductive mechanism across parasitic protozoa of the Leishmania genus, sexual recombination has long been suspected, based on hybrid marker profiles detected in field isolates from different geographical locations. The recent experimental demonstration of a sexual cycle in Leishmania within sand flies has confirmed the occurrence of hybridisation, but knowledge of the parasite life cycle in the wild still remains limited. Here, we use whole genome sequencing to investigate the frequency of sexual reproduction in Leishmania, by sequencing the genomes of 11 Leishmania infantum isolates from sand flies and 1 patient isolate in a focus of cutaneous leishmaniasis in the Ç ukurova province of southeast Turkey. This is the first genome-wide examination of a vector-isolated population of Leishmania parasites. A genome-wide pattern of patchy heterozygosity and SNP density was observed both within individual strains and across the whole group. Comparisons with other Leishmania donovani complex genome sequences suggest that these isolates are derived from a single cross of two diverse strains with subsequent recombination within the population. This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. This observation allowed us to estimate the relative rates of sexual and asexual reproduction within this population, to our knowledge the first quantitative estimate of these events during the Leishmania life cycle.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="7dc3672e62c6541e6c7baeea0cd1a3c3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":49083291,"asset_id":5938481,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/49083291/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938481"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938481"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938481; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938481]").text(description); $(".js-view-count[data-work-id=5938481]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938481; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938481']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "7dc3672e62c6541e6c7baeea0cd1a3c3" } } $('.js-work-strip[data-work-id=5938481]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938481,"title":"Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated leishmania population","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Although asexual reproduction via clonal propagation has been proposed as the principal reproductive mechanism across parasitic protozoa of the Leishmania genus, sexual recombination has long been suspected, based on hybrid marker profiles detected in field isolates from different geographical locations. The recent experimental demonstration of a sexual cycle in Leishmania within sand flies has confirmed the occurrence of hybridisation, but knowledge of the parasite life cycle in the wild still remains limited. Here, we use whole genome sequencing to investigate the frequency of sexual reproduction in Leishmania, by sequencing the genomes of 11 Leishmania infantum isolates from sand flies and 1 patient isolate in a focus of cutaneous leishmaniasis in the Ç ukurova province of southeast Turkey. This is the first genome-wide examination of a vector-isolated population of Leishmania parasites. A genome-wide pattern of patchy heterozygosity and SNP density was observed both within individual strains and across the whole group. Comparisons with other Leishmania donovani complex genome sequences suggest that these isolates are derived from a single cross of two diverse strains with subsequent recombination within the population. This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. 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This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. 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Here, we report a high-quality reference genome sequence for a strain of L. donovani from Nepal, and use this sequence to study variation in a set of 16 related clinical lines, isolated from visceral leishmaniasis patients from the same region, which also differ in their response to in vitro drug susceptibility.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="2751229"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="2751229"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 2751229; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=2751229]").text(description); $(".js-view-count[data-work-id=2751229]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 2751229; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='2751229']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=2751229]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":2751229,"title":"Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance","translated_title":"","metadata":{"abstract":"Abstract Visceral leishmaniasis is a potentially fatal disease endemic to large parts of Asia and Africa, primarily caused by the protozoan parasite Leishmania donovani. 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Here, we report a high-quality reference genome sequence for a strain of L. donovani from Nepal, and use this sequence to study variation in a set of 16 related clinical lines, isolated from visceral leishmaniasis patients from the same region, which also differ in their response to in vitro drug susceptibility.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[],"research_interests":[],"urls":[{"id":644585,"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227103/"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-2751229-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="2751167"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/2751167/Comparative_Genomics_of_the_Apicomplexan_Parasites_Toxoplasma_gondii_and_Neospora_caninum_Coccidia_Differing_in_Host_Range_and_Transmission_Strategy"><img alt="Research paper thumbnail of Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy" class="work-thumbnail" src="https://attachments.academia-assets.com/31008116/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/2751167/Comparative_Genomics_of_the_Apicomplexan_Parasites_Toxoplasma_gondii_and_Neospora_caninum_Coccidia_Differing_in_Host_Range_and_Transmission_Strategy">Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human po...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="a406de95b403b999eb41ea723c565e21" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":31008116,"asset_id":2751167,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/31008116/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="2751167"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="2751167"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 2751167; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=2751167]").text(description); $(".js-view-count[data-work-id=2751167]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 2751167; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='2751167']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "a406de95b403b999eb41ea723c565e21" } } $('.js-work-strip[data-work-id=2751167]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":2751167,"title":"Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy","translated_title":"","metadata":{"abstract":"Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. 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The generally well-supported and resolved phylogeny displayed the following relationships among the five nominate species sampled:(B. boulengeri ((B. taitanus, B. niedeni),(B. changamwensis, B. uluguruensis))).</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="fd8240fceecac47db72619cee4e43cd7" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":30723332,"asset_id":2751255,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/30723332/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="2751255"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="2751255"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 2751255; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=2751255]").text(description); $(".js-view-count[data-work-id=2751255]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 2751255; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='2751255']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "fd8240fceecac47db72619cee4e43cd7" } } $('.js-work-strip[data-work-id=2751255]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":2751255,"title":"Molecular phylogenetics of Boulengerula (Amphibia: Gymnophiona: Caeciliidae) and implications for taxonomy, biogeography and conservation","translated_title":"","metadata":{"abstract":"Abstract: Phylogenetic relationships of the East African caeciliid Boulengerula were reconstructed using 12S, 16S and cytb mitochondrial gene sequences for 32 samples from Kenya and Tanzania. 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This paper argues that eukaryotic genes derived from archaebacterial origins are more functionally important than the much more numerous eubacterial genes. 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profile--work_container" data-work-id="8008454"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008454/Phylogenomic_analyses_elucidate_the_evolutionary_relationships_of_bats"><img alt="Research paper thumbnail of Phylogenomic analyses elucidate the evolutionary relationships of bats" class="work-thumbnail" src="https://attachments.academia-assets.com/48255232/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008454/Phylogenomic_analyses_elucidate_the_evolutionary_relationships_of_bats">Phylogenomic analyses elucidate the evolutionary relationships of bats</a></div><div class="wp-workCard_item"><span>Current biology : CB</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal g...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups , yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) . Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic [7-9] or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes , we show that-contrary to recent suggestions-bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="ebbac085c20dc090cd4b5172be74ab9b" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255232,"asset_id":8008454,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255232/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008454"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008454"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008454; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008454]").text(description); $(".js-view-count[data-work-id=8008454]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008454; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008454']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "ebbac085c20dc090cd4b5172be74ab9b" } } $('.js-work-strip[data-work-id=8008454]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008454,"title":"Phylogenomic analyses elucidate the evolutionary relationships of bats","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","ai_title_tag":"Bats' Evolutionary Relationships Revealed","grobid_abstract":"Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups , yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) . Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic [7-9] or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes , we show that-contrary to recent suggestions-bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era.","publication_date":{"day":null,"month":null,"year":2013,"errors":{}},"publication_name":"Current biology : CB","grobid_abstract_attachment_id":48255232},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008454/Phylogenomic_analyses_elucidate_the_evolutionary_relationships_of_bats","translated_internal_url":"","created_at":"2014-08-18T01:12:17.417-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255232,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255232/thumbnails/1.jpg","file_name":"00463528bf07e3d93d000000.pdf","download_url":"https://www.academia.edu/attachments/48255232/download_file","bulk_download_file_name":"Phylogenomic_analyses_elucidate_the_evol.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255232/00463528bf07e3d93d000000-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DPhylogenomic_analyses_elucidate_the_evol.pdf\u0026Expires=1743265560\u0026Signature=FoE26hfm9AQ1~3WOWDoLKFKH-YC1t11xlOX0AOqdLvxshtXfFGNkIrHqqEsQ6JIw0z4NizhAIbPry-mqYLrG85AFIW0LEolZ94gA89tAQfQ5P14FT1bVJBum3U7Fyi-cwv0iL4FIFj4uArPtzOPsqHbJwQZiZ0HxYsQ1jQmCm8aqcT3rQ9ARytR18PFOXKuEWeblAB8mQMTxv9npQgqBt-KhO593vN9~TAx1Ik~oqYHgJMtFMwNznd91p~WZpmHMKoh2qMqjxLg71OvL2RaUsbmK0sh3OJfi-TujrbFetD8YPocPZRKRMQnjvA--e9zT5EtdEvrXw1o3LU4PzgKdWQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Phylogenomic_analyses_elucidate_the_evolutionary_relationships_of_bats","translated_slug":"","page_count":6,"language":"en","content_type":"Work","summary":"Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups , yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) . Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic [7-9] or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes , we show that-contrary to recent suggestions-bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255232,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255232/thumbnails/1.jpg","file_name":"00463528bf07e3d93d000000.pdf","download_url":"https://www.academia.edu/attachments/48255232/download_file","bulk_download_file_name":"Phylogenomic_analyses_elucidate_the_evol.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255232/00463528bf07e3d93d000000-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DPhylogenomic_analyses_elucidate_the_evol.pdf\u0026Expires=1743265560\u0026Signature=FoE26hfm9AQ1~3WOWDoLKFKH-YC1t11xlOX0AOqdLvxshtXfFGNkIrHqqEsQ6JIw0z4NizhAIbPry-mqYLrG85AFIW0LEolZ94gA89tAQfQ5P14FT1bVJBum3U7Fyi-cwv0iL4FIFj4uArPtzOPsqHbJwQZiZ0HxYsQ1jQmCm8aqcT3rQ9ARytR18PFOXKuEWeblAB8mQMTxv9npQgqBt-KhO593vN9~TAx1Ik~oqYHgJMtFMwNznd91p~WZpmHMKoh2qMqjxLg71OvL2RaUsbmK0sh3OJfi-TujrbFetD8YPocPZRKRMQnjvA--e9zT5EtdEvrXw1o3LU4PzgKdWQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":4207,"name":"Phylogenetics","url":"https://www.academia.edu/Documents/in/Phylogenetics"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":4967,"name":"Molecular Evolution","url":"https://www.academia.edu/Documents/in/Molecular_Evolution"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"},{"id":11186,"name":"Mammalogy","url":"https://www.academia.edu/Documents/in/Mammalogy"},{"id":18075,"name":"Bats (Mammalogy)","url":"https://www.academia.edu/Documents/in/Bats_Mammalogy_"},{"id":27230,"name":"Chiroptera","url":"https://www.academia.edu/Documents/in/Chiroptera"},{"id":34912,"name":"Phylogenomics","url":"https://www.academia.edu/Documents/in/Phylogenomics"},{"id":47884,"name":"Biological Sciences","url":"https://www.academia.edu/Documents/in/Biological_Sciences"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":170896,"name":"Echolocation","url":"https://www.academia.edu/Documents/in/Echolocation"},{"id":176486,"name":"Genome","url":"https://www.academia.edu/Documents/in/Genome"},{"id":191815,"name":"Biological evolution","url":"https://www.academia.edu/Documents/in/Biological_evolution"}],"urls":[{"id":3350935,"url":"http://dx.doi.org/10.1016/j.cub.2013.09.014"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008454-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008453"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008453/The_evolution_of_bat_vestibular_systems_in_the_face_of_potential_antagonistic_selection_pressures_for_flight_and_echolocation"><img alt="Research paper thumbnail of The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation" class="work-thumbnail" src="https://attachments.academia-assets.com/48255277/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008453/The_evolution_of_bat_vestibular_systems_in_the_face_of_potential_antagonistic_selection_pressures_for_flight_and_echolocation">The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation</a></div><div class="wp-workCard_item"><span>PloS one</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The vestibular system maintains the body's sense of balance and, therefore, was probably subject ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The vestibular system maintains the body's sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged semicircular canals. Second, many bats have enlarged cochleae associated with echolocation, and both cochleae and semicircular canals share a space within the petrosal bone. To determine how bat vestibular systems have evolved in the face of these pressures, we used micro-CT scans to compare canal morphology across species with contrasting flight and echolocation capabilities. We found no increase in canal radius in bats associated with the acquisition of powered flight, but canal radius did correlate with body mass in bat species from the suborder Yangochiroptera, and also in non-echolocating Old World fruit bats from the suborder Yinpterochiroptera. No such trend was seen in members of the Yinpterochiroptera that use laryngeal echolocation, although canal radius was associated with wing-tip roundedness in this group. We also found that the vestibular system scaled with cochlea size, although the relationship differed in species that use constant frequency echolocation. Across all bats, the shape of the anterior and lateral canals was associated with large cochlea size and small body size respectively, suggesting differential spatial constraints on each canal depending on its orientation within the skull. Thus in many echolocating bats, it seems that the combination of small body size and enlarged cochlea together act as a principal force on the vestibular system. The two main groups of echolocating bats displayed different canal morphologies, in terms of size and shape in relation to body mass and cochlear size, thus suggesting independent evolutionary pathways and offering tentative support for multiple acquisitions of echolocation.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8759fe958ed961cefadc27da0e8ee52a" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255277,"asset_id":8008453,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255277/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008453"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008453"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008453; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008453]").text(description); $(".js-view-count[data-work-id=8008453]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008453; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008453']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "8759fe958ed961cefadc27da0e8ee52a" } } $('.js-work-strip[data-work-id=8008453]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008453,"title":"The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"The vestibular system maintains the body's sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. 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No such trend was seen in members of the Yinpterochiroptera that use laryngeal echolocation, although canal radius was associated with wing-tip roundedness in this group. We also found that the vestibular system scaled with cochlea size, although the relationship differed in species that use constant frequency echolocation. Across all bats, the shape of the anterior and lateral canals was associated with large cochlea size and small body size respectively, suggesting differential spatial constraints on each canal depending on its orientation within the skull. Thus in many echolocating bats, it seems that the combination of small body size and enlarged cochlea together act as a principal force on the vestibular system. 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Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged semicircular canals. Second, many bats have enlarged cochleae associated with echolocation, and both cochleae and semicircular canals share a space within the petrosal bone. To determine how bat vestibular systems have evolved in the face of these pressures, we used micro-CT scans to compare canal morphology across species with contrasting flight and echolocation capabilities. We found no increase in canal radius in bats associated with the acquisition of powered flight, but canal radius did correlate with body mass in bat species from the suborder Yangochiroptera, and also in non-echolocating Old World fruit bats from the suborder Yinpterochiroptera. No such trend was seen in members of the Yinpterochiroptera that use laryngeal echolocation, although canal radius was associated with wing-tip roundedness in this group. We also found that the vestibular system scaled with cochlea size, although the relationship differed in species that use constant frequency echolocation. Across all bats, the shape of the anterior and lateral canals was associated with large cochlea size and small body size respectively, suggesting differential spatial constraints on each canal depending on its orientation within the skull. Thus in many echolocating bats, it seems that the combination of small body size and enlarged cochlea together act as a principal force on the vestibular system. The two main groups of echolocating bats displayed different canal morphologies, in terms of size and shape in relation to body mass and cochlear size, thus suggesting independent evolutionary pathways and offering tentative support for multiple acquisitions of echolocation.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255277,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255277/thumbnails/1.jpg","file_name":"The_Evolution_of_Bat_Vestibular_Systems_20160823-28130-dptk1r.pdf","download_url":"https://www.academia.edu/attachments/48255277/download_file","bulk_download_file_name":"The_evolution_of_bat_vestibular_systems.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255277/The_Evolution_of_Bat_Vestibular_Systems_20160823-28130-dptk1r-libre.pdf?1471956956=\u0026response-content-disposition=attachment%3B+filename%3DThe_evolution_of_bat_vestibular_systems.pdf\u0026Expires=1743265560\u0026Signature=RTmqyH~YdjIUkztXGO8zv7iJjXtWrDF40w0As2K7Wu~dh1QbxiDDp9SDI0Q12LdAOvIjERwKINHDjZK3MJZ7fFeMDqr3UzcdS9RbRlWHbe~rQdLtbLfQWr09TvQvfAB3pwOLyzkAI-nKMR3zoogke1c7x~tTc20Y2L-ez0MbrpVxsMUpU5eQzLkV25SZEIdeJCO39GuuGgmreMkuUqI7bniEGZKzt83cnhSDxyp6FzCJTWaeFmbgz~o7hO-brFis2HMjRSLsFx7dzcs2h7Z-eUsOmzP-OUASfv8hfSMkH3gPmn82NxO2Z22kCRUeAVBdunmxDrp5VCuwxL0gTKZG2Q__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":27230,"name":"Chiroptera","url":"https://www.academia.edu/Documents/in/Chiroptera"},{"id":28235,"name":"Multidisciplinary","url":"https://www.academia.edu/Documents/in/Multidisciplinary"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":170896,"name":"Echolocation","url":"https://www.academia.edu/Documents/in/Echolocation"},{"id":191815,"name":"Biological evolution","url":"https://www.academia.edu/Documents/in/Biological_evolution"},{"id":197299,"name":"Inner Ear","url":"https://www.academia.edu/Documents/in/Inner_Ear"},{"id":220780,"name":"PLoS one","url":"https://www.academia.edu/Documents/in/PLoS_one"},{"id":1151963,"name":"Cochlea","url":"https://www.academia.edu/Documents/in/Cochlea"},{"id":2253257,"name":"Wing","url":"https://www.academia.edu/Documents/in/Wing"}],"urls":[{"id":3350934,"url":"http://dx.doi.org/10.1371/journal.pone.0061998"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008453-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008452"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008452/New_approaches_for_unravelling_reassortment_pathways"><img alt="Research paper thumbnail of New approaches for unravelling reassortment pathways" class="work-thumbnail" src="https://attachments.academia-assets.com/48255288/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008452/New_approaches_for_unravelling_reassortment_pathways">New approaches for unravelling reassortment pathways</a></div><div class="wp-workCard_item"><span>BMC evolutionary biology</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: Every year the human population encounters epidemic outbreaks of influenza, and histo...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="b011408280dee1e815807bf70d0d632d" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255288,"asset_id":8008452,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255288/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008452"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008452"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008452; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008452]").text(description); $(".js-view-count[data-work-id=8008452]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008452; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008452']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "b011408280dee1e815807bf70d0d632d" } } $('.js-work-strip[data-work-id=8008452]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008452,"title":"New approaches for unravelling reassortment pathways","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","ai_title_tag":"Identifying Reassortant Influenza Strains","grobid_abstract":"Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.","publication_date":{"day":null,"month":null,"year":2013,"errors":{}},"publication_name":"BMC evolutionary biology","grobid_abstract_attachment_id":48255288},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008452/New_approaches_for_unravelling_reassortment_pathways","translated_internal_url":"","created_at":"2014-08-18T01:12:15.820-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255288,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255288/thumbnails/1.jpg","file_name":"1471-2148-13-1.pdf","download_url":"https://www.academia.edu/attachments/48255288/download_file","bulk_download_file_name":"New_approaches_for_unravelling_reassortm.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255288/1471-2148-13-1-libre.pdf?1471956956=\u0026response-content-disposition=attachment%3B+filename%3DNew_approaches_for_unravelling_reassortm.pdf\u0026Expires=1743265560\u0026Signature=dE53b9WVEbvWB8Mu51VKbIlkLITDTlVsAr~D6NW~~0jARLqTgbm5AGedkEUppHUEDa-Jto62eFk-Kiv~G4Rkk~zBAbryYdejBIFzPg2Navqmqvvd4nuthMeQfch68pkrLyIQCdEWxpZdT-6RMabFZKjVXRQFTKGkTnqJuJK88e~IYtWbiTygvOKll-t60~BulenfR-8nepu1xec2ceHUw4OUbJHqhx0~oHt6ZaEJ25-cc6sNe6b4ZOE697GCgrDdapOJXwZ248CW3w9GRMOXeLa6-efIGkrJelVUhiYMME~qe2I5ZGAFgjqGlikkLoGj3nlkpo6hc-24WstVgJWoow__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"New_approaches_for_unravelling_reassortment_pathways","translated_slug":"","page_count":14,"language":"en","content_type":"Work","summary":"Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255288,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255288/thumbnails/1.jpg","file_name":"1471-2148-13-1.pdf","download_url":"https://www.academia.edu/attachments/48255288/download_file","bulk_download_file_name":"New_approaches_for_unravelling_reassortm.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255288/1471-2148-13-1-libre.pdf?1471956956=\u0026response-content-disposition=attachment%3B+filename%3DNew_approaches_for_unravelling_reassortm.pdf\u0026Expires=1743265560\u0026Signature=dE53b9WVEbvWB8Mu51VKbIlkLITDTlVsAr~D6NW~~0jARLqTgbm5AGedkEUppHUEDa-Jto62eFk-Kiv~G4Rkk~zBAbryYdejBIFzPg2Navqmqvvd4nuthMeQfch68pkrLyIQCdEWxpZdT-6RMabFZKjVXRQFTKGkTnqJuJK88e~IYtWbiTygvOKll-t60~BulenfR-8nepu1xec2ceHUw4OUbJHqhx0~oHt6ZaEJ25-cc6sNe6b4ZOE697GCgrDdapOJXwZ248CW3w9GRMOXeLa6-efIGkrJelVUhiYMME~qe2I5ZGAFgjqGlikkLoGj3nlkpo6hc-24WstVgJWoow__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":428,"name":"Algorithms","url":"https://www.academia.edu/Documents/in/Algorithms"},{"id":2513,"name":"Molecular Biology","url":"https://www.academia.edu/Documents/in/Molecular_Biology"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"},{"id":25021,"name":"Hong Kong","url":"https://www.academia.edu/Documents/in/Hong_Kong"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":561000,"name":"influenza A virus","url":"https://www.academia.edu/Documents/in/influenza_A_virus"},{"id":880279,"name":"Bayes Theorem","url":"https://www.academia.edu/Documents/in/Bayes_Theorem-1"},{"id":1191613,"name":"Likelihood Functions","url":"https://www.academia.edu/Documents/in/Likelihood_Functions"}],"urls":[{"id":3350933,"url":"http://dx.doi.org/10.1186/1471-2148-13-1"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008452-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008450"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008450/The_genome_and_life_stage_specific_transcriptomes_of_Globodera_pallida_elucidate_key_aspects_of_plant_parasitism_by_a_cyst_nematode"><img alt="Research paper thumbnail of The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode" class="work-thumbnail" src="https://attachments.academia-assets.com/48255291/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008450/The_genome_and_life_stage_specific_transcriptomes_of_Globodera_pallida_elucidate_key_aspects_of_plant_parasitism_by_a_cyst_nematode">The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode</a></div><div class="wp-workCard_item"><span>Genome biology</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Globodera pallida is a devastating pathogen of potato crops, making it one of the most economical...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="e5e56efd61321808d5dac44bb94eced2" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255291,"asset_id":8008450,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255291/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008450"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008450"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008450; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008450]").text(description); $(".js-view-count[data-work-id=8008450]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008450; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008450']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "e5e56efd61321808d5dac44bb94eced2" } } $('.js-work-strip[data-work-id=8008450]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008450,"title":"The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. 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Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="1f615450f4c17016f546d12e8074d118" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255297,"asset_id":8008449,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255297/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008449"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008449"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008449; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008449]").text(description); $(".js-view-count[data-work-id=8008449]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008449; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008449']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "1f615450f4c17016f546d12e8074d118" } } $('.js-work-strip[data-work-id=8008449]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008449,"title":"Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.","publication_date":{"day":null,"month":null,"year":2012,"errors":{}},"publication_name":"PLoS pathogens","grobid_abstract_attachment_id":48255297},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008449/Comparative_genomics_of_the_apicomplexan_parasites_Toxoplasma_gondii_and_Neospora_caninum_Coccidia_differing_in_host_range_and_transmission_strategy","translated_internal_url":"","created_at":"2014-08-18T01:11:55.607-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255297,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255297/thumbnails/1.jpg","file_name":"journal.ppat.1002567.pdf","download_url":"https://www.academia.edu/attachments/48255297/download_file","bulk_download_file_name":"Comparative_genomics_of_the_apicomplexan.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255297/journal.ppat.1002567-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DComparative_genomics_of_the_apicomplexan.pdf\u0026Expires=1743265560\u0026Signature=bxUXUnxIyE8T7uXu4Wb57RYwlRLbU7bZ4CzH3vmSJ5JoK8N6bS8NrowtdpKDxReEMslpte9vfZncp7LNFyy4MHViY4FupBIA1wC8cNLsJwjlUxQHMiXhw~LHA~NX6i2Dyi8ATXSVHO0GeDWNbhvb35SH2hG9pH~wofDQaK7myKhb1AqEKSXqrYueA7ASRJEIYoFa8MKomsupJQUB7Xqg~XnpUgd2GpZpQNONb2G1mfiqyqebHAnUOJuX8EiFaNQFH4X6VqZkoQ9ccPTGA7iKoXtiRAGuAUABwxo0fLah7NtM9CjIJpRg7CPBtP2CxuHTq9oXEown0w7HnmVTMHxryQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Comparative_genomics_of_the_apicomplexan_parasites_Toxoplasma_gondii_and_Neospora_caninum_Coccidia_differing_in_host_range_and_transmission_strategy","translated_slug":"","page_count":15,"language":"en","content_type":"Work","summary":"Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255297,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255297/thumbnails/1.jpg","file_name":"journal.ppat.1002567.pdf","download_url":"https://www.academia.edu/attachments/48255297/download_file","bulk_download_file_name":"Comparative_genomics_of_the_apicomplexan.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255297/journal.ppat.1002567-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DComparative_genomics_of_the_apicomplexan.pdf\u0026Expires=1743265560\u0026Signature=bxUXUnxIyE8T7uXu4Wb57RYwlRLbU7bZ4CzH3vmSJ5JoK8N6bS8NrowtdpKDxReEMslpte9vfZncp7LNFyy4MHViY4FupBIA1wC8cNLsJwjlUxQHMiXhw~LHA~NX6i2Dyi8ATXSVHO0GeDWNbhvb35SH2hG9pH~wofDQaK7myKhb1AqEKSXqrYueA7ASRJEIYoFa8MKomsupJQUB7Xqg~XnpUgd2GpZpQNONb2G1mfiqyqebHAnUOJuX8EiFaNQFH4X6VqZkoQ9ccPTGA7iKoXtiRAGuAUABwxo0fLah7NtM9CjIJpRg7CPBtP2CxuHTq9oXEown0w7HnmVTMHxryQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":159,"name":"Microbiology","url":"https://www.academia.edu/Documents/in/Microbiology"},{"id":1290,"name":"Immunology","url":"https://www.academia.edu/Documents/in/Immunology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":5504,"name":"Comparative Genomics","url":"https://www.academia.edu/Documents/in/Comparative_Genomics"},{"id":6947,"name":"Medical Microbiology","url":"https://www.academia.edu/Documents/in/Medical_Microbiology"},{"id":13345,"name":"Apicomplexans","url":"https://www.academia.edu/Documents/in/Apicomplexans"},{"id":13346,"name":"Toxoplasma","url":"https://www.academia.edu/Documents/in/Toxoplasma"},{"id":19080,"name":"Zoonoses","url":"https://www.academia.edu/Documents/in/Zoonoses"},{"id":19652,"name":"Ecological Niche Modeling","url":"https://www.academia.edu/Documents/in/Ecological_Niche_Modeling"},{"id":27784,"name":"Gene expression","url":"https://www.academia.edu/Documents/in/Gene_expression"},{"id":37798,"name":"Toxoplasmosis","url":"https://www.academia.edu/Documents/in/Toxoplasmosis"},{"id":37801,"name":"Toxoplasma gondii","url":"https://www.academia.edu/Documents/in/Toxoplasma_gondii"},{"id":52873,"name":"Virulence","url":"https://www.academia.edu/Documents/in/Virulence"},{"id":74253,"name":"Neospora","url":"https://www.academia.edu/Documents/in/Neospora"},{"id":142138,"name":"Host-parasite interactions","url":"https://www.academia.edu/Documents/in/Host-parasite_interactions"},{"id":587939,"name":"Virulence factor","url":"https://www.academia.edu/Documents/in/Virulence_factor"},{"id":589504,"name":"Coccidiosis","url":"https://www.academia.edu/Documents/in/Coccidiosis"},{"id":750576,"name":"Host Range","url":"https://www.academia.edu/Documents/in/Host_Range"},{"id":906078,"name":"Neospora Caninum","url":"https://www.academia.edu/Documents/in/Neospora_Caninum"},{"id":965375,"name":"Vertical Transmission","url":"https://www.academia.edu/Documents/in/Vertical_Transmission"},{"id":999803,"name":"Gene Family","url":"https://www.academia.edu/Documents/in/Gene_Family"},{"id":1557716,"name":"Comparative Genomic Hybridization","url":"https://www.academia.edu/Documents/in/Comparative_Genomic_Hybridization"},{"id":1763968,"name":"Gene Expression Regulation","url":"https://www.academia.edu/Documents/in/Gene_Expression_Regulation"}],"urls":[{"id":3350930,"url":"http://dx.doi.org/10.1371/journal.ppat.1002567"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008449-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008447"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008447/Experimental_design_in_phylogenetics_testing_predictions_from_expected_information"><img alt="Research paper thumbnail of Experimental design in phylogenetics: testing predictions from expected information" class="work-thumbnail" src="https://attachments.academia-assets.com/48255271/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008447/Experimental_design_in_phylogenetics_testing_predictions_from_expected_information">Experimental design in phylogenetics: testing predictions from expected information</a></div><div class="wp-workCard_item"><span>Systematic biology</span><span>, 2012</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Taxon and character sampling are central to phylogenetic experimental design; yet, we lack genera...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species and studied how information (both expected and observed) and bootstrap support vary as each new taxon is individually added to our previous data set. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the 4th (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: Information is related to the ability to estimate branch length accurately and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well chosen) taxon may increase phylogenetic resolution and support in weakly supported parts of the tree without adding more characters/genes. Altogether our results corroborate that, although still underexplored, Goldman's method offers a powerful tool for experimental design in molecular phylogenetic studies. However, there are still several drawbacks to overcome, and further assessment of the method is needed in order to make it better understood, more accessible, and able to assess the addition of multiple taxa. [Bootstrap support; branch lengths; caecilians; experimental design; Gymnophiona; mitochondrial genome; phylogenetic information; rag1; taxon sampling.]</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="c0ec63aa8b3c9b59436159c81716f641" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255271,"asset_id":8008447,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255271/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008447"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008447"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008447; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008447]").text(description); $(".js-view-count[data-work-id=8008447]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008447; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008447']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "c0ec63aa8b3c9b59436159c81716f641" } } $('.js-work-strip[data-work-id=8008447]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008447,"title":"Experimental design in phylogenetics: testing predictions from expected information","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","ai_title_tag":"Enhancing Phylogenetic Design via Taxon Sampling","grobid_abstract":"Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species and studied how information (both expected and observed) and bootstrap support vary as each new taxon is individually added to our previous data set. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the 4th (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: Information is related to the ability to estimate branch length accurately and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well chosen) taxon may increase phylogenetic resolution and support in weakly supported parts of the tree without adding more characters/genes. Altogether our results corroborate that, although still underexplored, Goldman's method offers a powerful tool for experimental design in molecular phylogenetic studies. However, there are still several drawbacks to overcome, and further assessment of the method is needed in order to make it better understood, more accessible, and able to assess the addition of multiple taxa. [Bootstrap support; branch lengths; caecilians; experimental design; Gymnophiona; mitochondrial genome; phylogenetic information; rag1; taxon sampling.]","publication_date":{"day":null,"month":null,"year":2012,"errors":{}},"publication_name":"Systematic biology","grobid_abstract_attachment_id":48255271},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008447/Experimental_design_in_phylogenetics_testing_predictions_from_expected_information","translated_internal_url":"","created_at":"2014-08-18T01:11:54.880-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255271,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255271/thumbnails/1.jpg","file_name":"Experimental_Design_in_Phylogenetics_Tes20160823-20824-u8bxc5.pdf","download_url":"https://www.academia.edu/attachments/48255271/download_file","bulk_download_file_name":"Experimental_design_in_phylogenetics_tes.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255271/Experimental_Design_in_Phylogenetics_Tes20160823-20824-u8bxc5-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DExperimental_design_in_phylogenetics_tes.pdf\u0026Expires=1743265560\u0026Signature=JJiZC3QXPqBLPZjuBqKYuXVfuBGFikfTphW0WZ-LZ1WLKehZUW5lr0y8NWR8IDmFuSpZ3BEwxCB7US~HzxL2WOVEZP5Pua-frx~4uYDlKBjKwE~eFGcroetsoyePMmdamKDX1UeR~FC6ykOvwgFmJ-ff6PZqEhKAVCTX4fGNQHOQ8YZLP8A4uomzEe6DbUgn9hN6IX9HczIgtlbkZtlZSKwDL~65VLzcyUovmUzkdckrhA4jkQyY4osTiuziWrgb1LSVAWcg3dZAKV1nr7KmvHjQFwmrru7wzkOPhf~OT8dbrO0jCHNAxN5~yLwY88yCqXfIuTm-l97o3jhpEErUTw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Experimental_design_in_phylogenetics_testing_predictions_from_expected_information","translated_slug":"","page_count":14,"language":"en","content_type":"Work","summary":"Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species and studied how information (both expected and observed) and bootstrap support vary as each new taxon is individually added to our previous data set. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the 4th (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: Information is related to the ability to estimate branch length accurately and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well chosen) taxon may increase phylogenetic resolution and support in weakly supported parts of the tree without adding more characters/genes. Altogether our results corroborate that, although still underexplored, Goldman's method offers a powerful tool for experimental design in molecular phylogenetic studies. However, there are still several drawbacks to overcome, and further assessment of the method is needed in order to make it better understood, more accessible, and able to assess the addition of multiple taxa. [Bootstrap support; branch lengths; caecilians; experimental design; Gymnophiona; mitochondrial genome; phylogenetic information; rag1; taxon sampling.]","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255271,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255271/thumbnails/1.jpg","file_name":"Experimental_Design_in_Phylogenetics_Tes20160823-20824-u8bxc5.pdf","download_url":"https://www.academia.edu/attachments/48255271/download_file","bulk_download_file_name":"Experimental_design_in_phylogenetics_tes.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255271/Experimental_Design_in_Phylogenetics_Tes20160823-20824-u8bxc5-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DExperimental_design_in_phylogenetics_tes.pdf\u0026Expires=1743265560\u0026Signature=JJiZC3QXPqBLPZjuBqKYuXVfuBGFikfTphW0WZ-LZ1WLKehZUW5lr0y8NWR8IDmFuSpZ3BEwxCB7US~HzxL2WOVEZP5Pua-frx~4uYDlKBjKwE~eFGcroetsoyePMmdamKDX1UeR~FC6ykOvwgFmJ-ff6PZqEhKAVCTX4fGNQHOQ8YZLP8A4uomzEe6DbUgn9hN6IX9HczIgtlbkZtlZSKwDL~65VLzcyUovmUzkdckrhA4jkQyY4osTiuziWrgb1LSVAWcg3dZAKV1nr7KmvHjQFwmrru7wzkOPhf~OT8dbrO0jCHNAxN5~yLwY88yCqXfIuTm-l97o3jhpEErUTw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":3363,"name":"Systematic Biology","url":"https://www.academia.edu/Documents/in/Systematic_Biology"},{"id":4967,"name":"Molecular Evolution","url":"https://www.academia.edu/Documents/in/Molecular_Evolution"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":170540,"name":"Amphibians","url":"https://www.academia.edu/Documents/in/Amphibians"},{"id":222708,"name":"Mitochondrial Genome","url":"https://www.academia.edu/Documents/in/Mitochondrial_Genome"},{"id":2467566,"name":"Molecular Sequence Data","url":"https://www.academia.edu/Documents/in/Molecular_Sequence_Data"}],"urls":[{"id":3350928,"url":"http://dx.doi.org/10.1093/sysbio/sys028"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008447-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008445"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008445/Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals"><img alt="Research paper thumbnail of Genome-wide signatures of convergent evolution in echolocating mammals" class="work-thumbnail" src="https://attachments.academia-assets.com/48255259/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008445/Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals">Genome-wide signatures of convergent evolution in echolocating mammals</a></div><div class="wp-workCard_item"><span>Nature</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Evolution is typically thought to proceed through divergence of genes, proteins and ultimately ph...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="27022e1e29a12d29a112514c45b560bc" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255259,"asset_id":8008445,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255259/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008445"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008445"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008445; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008445]").text(description); $(".js-view-count[data-work-id=8008445]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008445; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008445']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "27022e1e29a12d29a112514c45b560bc" } } $('.js-work-strip[data-work-id=8008445]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008445,"title":"Genome-wide signatures of convergent evolution in echolocating mammals","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.","publication_date":{"day":null,"month":null,"year":2013,"errors":{}},"publication_name":"Nature","grobid_abstract_attachment_id":48255259},"translated_abstract":null,"internal_url":"https://www.academia.edu/8008445/Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals","translated_internal_url":"","created_at":"2014-08-18T01:11:52.526-07:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":48255259,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255259/thumbnails/1.jpg","file_name":"0c9605227ba4cedeb1000000.pdf","download_url":"https://www.academia.edu/attachments/48255259/download_file","bulk_download_file_name":"Genome_wide_signatures_of_convergent_evo.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255259/0c9605227ba4cedeb1000000-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DGenome_wide_signatures_of_convergent_evo.pdf\u0026Expires=1743265560\u0026Signature=R-~xx9ATcy5dBTm4wbgDlraIqt9WkEk~UShC4XYxGdhh9TgH71My7Za-SFnVD9BBuY3X3PcMz5MiAUtS7p5~I0RVFo9If8YXNRaVvXZKaAU0W4pkWGIYyg~7bHPnuyHP~igdtlAGdsYecQ6XcyyfL5~8EbvFo8AvqJHSprV9Q5b9ezp7WQ6XIynZ0CHmPHbZhdXJ-cj7NpoeXVy0qZ9S6SmEJfrIzUgZXAe4ql5XvW0ZzH0La5ND-2dL571iemOAu70rl0aw8Wy8N0yi~Uo1ZUTTnSNU5-KQkVsEmjyxrRf7R9nQe5Ltw2HoH05xPcKrxJVmpZ4to87fXcrrSI0MYg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals","translated_slug":"","page_count":9,"language":"en","content_type":"Work","summary":"Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":48255259,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/48255259/thumbnails/1.jpg","file_name":"0c9605227ba4cedeb1000000.pdf","download_url":"https://www.academia.edu/attachments/48255259/download_file","bulk_download_file_name":"Genome_wide_signatures_of_convergent_evo.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/48255259/0c9605227ba4cedeb1000000-libre.pdf?1471956957=\u0026response-content-disposition=attachment%3B+filename%3DGenome_wide_signatures_of_convergent_evo.pdf\u0026Expires=1743265560\u0026Signature=R-~xx9ATcy5dBTm4wbgDlraIqt9WkEk~UShC4XYxGdhh9TgH71My7Za-SFnVD9BBuY3X3PcMz5MiAUtS7p5~I0RVFo9If8YXNRaVvXZKaAU0W4pkWGIYyg~7bHPnuyHP~igdtlAGdsYecQ6XcyyfL5~8EbvFo8AvqJHSprV9Q5b9ezp7WQ6XIynZ0CHmPHbZhdXJ-cj7NpoeXVy0qZ9S6SmEJfrIzUgZXAe4ql5XvW0ZzH0La5ND-2dL571iemOAu70rl0aw8Wy8N0yi~Uo1ZUTTnSNU5-KQkVsEmjyxrRf7R9nQe5Ltw2HoH05xPcKrxJVmpZ4to87fXcrrSI0MYg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":2513,"name":"Molecular Biology","url":"https://www.academia.edu/Documents/in/Molecular_Biology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":4207,"name":"Phylogenetics","url":"https://www.academia.edu/Documents/in/Phylogenetics"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":4481,"name":"Evolutionary genetics","url":"https://www.academia.edu/Documents/in/Evolutionary_genetics"},{"id":4967,"name":"Molecular Evolution","url":"https://www.academia.edu/Documents/in/Molecular_Evolution"},{"id":5504,"name":"Comparative Genomics","url":"https://www.academia.edu/Documents/in/Comparative_Genomics"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"},{"id":13797,"name":"Marine Mammals","url":"https://www.academia.edu/Documents/in/Marine_Mammals"},{"id":15124,"name":"Convergence","url":"https://www.academia.edu/Documents/in/Convergence"},{"id":18075,"name":"Bats (Mammalogy)","url":"https://www.academia.edu/Documents/in/Bats_Mammalogy_"},{"id":27230,"name":"Chiroptera","url":"https://www.academia.edu/Documents/in/Chiroptera"},{"id":28235,"name":"Multidisciplinary","url":"https://www.academia.edu/Documents/in/Multidisciplinary"},{"id":33319,"name":"Nature","url":"https://www.academia.edu/Documents/in/Nature"},{"id":34912,"name":"Phylogenomics","url":"https://www.academia.edu/Documents/in/Phylogenomics"},{"id":41779,"name":"Mammals","url":"https://www.academia.edu/Documents/in/Mammals"},{"id":54065,"name":"Cetaceans","url":"https://www.academia.edu/Documents/in/Cetaceans"},{"id":54433,"name":"Phylogeny","url":"https://www.academia.edu/Documents/in/Phylogeny"},{"id":59693,"name":"Hearing","url":"https://www.academia.edu/Documents/in/Hearing"},{"id":75055,"name":"Dolphins","url":"https://www.academia.edu/Documents/in/Dolphins"},{"id":170896,"name":"Echolocation","url":"https://www.academia.edu/Documents/in/Echolocation"},{"id":176486,"name":"Genome","url":"https://www.academia.edu/Documents/in/Genome"},{"id":191815,"name":"Biological evolution","url":"https://www.academia.edu/Documents/in/Biological_evolution"}],"urls":[{"id":3350926,"url":"http://dx.doi.org/10.1038/nature12511"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008445-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008444"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008444/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery"><img alt="Research paper thumbnail of The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery" class="work-thumbnail" src="https://attachments.academia-assets.com/48255275/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008444/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery">The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery</a></div><div class="wp-workCard_item"><span>Genome biology</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic ne...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. Conclusions: The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="6060be248b46fbbebede47c7d422476e" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255275,"asset_id":8008444,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255275/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008444"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008444"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008444; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008444]").text(description); $(".js-view-count[data-work-id=8008444]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008444; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008444']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "6060be248b46fbbebede47c7d422476e" } } $('.js-work-strip[data-work-id=8008444]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008444,"title":"The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","ai_title_tag":"Genome and Transcriptome Analysis of Haemonchus contortus","grobid_abstract":"Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. 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Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-8008444-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="8008442"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/8008442/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_%CE%B2_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes"><img alt="Research paper thumbnail of Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes" class="work-thumbnail" src="https://attachments.academia-assets.com/48255280/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/8008442/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_%CE%B2_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes">Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes</a></div><div class="wp-workCard_item"><span>International journal for parasitology</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: High-molecular-weight glutenin subunits (HMW-GSs) have been considered as most import...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: High-molecular-weight glutenin subunits (HMW-GSs) have been considered as most important seed storage proteins for wheat flour quality. 1Ay subunits are of great interest because they are always silent in common wheat. The presence of expressed 1Ay subunits in diploid and tetraploid wheat genotypes makes it possible to investigate molecular information of active 1Ay genes.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8bf23c2c86302553333ba64718cd1ff3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":48255280,"asset_id":8008442,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/48255280/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="8008442"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="8008442"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 8008442; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=8008442]").text(description); $(".js-view-count[data-work-id=8008442]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 8008442; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='8008442']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "8bf23c2c86302553333ba64718cd1ff3" } } $('.js-work-strip[data-work-id=8008442]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":8008442,"title":"Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Background: High-molecular-weight glutenin subunits (HMW-GSs) have been considered as most important seed storage proteins for wheat flour quality. 1Ay subunits are of great interest because they are always silent in common wheat. 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class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938645/New_approaches_for_unravelling_reassortment_pathways"><img alt="Research paper thumbnail of New approaches for unravelling reassortment pathways" class="work-thumbnail" src="https://attachments.academia-assets.com/32910590/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938645/New_approaches_for_unravelling_reassortment_pathways">New approaches for unravelling reassortment pathways</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: Every year the human population encounters epidemic outbreaks of influenza, and histo...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.</span></div><div class="wp-workCard_item"><div class="carousel-container carousel-container--sm" id="profile-work-5938645-figures"><div class="prev-slide-container js-prev-button-container"><button aria-label="Previous" class="carousel-navigation-button js-profile-work-5938645-figures-prev"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">arrow_back_ios</span></button></div><div class="slides-container js-slides-container"><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044207/figure-3-trees-ns-and-na-confidence-intervals-and-spr"><img alt="Figure 3 Trees NS and NA, confidence intervals and SPR modifications. Subtree pruning and regrafting (SPR) modifications that the NA tree proposes on the NS tree, and the confidence interval around each tree (coloured shapes). Three paths are possible. The labels on the arrows refer to nodes involved in a move: m1 - move outgroup to cluster with hk1774, m2 — move hk1073 to cluster with hk1774, m2r — reverse of m2, m3 -— move hk1073 to cluster with outgroup, m4 — move env99 to cluster with quail99/sh39/hk1073 group. t1 - t6 are trees resulting from applying these SPR modifications to the NS tree. Arrows between two trees in the same confidence interval (Cl) reflect trivial differences (e.g. m1, black arrow), whereas ones between trees from different Cls are considered significant (e.g. m2, red arrow). We consider m2 as significant as we're interested in the minimum amount of significant branch moves between NS and NA. " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_003.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044209/figure-4-new-approaches-for-unravelling-reassortment"><img alt="" class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_004.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044203/figure-1-simulated-data-with-manually-introduced-spr"><img alt="Figure 1 Simulated data with manually introduced SPR modifications. The HA data was simulated on a tree modified by moving taxon ‘G’ to group with taxon ‘B’. (A) Output from the ML analysis for seven segments: MP, NA, NP, NS, PA, PB1 and PB2. A significant SPR was detected that would require moving taxon ‘G' to group with taxon 'B’, as suggested by the HA segment (direction of arc from empty to filled circle). Colours of arcs correspond to specific SPR operations. (B) HA tree: seven segments propose a significant SPR modification on the HA tree that would require moving taxon ‘G’ to group with taxon ‘F’. (C) Frequency network from Bayesian results. Edges point from segment proposing an SPR, to the segment whose tree needs to be modified (filled circle). Legend shows SPRs corresponding to the coloured edges. HA proposes moving taxon ‘G’ to group with taxon ‘B’ for the other seven segments. Conversely, the rest of the segments suggest that ‘G’ should move to cluster with ‘F’ on the HA tree. (D), (E) Overlap between MLreassort and Breassort. The x-axis represents the segments that propose the SPR move whereas the y-axis represents the segments whose trees need to be modified according to that SPR. The name of a tree segment is greyed out in the case where the SPR move is irrelevant, i.e. when the taxa involved in the move are sister-taxa. " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_001.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044205/figure-2-peqmps-avmitisvuipt-uum-ulstahiles-moeuweeh-lees-ui"><img alt="PEQMPS 2 AVMITISVUIPT UUM UlStaHILes MOEUWEEH Lees UI Le PIU Kong dataset. The intensity of the squares corresponds to the degree of distance. Distances range from 0 to 6, representing the number of bipartitions present in one tree but not in the other. Some trees have the same topology (NP and PB1, NS and PB2) whereas the NA tree seems to be most distant to the other trees (distance of 6). AU p values). We have corrected these p values using the Benjamini and Hochberg [37] test (BH test) and note that the correction has little impact on the resulting confidence intervals (data not shown). This means that for these 24 tree pairs, the topological differences can be accounted for by stochastic errors; 46% (26/56) of cases with non-overlapping confidence regions remained. Sig- nificant edits (SPR operations that result in a significant change in likelihood score) between trees with non- overlapping confidence regions were determined and depicted on each ML tree (shown in Additional file 1: Figure $1). In the cases where the arcs are bidirectional, " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_002.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044211/figure-5-network-of-the-most-frequent-sprs-from-breassort"><img alt="Figure 5 Network of the most frequent SPRs from Breassort. Each node represents the set of trees for the corresponding segment. Edge colours correspond to different types of SPR operations, as shown. Edges point from a segment that proposes the branch swap, to the one that needs to be modified (ending in filled circle). For example, the orange edge going from NA to NS depicts the following operation: cutting the branch leading to A/HongKong/1073/99 H9N2 and reconnecting it to the branch ending in A/HongKong/1774/99 H3N2. The NS tree is the one being modified, and the NA tree proposes this modification. " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_005.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044212/figure-6-combined-sprs-from-mlreassort-and-breassort-each"><img alt="Figure 6 Combined SPRs from MLreassort and Breassort. Each plot depicts an SPR move, with symbols indicating the cases when this move is significant. Circles represent results from the maximum likelihood-based approach, while crosses represent results from applying the algorithm based on a Bayesian framework. The x-axis shows the segments that propose the specified SPR, while the y-axis shows the segments whose trees need to be modified. The name of a tree segment is greyed out in the case where the SPR move is irrelevant, i.e. when the taxa involved in the move are sister-taxa. For example, moving hk1073 to group with hk1774 in the NA tree is irrelevant, as the NA tree already has these grouping together. " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/figure_006.jpg" /></a></figure><figure class="figure-slide-container"><a href="https://www.academia.edu/figures/35044214/table-1-alignments-and-models-for-hong-kong-dataset-the"><img alt="Table 1 Alignments and models for Hong Kong 1999 dataset the source and recipient taxa cannot be determined with certainty. Bayesian phylogenetics (Breassort) was also used to infer the evolutionary histories of each segment, by car- rying out 28 pairwise comparisons of sets of trees using 95% confidence intervals (as described in methods). In 57% (16 out of 28) of cases the two sets of trees do not overlap, which indicates that the trees in one set cannot be used to explain the data from which the trees in the other set are derived. The analysis was repeated using dif- ferent thresholds (90%, 95%, 99%, 99.9%, 3 replicates each) for determining confidence intervals (Additional file 1: Figure $3). Small variations in the networks are expected to occur due to the reduction of multi-dimensional space to 2D, and the arbitrary choice of trees to compare from each convex hull. However, consistent signals were identi- fied irrespective of the analyses, and variations between different CI thresholds are not greater than those observed when repeating the analysis with the same parameters. The findings from both algorithms are discussed below, starting with the example of a specific pair of segments: NS (non-structural) and NA (neuraminidase). " class="figure-slide-image" src="https://figures.academia-assets.com/32910590/table_001.jpg" /></a></figure></div><div class="next-slide-container js-next-button-container"><button aria-label="Next" class="carousel-navigation-button js-profile-work-5938645-figures-next"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">arrow_forward_ios</span></button></div></div></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="cade0040df109ee8d5913ee03d76b2d2" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910590,"asset_id":5938645,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910590/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938645"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938645"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938645; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938645]").text(description); $(".js-view-count[data-work-id=5938645]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938645; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938645']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "cade0040df109ee8d5913ee03d76b2d2" } } $('.js-work-strip[data-work-id=5938645]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938645,"title":"New approaches for unravelling reassortment pathways","translated_title":"","metadata":{"ai_title_tag":"Detecting Reassortment Pathways in Influenza Strains","grobid_abstract":"Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.","grobid_abstract_attachment_id":32910590},"translated_abstract":null,"internal_url":"https://www.academia.edu/5938645/New_approaches_for_unravelling_reassortment_pathways","translated_internal_url":"","created_at":"2014-02-03T18:21:40.622-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":32910590,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910590/thumbnails/1.jpg","file_name":"SvintiCottonMcInerney_2013_NewApproachesToUnravellingReassortmentPathways_BMCEvolutionaryBiology.pdf","download_url":"https://www.academia.edu/attachments/32910590/download_file","bulk_download_file_name":"New_approaches_for_unravelling_reassortm.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910590/SvintiCottonMcInerney_2013_NewApproachesToUnravellingReassortmentPathways_BMCEvolutionaryBiology-libre.pdf?1392028819=\u0026response-content-disposition=attachment%3B+filename%3DNew_approaches_for_unravelling_reassortm.pdf\u0026Expires=1743265560\u0026Signature=O0aPHe~UmxeTs5Xf1km04km1rDg5cYVnOnqOO0qR62uEtHerZDCqpqtKuhy5WouRjF2FG2uX0ULb-zKtZ7nQq3pG7wgEgUbtwHVeSrwJjWVBo9kiiJZhXZiv1nPYJVfXEDSQzZJm7t3AoZ-h6K2RKFciSFYIPka7qTHamU-NR69vIyO7U9w6uVCUNFTIPjrm2hiKyVuaXepghAduG~KGhwBuedA7~wY9h0hWg~DoH9jL3PCH7vuUeDC4EZJfIXuxx7UFoCLfSaWqoEX9X-FPsgwez7TsJ34lu9iZh6~opH82Za36B6julQeGn9KBYc3YrzLevCEO4ueQtfF2qAM59g__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"New_approaches_for_unravelling_reassortment_pathways","translated_slug":"","page_count":14,"language":"en","content_type":"Work","summary":"Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":32910590,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910590/thumbnails/1.jpg","file_name":"SvintiCottonMcInerney_2013_NewApproachesToUnravellingReassortmentPathways_BMCEvolutionaryBiology.pdf","download_url":"https://www.academia.edu/attachments/32910590/download_file","bulk_download_file_name":"New_approaches_for_unravelling_reassortm.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910590/SvintiCottonMcInerney_2013_NewApproachesToUnravellingReassortmentPathways_BMCEvolutionaryBiology-libre.pdf?1392028819=\u0026response-content-disposition=attachment%3B+filename%3DNew_approaches_for_unravelling_reassortm.pdf\u0026Expires=1743265560\u0026Signature=O0aPHe~UmxeTs5Xf1km04km1rDg5cYVnOnqOO0qR62uEtHerZDCqpqtKuhy5WouRjF2FG2uX0ULb-zKtZ7nQq3pG7wgEgUbtwHVeSrwJjWVBo9kiiJZhXZiv1nPYJVfXEDSQzZJm7t3AoZ-h6K2RKFciSFYIPka7qTHamU-NR69vIyO7U9w6uVCUNFTIPjrm2hiKyVuaXepghAduG~KGhwBuedA7~wY9h0hWg~DoH9jL3PCH7vuUeDC4EZJfIXuxx7UFoCLfSaWqoEX9X-FPsgwez7TsJ34lu9iZh6~opH82Za36B6julQeGn9KBYc3YrzLevCEO4ueQtfF2qAM59g__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":2513,"name":"Molecular Biology","url":"https://www.academia.edu/Documents/in/Molecular_Biology"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (true) { Aedu.setUpFigureCarousel('profile-work-5938645-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938644"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938644/Phylogenomic_Analyses_Elucidate_the_Evolutionary_Relationships_of_Bats"><img alt="Research paper thumbnail of Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats" class="work-thumbnail" src="https://attachments.academia-assets.com/32910587/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938644/Phylogenomic_Analyses_Elucidate_the_Evolutionary_Relationships_of_Bats">Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal g...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups , yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) . Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes , we show that-contrary to recent suggestions-bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="2c22df9feaa393268430880b972cd5d0" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910587,"asset_id":5938644,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910587/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938644"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938644"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938644; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938644]").text(description); $(".js-view-count[data-work-id=5938644]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938644; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938644']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "2c22df9feaa393268430880b972cd5d0" } } $('.js-work-strip[data-work-id=5938644]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938644,"title":"Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats","translated_title":"","metadata":{"grobid_abstract":"Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups , yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) . 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We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. 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Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes , we show that-contrary to recent suggestions-bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. 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However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="4b25fc31009394f2d6f91afc1970d858" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910586,"asset_id":5938643,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910586/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938643"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938643"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938643; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938643]").text(description); $(".js-view-count[data-work-id=5938643]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938643; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938643']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "4b25fc31009394f2d6f91afc1970d858" } } $('.js-work-strip[data-work-id=5938643]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938643,"title":"Genome-wide signatures of convergent evolution in echolocating mammals","translated_title":"","metadata":{"grobid_abstract":"Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.","grobid_abstract_attachment_id":32910586},"translated_abstract":null,"internal_url":"https://www.academia.edu/5938643/Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals","translated_internal_url":"","created_at":"2014-02-03T18:21:40.309-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":32910586,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910586/thumbnails/1.jpg","file_name":"ParkerTsagkogeogaCottonLiuProveroStupkaRossiter_2013_GenomeWideSignaturesOfConvergentEvolutionInEcholocatingMammals_Nature.pdf","download_url":"https://www.academia.edu/attachments/32910586/download_file","bulk_download_file_name":"Genome_wide_signatures_of_convergent_evo.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910586/ParkerTsagkogeogaCottonLiuProveroStupkaRossiter_2013_GenomeWideSignaturesOfConvergentEvolutionInEcholocatingMammals_Nature-libre.pdf?1392038841=\u0026response-content-disposition=attachment%3B+filename%3DGenome_wide_signatures_of_convergent_evo.pdf\u0026Expires=1743265560\u0026Signature=ONnargV~-f8p~8rElJA3hQ94KYfWSijslkrkcGi6k4gWHIVeEViv6ZLY-sgYbGI~O6j-Vn1F8hhlNZhoLGoE4GBO2~e7YwI7ok9OA3yp0QpCac6QCe1-FHE8cKwtZokXoRE7WWxe45ZtILy4g1jkbVA6dbQhRPKfWo11oj3lA6VrlgVK1V302pqhdjaieUPjLf4bsSbYPtuLgD8VZ8~E32~7S4eigNkSZt-orVHXDsGlChZ2TaccA8Ao4JLz5rMyUHWPm9eMwUqm2TiuMUJnFL4QkzOhWFvvS3aa1~jPDPk9uvbYEAxsz6oi3d2BN3UEiVHY6sI0oCkL6WYA~8GAvQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Genome_wide_signatures_of_convergent_evolution_in_echolocating_mammals","translated_slug":"","page_count":9,"language":"en","content_type":"Work","summary":"Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1-3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4,5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9,10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":32910586,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910586/thumbnails/1.jpg","file_name":"ParkerTsagkogeogaCottonLiuProveroStupkaRossiter_2013_GenomeWideSignaturesOfConvergentEvolutionInEcholocatingMammals_Nature.pdf","download_url":"https://www.academia.edu/attachments/32910586/download_file","bulk_download_file_name":"Genome_wide_signatures_of_convergent_evo.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910586/ParkerTsagkogeogaCottonLiuProveroStupkaRossiter_2013_GenomeWideSignaturesOfConvergentEvolutionInEcholocatingMammals_Nature-libre.pdf?1392038841=\u0026response-content-disposition=attachment%3B+filename%3DGenome_wide_signatures_of_convergent_evo.pdf\u0026Expires=1743265560\u0026Signature=ONnargV~-f8p~8rElJA3hQ94KYfWSijslkrkcGi6k4gWHIVeEViv6ZLY-sgYbGI~O6j-Vn1F8hhlNZhoLGoE4GBO2~e7YwI7ok9OA3yp0QpCac6QCe1-FHE8cKwtZokXoRE7WWxe45ZtILy4g1jkbVA6dbQhRPKfWo11oj3lA6VrlgVK1V302pqhdjaieUPjLf4bsSbYPtuLgD8VZ8~E32~7S4eigNkSZt-orVHXDsGlChZ2TaccA8Ao4JLz5rMyUHWPm9eMwUqm2TiuMUJnFL4QkzOhWFvvS3aa1~jPDPk9uvbYEAxsz6oi3d2BN3UEiVHY6sI0oCkL6WYA~8GAvQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics"},{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology"},{"id":156,"name":"Genetics","url":"https://www.academia.edu/Documents/in/Genetics"},{"id":2513,"name":"Molecular Biology","url":"https://www.academia.edu/Documents/in/Molecular_Biology"},{"id":3216,"name":"Genomics","url":"https://www.academia.edu/Documents/in/Genomics"},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology"},{"id":10882,"name":"Evolution","url":"https://www.academia.edu/Documents/in/Evolution"}],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-5938643-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938566"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938566/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_b_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes"><img alt="Research paper thumbnail of Characterization and comparative analysis of the complete Haemonchus contortus b-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes" class="work-thumbnail" src="https://attachments.academia-assets.com/32910545/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938566/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_b_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes">Characterization and comparative analysis of the complete Haemonchus contortus b-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Parasitic nematode β-tubulin genes are of particular interest because they are the targets of ben...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Parasitic nematode β-tubulin genes are of particular interest because they are the targets of benzimidazole drugs. However, in spite of this, the full β-tubulin gene family has not been characterized for any parasitic nematode to date. Haemonchus contortus is the parasite species for which we understand benzimidazole resistance the best and its close phylogenetic relationship with Caenorhabditis elegans potentially allows inferences of gene function by comparative analysis. Consequently, we have characterized the full β-tubulin gene family in H. contortus. Further to the previously identified Hco-tbb-iso-1 and Hco-tbb-iso-2 genes, we have characterized two additional family members designated Hco-tbb-iso-3 and Hco-tbb-iso-4. We show that Hco-tbb-iso-1 is not a one-to-one orthologue with Cel-ben-1, the only β-tubulin gene in C. elegans that is a benzimidazole drug target. Instead, both Hco-tbb-iso-1 and Hco-tbb-iso-2 have a complex evolutionary relationship with three C. elegans β-tubulin genes: Cel-ben-1, Cel-tbb-1 and Cel-tbb-2. Furthermore, we show that both Hco-tbb-iso-1 and Hco-tbb-iso-2 are highly expressed in adult worms; in contrast, Hco-tbb-iso-3 and Hco-tbb-iso-4 are expressed only at very low levels and are orthologous to the Cel-mec-7 and Cel-tbb-4 genes, respectively, suggesting that they have specialized functional roles. Indeed, we have found that the expression pattern of Hco-tbb-iso-3 in H. contortus is identical to that of Cel-mec-7 in C. elegans, being expressed in just six "touch receptor" mechano-sensory neurons. These results suggest that further investigation is warranted into the potential involvement of strongylid isotype-2 β-tubulin genes in mechanisms of benzimidazole resistance.Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="218c9bfc9c698cdb1476e293fa5e604d" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910545,"asset_id":5938566,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910545/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938566"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938566"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938566; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938566]").text(description); $(".js-view-count[data-work-id=5938566]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938566; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938566']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "218c9bfc9c698cdb1476e293fa5e604d" } } $('.js-work-strip[data-work-id=5938566]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938566,"title":"Characterization and comparative analysis of the complete Haemonchus contortus b-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes","translated_title":"","metadata":{"abstract":"Parasitic nematode β-tubulin genes are of particular interest because they are the targets of benzimidazole drugs. However, in spite of this, the full β-tubulin gene family has not been characterized for any parasitic nematode to date. Haemonchus contortus is the parasite species for which we understand benzimidazole resistance the best and its close phylogenetic relationship with Caenorhabditis elegans potentially allows inferences of gene function by comparative analysis. Consequently, we have characterized the full β-tubulin gene family in H. contortus. Further to the previously identified Hco-tbb-iso-1 and Hco-tbb-iso-2 genes, we have characterized two additional family members designated Hco-tbb-iso-3 and Hco-tbb-iso-4. We show that Hco-tbb-iso-1 is not a one-to-one orthologue with Cel-ben-1, the only β-tubulin gene in C. elegans that is a benzimidazole drug target. Instead, both Hco-tbb-iso-1 and Hco-tbb-iso-2 have a complex evolutionary relationship with three C. elegans β-tubulin genes: Cel-ben-1, Cel-tbb-1 and Cel-tbb-2. Furthermore, we show that both Hco-tbb-iso-1 and Hco-tbb-iso-2 are highly expressed in adult worms; in contrast, Hco-tbb-iso-3 and Hco-tbb-iso-4 are expressed only at very low levels and are orthologous to the Cel-mec-7 and Cel-tbb-4 genes, respectively, suggesting that they have specialized functional roles. Indeed, we have found that the expression pattern of Hco-tbb-iso-3 in H. contortus is identical to that of Cel-mec-7 in C. elegans, being expressed in just six \"touch receptor\" mechano-sensory neurons. These results suggest that further investigation is warranted into the potential involvement of strongylid isotype-2 β-tubulin genes in mechanisms of benzimidazole resistance.Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.","ai_title_tag":"H. contortus β-Tubulin Gene Family and Resistance"},"translated_abstract":"Parasitic nematode β-tubulin genes are of particular interest because they are the targets of benzimidazole drugs. However, in spite of this, the full β-tubulin gene family has not been characterized for any parasitic nematode to date. Haemonchus contortus is the parasite species for which we understand benzimidazole resistance the best and its close phylogenetic relationship with Caenorhabditis elegans potentially allows inferences of gene function by comparative analysis. Consequently, we have characterized the full β-tubulin gene family in H. contortus. Further to the previously identified Hco-tbb-iso-1 and Hco-tbb-iso-2 genes, we have characterized two additional family members designated Hco-tbb-iso-3 and Hco-tbb-iso-4. We show that Hco-tbb-iso-1 is not a one-to-one orthologue with Cel-ben-1, the only β-tubulin gene in C. elegans that is a benzimidazole drug target. Instead, both Hco-tbb-iso-1 and Hco-tbb-iso-2 have a complex evolutionary relationship with three C. elegans β-tubulin genes: Cel-ben-1, Cel-tbb-1 and Cel-tbb-2. Furthermore, we show that both Hco-tbb-iso-1 and Hco-tbb-iso-2 are highly expressed in adult worms; in contrast, Hco-tbb-iso-3 and Hco-tbb-iso-4 are expressed only at very low levels and are orthologous to the Cel-mec-7 and Cel-tbb-4 genes, respectively, suggesting that they have specialized functional roles. Indeed, we have found that the expression pattern of Hco-tbb-iso-3 in H. contortus is identical to that of Cel-mec-7 in C. elegans, being expressed in just six \"touch receptor\" mechano-sensory neurons. These results suggest that further investigation is warranted into the potential involvement of strongylid isotype-2 β-tubulin genes in mechanisms of benzimidazole resistance.Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.","internal_url":"https://www.academia.edu/5938566/Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_b_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes","translated_internal_url":"","created_at":"2014-02-03T18:16:03.738-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":32910545,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910545/thumbnails/1.jpg","file_name":"SaundersWasmuthBeechLaingHuntNaghraCottonBerrimanBrittonGilleard_2013_CharacterizationAndComparativeAnalysisOfTheCompleteHaemonchusConto.pdf","download_url":"https://www.academia.edu/attachments/32910545/download_file","bulk_download_file_name":"Characterization_and_comparative_analysi.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910545/SaundersWasmuthBeechLaingHuntNaghraCottonBerrimanBrittonGilleard_2013_CharacterizationAndComparativeAnalysisOfTheCompleteHaemonchusConto-libre.pdf?1392033993=\u0026response-content-disposition=attachment%3B+filename%3DCharacterization_and_comparative_analysi.pdf\u0026Expires=1743265560\u0026Signature=MIxtdqLB0jf1Q6Voh7qdD0W61RVA7OreJEAwW~RRAVEf6UNCmccy2Pk~QxLZDas23jV-hmc4hrfOFGW2fvAWpu2B0~NiqhRkHfMhHF2-H-sYVdZRFQYwDNqGabPxgkAsMX-ly8rDf-Te93bwbeTQ~2zojVEw93VdSKGImo5KCb7Qu2LwGgFL-nlRBxxD4hQPPLKEPOTHeK4Qd1Nuh8v2Z93ffUzo8ISwooCcW0eVx4gz6mqT2vBx-V-BdI4YAcu5A8hGjE4CvVev2ZFJdlUVU4TMko4g7znHBDqDVK~QTR8-f2IzgPmurhraNJ~CA7f-ybMzNRGOxfixS~1u~dyvCw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"Characterization_and_comparative_analysis_of_the_complete_Haemonchus_contortus_b_tubulin_gene_family_and_implications_for_benzimidazole_resistance_in_strongylid_nematodes","translated_slug":"","page_count":11,"language":"en","content_type":"Work","summary":"Parasitic nematode β-tubulin genes are of particular interest because they are the targets of benzimidazole drugs. However, in spite of this, the full β-tubulin gene family has not been characterized for any parasitic nematode to date. Haemonchus contortus is the parasite species for which we understand benzimidazole resistance the best and its close phylogenetic relationship with Caenorhabditis elegans potentially allows inferences of gene function by comparative analysis. Consequently, we have characterized the full β-tubulin gene family in H. contortus. Further to the previously identified Hco-tbb-iso-1 and Hco-tbb-iso-2 genes, we have characterized two additional family members designated Hco-tbb-iso-3 and Hco-tbb-iso-4. We show that Hco-tbb-iso-1 is not a one-to-one orthologue with Cel-ben-1, the only β-tubulin gene in C. elegans that is a benzimidazole drug target. Instead, both Hco-tbb-iso-1 and Hco-tbb-iso-2 have a complex evolutionary relationship with three C. elegans β-tubulin genes: Cel-ben-1, Cel-tbb-1 and Cel-tbb-2. Furthermore, we show that both Hco-tbb-iso-1 and Hco-tbb-iso-2 are highly expressed in adult worms; in contrast, Hco-tbb-iso-3 and Hco-tbb-iso-4 are expressed only at very low levels and are orthologous to the Cel-mec-7 and Cel-tbb-4 genes, respectively, suggesting that they have specialized functional roles. Indeed, we have found that the expression pattern of Hco-tbb-iso-3 in H. contortus is identical to that of Cel-mec-7 in C. elegans, being expressed in just six \"touch receptor\" mechano-sensory neurons. These results suggest that further investigation is warranted into the potential involvement of strongylid isotype-2 β-tubulin genes in mechanisms of benzimidazole resistance.Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":32910545,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910545/thumbnails/1.jpg","file_name":"SaundersWasmuthBeechLaingHuntNaghraCottonBerrimanBrittonGilleard_2013_CharacterizationAndComparativeAnalysisOfTheCompleteHaemonchusConto.pdf","download_url":"https://www.academia.edu/attachments/32910545/download_file","bulk_download_file_name":"Characterization_and_comparative_analysi.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910545/SaundersWasmuthBeechLaingHuntNaghraCottonBerrimanBrittonGilleard_2013_CharacterizationAndComparativeAnalysisOfTheCompleteHaemonchusConto-libre.pdf?1392033993=\u0026response-content-disposition=attachment%3B+filename%3DCharacterization_and_comparative_analysi.pdf\u0026Expires=1743265560\u0026Signature=MIxtdqLB0jf1Q6Voh7qdD0W61RVA7OreJEAwW~RRAVEf6UNCmccy2Pk~QxLZDas23jV-hmc4hrfOFGW2fvAWpu2B0~NiqhRkHfMhHF2-H-sYVdZRFQYwDNqGabPxgkAsMX-ly8rDf-Te93bwbeTQ~2zojVEw93VdSKGImo5KCb7Qu2LwGgFL-nlRBxxD4hQPPLKEPOTHeK4Qd1Nuh8v2Z93ffUzo8ISwooCcW0eVx4gz6mqT2vBx-V-BdI4YAcu5A8hGjE4CvVev2ZFJdlUVU4TMko4g7znHBDqDVK~QTR8-f2IzgPmurhraNJ~CA7f-ybMzNRGOxfixS~1u~dyvCw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[],"urls":[{"id":2348733,"url":"http://www.ncbi.nlm.nih.gov/pubmed/23416426"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-5938566-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938512"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938512/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery"><img alt="Research paper thumbnail of The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery" class="work-thumbnail" src="https://attachments.academia-assets.com/32910513/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938512/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery">The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic ne...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. Conclusions: The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="7d2b813d818d6ad0e3066bc5c6d6c599" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":32910513,"asset_id":5938512,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/32910513/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938512"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938512"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938512; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938512]").text(description); $(".js-view-count[data-work-id=5938512]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938512; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938512']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "7d2b813d818d6ad0e3066bc5c6d6c599" } } $('.js-work-strip[data-work-id=5938512]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938512,"title":"The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery","translated_title":"","metadata":{"ai_title_tag":"Genome and Transcriptome of Haemonchus contortus","grobid_abstract":"Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. Conclusions: The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.","grobid_abstract_attachment_id":32910513},"translated_abstract":null,"internal_url":"https://www.academia.edu/5938512/The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery","translated_internal_url":"","created_at":"2014-02-03T18:12:26.360-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":32910513,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910513/thumbnails/1.jpg","file_name":"LaingEtAl_2013_TheGenomeAndTranscriptomeOfHaemonchusContortusAKeyModelParasiteForDrugAndVaccineDiscovery_GenomeBiology.pdf","download_url":"https://www.academia.edu/attachments/32910513/download_file","bulk_download_file_name":"The_genome_and_transcriptome_of_Haemonch.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910513/LaingEtAl_2013_TheGenomeAndTranscriptomeOfHaemonchusContortusAKeyModelParasiteForDrugAndVaccineDiscovery_GenomeBiology-libre.pdf?1392033125=\u0026response-content-disposition=attachment%3B+filename%3DThe_genome_and_transcriptome_of_Haemonch.pdf\u0026Expires=1743265560\u0026Signature=PvXWAfFVIHLPXmHc5Qu0nLbdHxNbF--Uq9LxZzeyx7z~8pqYbrTpgu6vemv~XGBaFf6xxqYE4YzAXnUHThKT29AXc6LTzz5dAA3WkjE2JP2Zds4qNaJKxYUAp2y7W4leIIYfDWpnvA15Rp3ePai~IrDy0rcYykZnAgXL3aRWDi4wlQH5bYr-auavwEnNZuQ3KYYB~496yF3AbuJOQ3xhJlcVIwStXnvwSL827E4wAiA7PR8cgS44XlMaMlO~V2fAfOwQ2CKbyu7nFYrnGnc6qm1KRaO-JLuH6v18qRuJAv0ZnUhnbsaIaWU0vaRl7sKNbBHObNJeliRMyM3bjeSRkA__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"The_genome_and_transcriptome_of_Haemonchus_contortus_a_key_model_parasite_for_drug_and_vaccine_discovery","translated_slug":"","page_count":16,"language":"en","content_type":"Work","summary":"Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. Conclusions: The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":32910513,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/32910513/thumbnails/1.jpg","file_name":"LaingEtAl_2013_TheGenomeAndTranscriptomeOfHaemonchusContortusAKeyModelParasiteForDrugAndVaccineDiscovery_GenomeBiology.pdf","download_url":"https://www.academia.edu/attachments/32910513/download_file","bulk_download_file_name":"The_genome_and_transcriptome_of_Haemonch.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/32910513/LaingEtAl_2013_TheGenomeAndTranscriptomeOfHaemonchusContortusAKeyModelParasiteForDrugAndVaccineDiscovery_GenomeBiology-libre.pdf?1392033125=\u0026response-content-disposition=attachment%3B+filename%3DThe_genome_and_transcriptome_of_Haemonch.pdf\u0026Expires=1743265560\u0026Signature=PvXWAfFVIHLPXmHc5Qu0nLbdHxNbF--Uq9LxZzeyx7z~8pqYbrTpgu6vemv~XGBaFf6xxqYE4YzAXnUHThKT29AXc6LTzz5dAA3WkjE2JP2Zds4qNaJKxYUAp2y7W4leIIYfDWpnvA15Rp3ePai~IrDy0rcYykZnAgXL3aRWDi4wlQH5bYr-auavwEnNZuQ3KYYB~496yF3AbuJOQ3xhJlcVIwStXnvwSL827E4wAiA7PR8cgS44XlMaMlO~V2fAfOwQ2CKbyu7nFYrnGnc6qm1KRaO-JLuH6v18qRuJAv0ZnUhnbsaIaWU0vaRl7sKNbBHObNJeliRMyM3bjeSRkA__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[],"urls":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-5938512-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938482"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938482/The_peculiar_epidemiology_of_dracunculiasis_in_chad"><img alt="Research paper thumbnail of The peculiar epidemiology of dracunculiasis in chad" class="work-thumbnail" src="https://attachments.academia-assets.com/49083292/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938482/The_peculiar_epidemiology_of_dracunculiasis_in_chad">The peculiar epidemiology of dracunculiasis in chad</a></div><div class="wp-workCard_item"><span>The American journal of tropical medicine and hygiene</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Dracunculiasis was rediscovered in Chad in 2010 after an apparent absence of 10 years. In April 2...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Dracunculiasis was rediscovered in Chad in 2010 after an apparent absence of 10 years. In April 2012 active village-based surveillance was initiated to determine where, when, and how transmission of the disease was occurring, and to implement interventions to interrupt it. The current epidemiologic pattern of the disease in Chad is unlike that seen previously in Chad or other endemic countries, i.e., no clustering of cases by village or association with a common water source, the average number of worms per person was small, and a large number of dogs were found to be infected. Molecular sequencing suggests these infections were all caused by Dracunculus medinensis. It appears that the infection in dogs is serving as the major driving force sustaining transmission in Chad, that an aberrant life cycle involving a paratenic host common to people and dogs is occurring, and that the cases in humans are sporadic and incidental.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="4c1966b079000edb75b9e356a61922f3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":49083292,"asset_id":5938482,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/49083292/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938482"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938482"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938482; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938482]").text(description); $(".js-view-count[data-work-id=5938482]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938482; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938482']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "4c1966b079000edb75b9e356a61922f3" } } $('.js-work-strip[data-work-id=5938482]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938482,"title":"The peculiar epidemiology of dracunculiasis in chad","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Dracunculiasis was rediscovered in Chad in 2010 after an apparent absence of 10 years. In April 2012 active village-based surveillance was initiated to determine where, when, and how transmission of the disease was occurring, and to implement interventions to interrupt it. The current epidemiologic pattern of the disease in Chad is unlike that seen previously in Chad or other endemic countries, i.e., no clustering of cases by village or association with a common water source, the average number of worms per person was small, and a large number of dogs were found to be infected. Molecular sequencing suggests these infections were all caused by Dracunculus medinensis. It appears that the infection in dogs is serving as the major driving force sustaining transmission in Chad, that an aberrant life cycle involving a paratenic host common to people and dogs is occurring, and that the cases in humans are sporadic and incidental.","publication_date":{"day":null,"month":null,"year":2014,"errors":{}},"publication_name":"The American journal of tropical medicine and hygiene","grobid_abstract_attachment_id":49083292},"translated_abstract":null,"internal_url":"https://www.academia.edu/5938482/The_peculiar_epidemiology_of_dracunculiasis_in_chad","translated_internal_url":"","created_at":"2014-02-03T18:10:14.083-08:00","preview_url":null,"current_user_can_edit":null,"current_user_is_owner":null,"owner_id":435804,"coauthors_can_edit":true,"document_type":"paper","co_author_tags":[],"downloadable_attachments":[{"id":49083292,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/49083292/thumbnails/1.jpg","file_name":"The_Peculiar_Epidemiology_of_Dracunculia20160924-14558-yubiwf.pdf","download_url":"https://www.academia.edu/attachments/49083292/download_file","bulk_download_file_name":"The_peculiar_epidemiology_of_dracunculia.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/49083292/The_Peculiar_Epidemiology_of_Dracunculia20160924-14558-yubiwf-libre.pdf?1474720240=\u0026response-content-disposition=attachment%3B+filename%3DThe_peculiar_epidemiology_of_dracunculia.pdf\u0026Expires=1743265561\u0026Signature=MMH2aK5Ywpbp~wj~THxH1uxeKGK-Rimaw5lP70AEBj0ncLjwCCyOE3CTD1cY3tyZDC51bDJYbtAgyU9bKW6SBXbiqnJbI6of7H~x8w35AWNOs~7n8Uc7s8FlCJAE5RY-e-dSLbNVJTfOrWC9lV1~UQ7FQuCRf4mKksSpqKwAhweVb-JniET1qmBF1NHyya~Dlmm9N9v1M3nqfGFmSTD0cudYSjFGl1X5M-ZDmIa7zJGr2rDEENiHK1d83uWwno7jlCR5SJH13ZaqO0-qZ4etyofWIF-zNU5L4xIVp3TPq9D18b4DqWP~VUDc3idO7UsgiQ96JnXV1Rnk4eZBCwNxQg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"slug":"The_peculiar_epidemiology_of_dracunculiasis_in_chad","translated_slug":"","page_count":10,"language":"en","content_type":"Work","summary":"Dracunculiasis was rediscovered in Chad in 2010 after an apparent absence of 10 years. In April 2012 active village-based surveillance was initiated to determine where, when, and how transmission of the disease was occurring, and to implement interventions to interrupt it. The current epidemiologic pattern of the disease in Chad is unlike that seen previously in Chad or other endemic countries, i.e., no clustering of cases by village or association with a common water source, the average number of worms per person was small, and a large number of dogs were found to be infected. Molecular sequencing suggests these infections were all caused by Dracunculus medinensis. It appears that the infection in dogs is serving as the major driving force sustaining transmission in Chad, that an aberrant life cycle involving a paratenic host common to people and dogs is occurring, and that the cases in humans are sporadic and incidental.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[{"id":49083292,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/49083292/thumbnails/1.jpg","file_name":"The_Peculiar_Epidemiology_of_Dracunculia20160924-14558-yubiwf.pdf","download_url":"https://www.academia.edu/attachments/49083292/download_file","bulk_download_file_name":"The_peculiar_epidemiology_of_dracunculia.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/49083292/The_Peculiar_Epidemiology_of_Dracunculia20160924-14558-yubiwf-libre.pdf?1474720240=\u0026response-content-disposition=attachment%3B+filename%3DThe_peculiar_epidemiology_of_dracunculia.pdf\u0026Expires=1743265561\u0026Signature=MMH2aK5Ywpbp~wj~THxH1uxeKGK-Rimaw5lP70AEBj0ncLjwCCyOE3CTD1cY3tyZDC51bDJYbtAgyU9bKW6SBXbiqnJbI6of7H~x8w35AWNOs~7n8Uc7s8FlCJAE5RY-e-dSLbNVJTfOrWC9lV1~UQ7FQuCRf4mKksSpqKwAhweVb-JniET1qmBF1NHyya~Dlmm9N9v1M3nqfGFmSTD0cudYSjFGl1X5M-ZDmIa7zJGr2rDEENiHK1d83uWwno7jlCR5SJH13ZaqO0-qZ4etyofWIF-zNU5L4xIVp3TPq9D18b4DqWP~VUDc3idO7UsgiQ96JnXV1Rnk4eZBCwNxQg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}],"research_interests":[{"id":29570,"name":"Chad","url":"https://www.academia.edu/Documents/in/Chad"},{"id":52438,"name":"Dogs","url":"https://www.academia.edu/Documents/in/Dogs"},{"id":1739635,"name":"Dracunculiasis","url":"https://www.academia.edu/Documents/in/Dracunculiasis"}],"urls":[{"id":2348706,"url":"http://dx.doi.org/10.4269/ajtmh.13-0554"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-5938482-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="5938481"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/5938481/Genomic_confirmation_of_hybridisation_and_recent_inbreeding_in_a_vector_isolated_leishmania_population"><img alt="Research paper thumbnail of Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated leishmania population" class="work-thumbnail" src="https://attachments.academia-assets.com/49083291/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/5938481/Genomic_confirmation_of_hybridisation_and_recent_inbreeding_in_a_vector_isolated_leishmania_population">Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated leishmania population</a></div><div class="wp-workCard_item"><span>PLoS genetics</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Although asexual reproduction via clonal propagation has been proposed as the principal reproduct...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Although asexual reproduction via clonal propagation has been proposed as the principal reproductive mechanism across parasitic protozoa of the Leishmania genus, sexual recombination has long been suspected, based on hybrid marker profiles detected in field isolates from different geographical locations. The recent experimental demonstration of a sexual cycle in Leishmania within sand flies has confirmed the occurrence of hybridisation, but knowledge of the parasite life cycle in the wild still remains limited. Here, we use whole genome sequencing to investigate the frequency of sexual reproduction in Leishmania, by sequencing the genomes of 11 Leishmania infantum isolates from sand flies and 1 patient isolate in a focus of cutaneous leishmaniasis in the Ç ukurova province of southeast Turkey. This is the first genome-wide examination of a vector-isolated population of Leishmania parasites. A genome-wide pattern of patchy heterozygosity and SNP density was observed both within individual strains and across the whole group. Comparisons with other Leishmania donovani complex genome sequences suggest that these isolates are derived from a single cross of two diverse strains with subsequent recombination within the population. This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. This observation allowed us to estimate the relative rates of sexual and asexual reproduction within this population, to our knowledge the first quantitative estimate of these events during the Leishmania life cycle.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="7dc3672e62c6541e6c7baeea0cd1a3c3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":49083291,"asset_id":5938481,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/49083291/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="5938481"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="5938481"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5938481; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5938481]").text(description); $(".js-view-count[data-work-id=5938481]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 5938481; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='5938481']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "7dc3672e62c6541e6c7baeea0cd1a3c3" } } $('.js-work-strip[data-work-id=5938481]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":5938481,"title":"Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated leishmania population","translated_title":"","metadata":{"publisher":"ncbi.nlm.nih.gov","grobid_abstract":"Although asexual reproduction via clonal propagation has been proposed as the principal reproductive mechanism across parasitic protozoa of the Leishmania genus, sexual recombination has long been suspected, based on hybrid marker profiles detected in field isolates from different geographical locations. The recent experimental demonstration of a sexual cycle in Leishmania within sand flies has confirmed the occurrence of hybridisation, but knowledge of the parasite life cycle in the wild still remains limited. Here, we use whole genome sequencing to investigate the frequency of sexual reproduction in Leishmania, by sequencing the genomes of 11 Leishmania infantum isolates from sand flies and 1 patient isolate in a focus of cutaneous leishmaniasis in the Ç ukurova province of southeast Turkey. This is the first genome-wide examination of a vector-isolated population of Leishmania parasites. A genome-wide pattern of patchy heterozygosity and SNP density was observed both within individual strains and across the whole group. Comparisons with other Leishmania donovani complex genome sequences suggest that these isolates are derived from a single cross of two diverse strains with subsequent recombination within the population. This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. 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This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. 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Here, we report a high-quality reference genome sequence for a strain of L. donovani from Nepal, and use this sequence to study variation in a set of 16 related clinical lines, isolated from visceral leishmaniasis patients from the same region, which also differ in their response to in vitro drug susceptibility.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="2751229"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="2751229"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 2751229; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=2751229]").text(description); $(".js-view-count[data-work-id=2751229]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 2751229; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='2751229']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=2751229]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":2751229,"title":"Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance","translated_title":"","metadata":{"abstract":"Abstract Visceral leishmaniasis is a potentially fatal disease endemic to large parts of Asia and Africa, primarily caused by the protozoan parasite Leishmania donovani. 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Here, we report a high-quality reference genome sequence for a strain of L. donovani from Nepal, and use this sequence to study variation in a set of 16 related clinical lines, isolated from visceral leishmaniasis patients from the same region, which also differ in their response to in vitro drug susceptibility.","owner":{"id":435804,"first_name":"James","middle_initials":null,"last_name":"Cotton","page_name":"JamesCotton","domain_name":"sanger","created_at":"2011-05-12T21:07:22.258-07:00","display_name":"James Cotton","url":"https://sanger.academia.edu/JamesCotton"},"attachments":[],"research_interests":[],"urls":[{"id":644585,"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227103/"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") if (false) { Aedu.setUpFigureCarousel('profile-work-2751229-figures'); } }); </script> <div class="js-work-strip profile--work_container" data-work-id="2751167"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/2751167/Comparative_Genomics_of_the_Apicomplexan_Parasites_Toxoplasma_gondii_and_Neospora_caninum_Coccidia_Differing_in_Host_Range_and_Transmission_Strategy"><img alt="Research paper thumbnail of Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy" class="work-thumbnail" src="https://attachments.academia-assets.com/31008116/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/2751167/Comparative_Genomics_of_the_Apicomplexan_Parasites_Toxoplasma_gondii_and_Neospora_caninum_Coccidia_Differing_in_Host_Range_and_Transmission_Strategy">Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human po...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="a406de95b403b999eb41ea723c565e21" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":31008116,"asset_id":2751167,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/31008116/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="2751167"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="2751167"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 2751167; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=2751167]").text(description); $(".js-view-count[data-work-id=2751167]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 2751167; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='2751167']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "a406de95b403b999eb41ea723c565e21" } } $('.js-work-strip[data-work-id=2751167]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":2751167,"title":"Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy","translated_title":"","metadata":{"abstract":"Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. 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The generally well-supported and resolved phylogeny displayed the following relationships among the five nominate species sampled:(B. boulengeri ((B. taitanus, B. niedeni),(B. changamwensis, B. uluguruensis))).</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="fd8240fceecac47db72619cee4e43cd7" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":30723332,"asset_id":2751255,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/30723332/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="2751255"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="2751255"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 2751255; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=2751255]").text(description); $(".js-view-count[data-work-id=2751255]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 2751255; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='2751255']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "fd8240fceecac47db72619cee4e43cd7" } } $('.js-work-strip[data-work-id=2751255]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":2751255,"title":"Molecular phylogenetics of Boulengerula (Amphibia: Gymnophiona: Caeciliidae) and implications for taxonomy, biogeography and conservation","translated_title":"","metadata":{"abstract":"Abstract: Phylogenetic relationships of the East African caeciliid Boulengerula were reconstructed using 12S, 16S and cytb mitochondrial gene sequences for 32 samples from Kenya and Tanzania. 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This paper argues that eukaryotic genes derived from archaebacterial origins are more functionally important than the much more numerous eubacterial genes. 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