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(PDF) Rate of Adaptation in Large Sexual Populations | Boris Shraiman - Academia.edu

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In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for populations in" /> <title>(PDF) Rate of Adaptation in Large Sexual Populations | Boris Shraiman - Academia.edu</title> <link rel="canonical" href="https://www.academia.edu/102452320/Rate_of_Adaptation_in_Large_Sexual_Populations" /> <script async src="https://www.googletagmanager.com/gtag/js?id=G-5VKX33P2DS"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-5VKX33P2DS', { cookie_domain: 'academia.edu', send_page_view: false, }); gtag('event', 'page_view', { 'controller': "single_work", 'action': "show", 'controller_action': 'single_work#show', 'logged_in': 'false', 'edge': 'unknown', // Send nil if there is no A/B test bucket, in case some records get logged // with missing data - that way we can distinguish between the two cases. // ab_test_bucket should be of the form <ab_test_name>:<bucket> 'ab_test_bucket': null, }) </script> <script> var $controller_name = 'single_work'; var $action_name = "show"; var $rails_env = 'production'; var $app_rev = '49879c2402910372f4abc62630a427bbe033d190'; var $domain = 'academia.edu'; var $app_host = "academia.edu"; var $asset_host = "academia-assets.com"; var $start_time = new Date().getTime(); var $recaptcha_key = "6LdxlRMTAAAAADnu_zyLhLg0YF9uACwz78shpjJB"; var $recaptcha_invisible_key = "6Lf3KHUUAAAAACggoMpmGJdQDtiyrjVlvGJ6BbAj"; var $disableClientRecordHit = false; </script> <script> window.require = { config: function() { return function() {} } } </script> <script> window.Aedu = window.Aedu || {}; window.Aedu.hit_data = null; window.Aedu.serverRenderTime = new Date(1732437721000); window.Aedu.timeDifference = new Date().getTime() - 1732437721000; </script> <script type="application/ld+json">{"@context":"https://schema.org","@type":"ScholarlyArticle","abstract":"Adaptation often involves the acquisition of a large number of genomic changes that arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for populations in which genetic information is exchanged, beneficial mutations can arise in different individuals and be combined later. In large populations, when the product of the population size N and the total beneficial mutation rate Ub is large, many new beneficial alleles can be segregating in the population simultaneously. We calculate the rate of adaptation, v, in several models of such sexual populations and show that v is linear in NUb only in sufficiently small populations. In large populations, v increases much more slowly as log NUb. The prefactor of this logarithm, however, increases as the square of the recombination rate. This acceleration of adaptation by recombination implies a strong evolutionary advantage of sex.","author":[{"@context":"https://schema.org","@type":"Person","name":"Boris Shraiman"}],"contributor":[],"dateCreated":"2023-05-27","dateModified":null,"datePublished":"2009-01-01","headline":"Rate of Adaptation in Large Sexual Populations","inLanguage":"en","keywords":["Evolutionary Biology","Genetics","Physics","Sex","Molecular Evolution","Biology","Medicine","Probability","Population","Mutation","Investigations","Asexual Reproduction","Reproducibility of Results","Genetic Recombination","Recombination","Mutation Rate"],"locationCreated":null,"publication":"Genetics","publisher":{"@context":"https://schema.org","@type":"Organization","name":"Oxford University Press 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window.loswp.showSignupCaptcha = false window.loswp.willEdgeCache = false; window.loswp.work = {"work":{"id":102452320,"created_at":"2023-05-27T13:25:52.785-07:00","from_world_paper_id":234602740,"updated_at":"2023-05-27T13:48:04.480-07:00","_data":{"abstract":"Adaptation often involves the acquisition of a large number of genomic changes that arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for populations in which genetic information is exchanged, beneficial mutations can arise in different individuals and be combined later. In large populations, when the product of the population size N and the total beneficial mutation rate Ub is large, many new beneficial alleles can be segregating in the population simultaneously. We calculate the rate of adaptation, v, in several models of such sexual populations and show that v is linear in NUb only in sufficiently small populations. In large populations, v increases much more slowly as log NUb. The prefactor of this logarithm, however, increases as the square of the recombination rate. This acceleration of adaptation by recombination implies a strong evolutionary advantage of sex.","publisher":"Oxford University Press (OUP)","publication_date":"2009,,","publication_name":"Genetics"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"Rate of Adaptation in Large Sexual Populations","broadcastable":false,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [49581400]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "control"; window.loswp.useOptimizedScribd4genScript = false; window.loswp.appleClientId = 'edu.academia.applesignon';</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;swp-splash-paper-cover&quot;,&quot;attachmentId&quot;:102719183,&quot;attachmentType&quot;:&quot;pdf&quot;}"><img alt="First page of “Rate of Adaptation in Large Sexual Populations”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/102719183/mini_magick20230527-1-e7y5ih.png?1685219215" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/assets/single_work_splash/adobe.icon-574afd46eb6b03a77a153a647fb47e30546f9215c0ee6a25df597a779717f9ef.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">Rate of Adaptation in Large Sexual Populations</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="49581400" href="https://independent.academia.edu/BorisShraiman"><img alt="Profile image of Boris Shraiman" class="ds-work-card--author-avatar" src="//a.academia-assets.com/images/s65_no_pic.png" />Boris Shraiman</a></div><p class="ds-work-card--detail ds2-5-body-sm">2009, Genetics</p><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">Adaptation often involves the acquisition of a large number of genomic changes that arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for populations in which genetic information is exchanged, beneficial mutations can arise in different individuals and be combined later. In large populations, when the product of the population size N and the total beneficial mutation rate Ub is large, many new beneficial alleles can be segregating in the population simultaneously. We calculate the rate of adaptation, v, in several models of such sexual populations and show that v is linear in NUb only in sufficiently small populations. In large populations, v increases much more slowly as log NUb. The prefactor of this logarithm, however, increases as the square of the recombination rate. This acceleration of adaptation by recombination implies a strong evolutionary advantage of sex.</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;continue-reading-button--work-card&quot;,&quot;attachmentId&quot;:102719183,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;workUrl&quot;:&quot;https://www.academia.edu/102452320/Rate_of_Adaptation_in_Large_Sexual_Populations&quot;}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;download-pdf-button--work-card&quot;,&quot;attachmentId&quot;:102719183,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;workUrl&quot;:&quot;https://www.academia.edu/102452320/Rate_of_Adaptation_in_Large_Sexual_Populations&quot;}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div></div><div data-auto_select="false" data-client_id="331998490334-rsn3chp12mbkiqhl6e7lu2q0mlbu0f1b" data-doc_id="102719183" data-landing_url="https://www.academia.edu/102452320/Rate_of_Adaptation_in_Large_Sexual_Populations" data-login_uri="https://www.academia.edu/registrations/google_one_tap" data-moment_callback="onGoogleOneTapEvent" id="g_id_onload"></div><div class="ds-top-related-works--grid-container"><div class="ds-related-content--container ds-top-related-works--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="0" data-entity-id="74728995" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/74728995/Distribution_of_fixed_beneficial_mutations_and_the_rate_of_adaptation_in_asexual_populations">Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="194511207" href="https://independent.academia.edu/IgorRouzine">Igor Rouzine</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Proceedings of the National Academy of Sciences, 2012</p><p class="ds-related-work--abstract ds2-5-body-sm">When large asexual populations adapt, competition between simultaneously segregating mutations slows the rate of adaptation and restricts the set of mutations that eventually fix. This phenomenon of interference arises from competition between mutations of different strengths as well as competition between mutations that arise on different fitness backgrounds. Previous work has explored each of these effects in isolation, but the way they combine to influence the dynamics of adaptation remains largely unknown. Here, we describe a theoretical model to treat both aspects of interference in large populations. We calculate the rate of adaptation and the distribution of fixed mutational effects accumulated by the population. We focus particular attention on the case when the effects of beneficial mutations are exponentially distributed, as well as on a more general class of exponential-like distributions. In both cases, we show that the rate of adaptation and the influence of genetic bac...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations&quot;,&quot;attachmentId&quot;:82774193,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/74728995/Distribution_of_fixed_beneficial_mutations_and_the_rate_of_adaptation_in_asexual_populations&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/74728995/Distribution_of_fixed_beneficial_mutations_and_the_rate_of_adaptation_in_asexual_populations"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="94012927" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/94012927/The_Evolution_of_Mutation_Rate_in_Finite_Asexual_Populations">The Evolution of Mutation Rate in Finite Asexual Populations</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="251526311" href="https://independent.academia.edu/JeanBaptisteAndr%C3%A92">Jean-Baptiste André</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Genetics, 2005</p><p class="ds-related-work--abstract ds2-5-body-sm">In this article, we model analytically the evolution of mutation rate in asexual organisms. Three selective forces are present. First, everything else being equal, individuals with higher mutation rate have a larger fitness, thanks to the energy and time saved by not replicating DNA accurately. Second, as a flip side, the genome of these individuals is replicated with errors that may negatively affect fitness. Third, and conversely, replication errors have a potential benefit if beneficial mutations are to be generated. Our model describes the fate of modifiers of mutation rate under the three forces and allows us to predict the long-term evolutionary trajectory of mutation rate. We obtain three major results. First, in asexuals, the needs for both adaptation and genome preservation are not evolutionary forces that can stabilize mutation rate at an intermediate optimum. 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data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Coalescence and genetic diversity in sexual populations under selection&quot;,&quot;attachmentId&quot;:65007603,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/44556156/Coalescence_and_genetic_diversity_in_sexual_populations_under_selection&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/44556156/Coalescence_and_genetic_diversity_in_sexual_populations_under_selection"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="109469724" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/109469724/The_Effect_of_Deleterious_Alleles_on_Adaptation_in_Asexual_Populations">The Effect of Deleterious Alleles on Adaptation in Asexual Populations</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="328715" href="https://oxford.academia.edu/NBarton">Nick Barton</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Genetics, 2002</p><p class="ds-related-work--abstract ds2-5-body-sm">We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles ari...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;The Effect of Deleterious Alleles on Adaptation in Asexual Populations&quot;,&quot;attachmentId&quot;:107585930,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/109469724/The_Effect_of_Deleterious_Alleles_on_Adaptation_in_Asexual_Populations&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/109469724/The_Effect_of_Deleterious_Alleles_on_Adaptation_in_Asexual_Populations"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="17478895" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/17478895/Diminishing_Returns_from_Mutation_Supply_Rate_in_Asexual_Populations">Diminishing Returns from Mutation Supply Rate in Asexual Populations</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="37236119" href="https://independent.academia.edu/BlanchardJeffrey">Jeffrey Blanchard</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Science, 1999</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Diminishing Returns from Mutation Supply Rate in Asexual Populations&quot;,&quot;attachmentId&quot;:39533030,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/17478895/Diminishing_Returns_from_Mutation_Supply_Rate_in_Asexual_Populations&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/17478895/Diminishing_Returns_from_Mutation_Supply_Rate_in_Asexual_Populations"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="20032175" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/20032175/Lineage_dynamics_and_mutation_selection_balance_in_non_adapting_asexual_populations">Lineage dynamics and mutation–selection balance in non-adapting asexual populations</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="40961375" href="https://ufscar-br.academia.edu/AColato">A. 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2012</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;CONTRASTING DYNAMICS OF A MUTATOR ALLELE IN ASEXUAL POPULATIONS OF DIFFERING SIZE&quot;,&quot;attachmentId&quot;:47414989,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/10392344/CONTRASTING_DYNAMICS_OF_A_MUTATOR_ALLELE_IN_ASEXUAL_POPULATIONS_OF_DIFFERING_SIZE&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/10392344/CONTRASTING_DYNAMICS_OF_A_MUTATOR_ALLELE_IN_ASEXUAL_POPULATIONS_OF_DIFFERING_SIZE"><span 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