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Are we close to a consensus?" /> <meta name="keywords" content="Archaeplastida; Glaucophyta; monophyly; phylogenomics; phylogenetic analyses; primary plastid; Rhodophyta; Viridiplantae" /> <link rel="icon" href="https://pbsociety.org.pl/journals/public/journals/1/journalFavicon_en_US.png" type="ERROR: cannot open `/var/lib/php/ptb/php8VKuKU' (No such file or directory)" /> <link rel="schema.DC" href="http://purl.org/dc/elements/1.1/" /> <meta name="DC.Contributor.Sponsor" xml:lang="en" content=""/> <meta name="DC.Creator.PersonalName" content="Paweł Mackiewicz"/> <meta name="DC.Creator.PersonalName" content="Przemysław Gagat"/> <meta name="DC.Date.created" scheme="ISO8601" content="2014-12-31"/> <meta name="DC.Date.dateSubmitted" scheme="ISO8601" content="2014-11-21"/> <meta name="DC.Date.issued" scheme="ISO8601" content="2014-12-31"/> <meta name="DC.Date.modified" scheme="ISO8601" content="2014-12-31"/> <meta name="DC.Description" xml:lang="en" content="One of the key evolutionary events on the scale of the biosphere was an endosymbiosis between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid. Such an organelle is characteristic of three eukaryotic lineages, glaucophytes, red algae and green plants. The three groups are usually united under the common name Archaeplastida or Plantae in modern taxonomic classifications, which indicates they are considered monophyletic. The methods generally used to verify this monophyly are phylogenetic analyses. In this article we review up-to-date results of such analyses and discussed their inconsistencies. Although phylogenies of plastid genes suggest a single primary endosymbiosis, which is assumed to mean a common origin of the Archaeplastida, different phylogenetic trees based on nuclear markers show monophyly, paraphyly, polyphyly or unresolved topologies of Archaeplastida hosts. The difficulties in reconstructing host cell relationships could result from stochastic and systematic biases in data sets, including different substitution rates and patterns, gene paralogy and horizontal/endosymbiotic gene transfer into eukaryotic lineages, which attract Archaeplastida in phylogenetic trees. Based on results to date, it is neither possible to confirm nor refute alternative evolutionary scenarios to a single primary endosymbiosis. Nevertheless, if trees supporting monophyly are considered, relationships inferred among Archaeplastida lineages can be discussed. Phylogenetic analyses based on nuclear genes clearly show the earlier divergence of glaucophytes from red algae and green plants. Plastid genes suggest a more complicated history, but at least some studies are congruent with this concept. Additional research involving more representatives of glaucophytes and many understudied lineages of Eukaryota can improve inferring phylogenetic relationships related to the Archaeplastida. In addition, alternative approaches not directly dependent on phylogenetic methods should be developed."/> <meta name="DC.Format" scheme="IMT" content="application/pdf"/> <meta name="DC.Identifier" content="asbp.2014.044"/> <meta name="DC.Identifier.pageNumber" content="263-280"/> <meta name="DC.Identifier.DOI" content="10.5586/asbp.2014.044"/> <meta name="DC.Identifier.URI" content="https://pbsociety.org.pl/journals/index.php/asbp/article/view/asbp.2014.044"/> <meta name="DC.Language" scheme="ISO639-1" content="en"/> <meta name="DC.Rights" content="Copyright (c) 2014 Paweł Mackiewicz, Przemysław Gagat" /> <meta name="DC.Rights" content="http://creativecommons.org/licenses/by/3.0"/> <meta name="DC.Source" content="Acta Societatis Botanicorum Poloniae"/> <meta name="DC.Source.ISSN" content="2083-9480"/> <meta name="DC.Source.Issue" content="4"/> <meta name="DC.Source.URI" content="https://pbsociety.org.pl/journals/index.php/asbp"/> <meta name="DC.Source.Volume" content="83"/> <meta name="DC.Subject" xml:lang="en" content="Archaeplastida"/> <meta name="DC.Subject" xml:lang="en" content="Glaucophyta"/> <meta name="DC.Subject" xml:lang="en" content="monophyly"/> <meta name="DC.Subject" xml:lang="en" content="phylogenomics"/> <meta name="DC.Subject" xml:lang="en" content="phylogenetic analyses"/> <meta name="DC.Subject" xml:lang="en" content="primary plastid"/> <meta name="DC.Subject" xml:lang="en" content="Rhodophyta"/> <meta name="DC.Subject" xml:lang="en" content="Viridiplantae"/> <meta name="DC.Title" content="Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?"/> <meta name="DC.Type" content="Text.Serial.Journal"/> <meta name="DC.Type.articleType" content="Evolution of Plant Cells"/> <meta name="gs_meta_revision" content="1.1" /> <meta name="citation_journal_title" content="Acta Societatis Botanicorum Poloniae"/> <meta name="citation_issn" content="2083-9480"/> <meta name="citation_author" content="Paweł Mackiewicz"/> <meta name="citation_author_institution" content="Department of Genomics, Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-383 Wrocław"/> <meta name="citation_author" content="Przemysław Gagat"/> <meta name="citation_author_institution" content="Department of Genomics, Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-383 Wrocław"/> <meta name="citation_title" content="Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?"/> <meta name="citation_date" content="2014/12/31"/> <meta name="citation_volume" content="83"/> <meta name="citation_issue" content="4"/> <meta name="citation_firstpage" content="263"/> <meta name="citation_lastpage" content="280"/> <meta name="citation_doi" content="10.5586/asbp.2014.044"/> <meta name="citation_abstract_html_url" content="https://pbsociety.org.pl/journals/index.php/asbp/article/view/asbp.2014.044"/> <meta name="citation_language" content="en"/> <meta name="citation_keywords" xml:lang="en" content="Archaeplastida"/> <meta name="citation_keywords" xml:lang="en" content="Glaucophyta"/> <meta name="citation_keywords" xml:lang="en" content="monophyly"/> <meta name="citation_keywords" xml:lang="en" content="phylogenomics"/> <meta name="citation_keywords" xml:lang="en" content="phylogenetic analyses"/> <meta name="citation_keywords" xml:lang="en" content="primary plastid"/> <meta name="citation_keywords" xml:lang="en" content="Rhodophyta"/> 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id="articleTitle"><h3>Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?</h3></div> <div id="authorString"><em>Paweł Mackiewicz, Przemysław Gagat</em></div> <br /> <div id="articleAbstract"> <h4>Abstract</h4> <br /> <div>One of the key evolutionary events on the scale of the biosphere was an endosymbiosis between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid. Such an organelle is characteristic of three eukaryotic lineages, glaucophytes, red algae and green plants. The three groups are usually united under the common name Archaeplastida or Plantae in modern taxonomic classifications, which indicates they are considered monophyletic. The methods generally used to verify this monophyly are phylogenetic analyses. In this article we review up-to-date results of such analyses and discussed their inconsistencies. Although phylogenies of plastid genes suggest a single primary endosymbiosis, which is assumed to mean a common origin of the Archaeplastida, different phylogenetic trees based on nuclear markers show monophyly, paraphyly, polyphyly or unresolved topologies of Archaeplastida hosts. The difficulties in reconstructing host cell relationships could result from stochastic and systematic biases in data sets, including different substitution rates and patterns, gene paralogy and horizontal/endosymbiotic gene transfer into eukaryotic lineages, which attract Archaeplastida in phylogenetic trees. Based on results to date, it is neither possible to confirm nor refute alternative evolutionary scenarios to a single primary endosymbiosis. Nevertheless, if trees supporting monophyly are considered, relationships inferred among Archaeplastida lineages can be discussed. Phylogenetic analyses based on nuclear genes clearly show the earlier divergence of glaucophytes from red algae and green plants. Plastid genes suggest a more complicated history, but at least some studies are congruent with this concept. Additional research involving more representatives of glaucophytes and many understudied lineages of Eukaryota can improve inferring phylogenetic relationships related to the Archaeplastida. In addition, alternative approaches not directly dependent on phylogenetic methods should be developed.</div> <br /> </div> <div id="articleSubject"> <h4>Keywords</h4> <br /> <div>Archaeplastida; Glaucophyta; monophyly; phylogenomics; phylogenetic analyses; primary plastid; Rhodophyta; Viridiplantae</div> <br /> </div> <div id="articleFullText"> <h4>Full Text:</h4> <a href="https://pbsociety.org.pl/journals/index.php/asbp/article/view/asbp.2014.044/3989" class="file" target="_parent">PDF</a> </div> <div id="articleCitations"> <h4>References</h4> <br /> <div> <p>Delwiche CF, Timme RE. Plants. Curr Biol. 2011;21(11):R417–R422. http://dx.doi.org/10.1016/j.cub.2011.04.021</p> <p>Schenk HE. Glaucocystophytes. In: Encyclopedia of life sciences. Chichester: John Wiley & Sons; 2001. http://dx.doi.org/10.1038/npg.els.0003061</p> <p>Thomas DN. Seaweeds. London: Natural History Museum; 2002.</p> <p>Lewis LA, McCourt RM. Green algae and the origin of land plants. Am J Bot. 2004;91(10):1535–1556. http://dx.doi.org/10.3732/ajb.91.10.1535</p> <p>Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, et al. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol. 2005;52(5):399–451. http://dx.doi.org/10.1111/j.1550-7408.2005.00053.x</p> <p>Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, et al. The revised classification of eukaryotes. J Eukaryot Microbiol. 2012;59(5):429–514. http://dx.doi.org/10.1111/j.1550-7408.2012.00644.x</p> <p>Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, Pearlman RE, et al. The tree of eukaryotes. 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Bioscience. 2009;59(6):471–481. http://dx.doi.org/10.1525/bio.2009.59.6.5</p> </div> <br /> </div> <br /> <br /> DOI: <a id="pub-id::doi" href="https://doi.org/10.5586/asbp.2014.044">https://doi.org/10.5586/asbp.2014.044</a> <span class="Z3988" title="ctx_ver=Z39.88-2004&rft_id=https%3A%2F%2Fpbsociety.org.pl%2Fjournals%2Findex.php%2Fasbp%2Farticle%2Fview%2F4662&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.title=Acta+Societatis+Botanicorum+Poloniae&rft.jtitle=Acta+Societatis+Botanicorum+Poloniae&rft.atitle=Monophyly+of+Archaeplastida+supergroup+and+relationships+among+its+lineages+in+the+light+of+phylogenetic+and+phylogenomic+studies.+Are+we+close+to+a+consensus%3F&rft.artnum=asbp.2014.044&rft.stitle=Acta+Soc+Bot+Pol&rft.volume=83&rft.issue=4&rft.aulast=Mackiewicz&rft.aufirst=Pawe%C5%82&rft.auinit=&rft.date=2014-12-31&rft.au=Pawe%C5%82+Mackiewicz&rft.au=Przemys%C5%82aw+Gagat&rft_id=info%3Adoi%2F10.5586%2Fasbp.2014.044&rft.pages=263-280&rft.eissn=2083-9480"></span>  <script type="text/javascript"> var gaJsHost = (("https:" == document.location.protocol) ? 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