Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
Identifieur interne : 000150 ( Ncbi/Merge ); précédent : 000149; suivant : 000151Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
Auteurs : Laura Wegener Parfrey [États-Unis] ; Jessica Grant [États-Unis] ; Yonas I. Tekle [États-Unis] ; Erica Lasek-Nesselquist [États-Unis] ; Hilary G. Morrison [États-Unis] ; Mitchell L. Sogin [États-Unis] ; David J. Patterson [États-Unis] ; Laura A. Katz [États-Unis]Source :
- Systematic Biology [ 1063-5157 ] ; 2010.
Abstract
An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level “supergroups,” many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88–451) and levels of missing data (17–69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup “Chromalveolata” is rejected. Furthermore, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support (BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.
Url:
DOI: 10.1093/sysbio/syq037
PubMed: 20656852
PubMed Central: 2950834
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<front><div type="abstract" xml:lang="en"><p>An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level “supergroups,” many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88–451) and levels of missing data (17–69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup “Chromalveolata” is rejected. Furthermore, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support (BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.</p>
</div>
</front>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Syst Biol</journal-id>
<journal-id journal-id-type="hwp">sysbio</journal-id>
<journal-id journal-id-type="publisher-id">sysbio</journal-id>
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<issn pub-type="epub">1076-836X</issn>
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<article-categories><subj-group subj-group-type="heading"><subject>Regular Articles</subject>
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</article-categories>
<title-group><article-title>Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Parfrey</surname>
<given-names>Laura Wegener</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Grant</surname>
<given-names>Jessica</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tekle</surname>
<given-names>Yonas I.</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
<xref ref-type="aff" rid="aff6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lasek-Nesselquist</surname>
<given-names>Erica</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
<xref ref-type="aff" rid="aff4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Morrison</surname>
<given-names>Hilary G.</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sogin</surname>
<given-names>Mitchell L.</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Patterson</surname>
<given-names>David J.</given-names>
</name>
<xref ref-type="aff" rid="aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Katz</surname>
<given-names>Laura A.</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="aff" rid="aff2">2</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, MA 01003, USA</aff>
<aff id="aff2"><label>2</label>
Department of Biological Sciences, Smith College, 44 College Lane, Northampton, MA 01063, USA</aff>
<aff id="aff3"><label>3</label>
Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA</aff>
<aff id="aff4"><label>4</label>
Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, RI 02912, USA</aff>
<aff id="aff5"><label>5</label>
Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA</aff>
<aff id="aff6"><label>6</label>
Present address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520, USA</aff>
<author-notes><corresp id="cor1"><label>*</label>
Correspondence to be sent to: Laura A. Katz, 44 College Lane, Northampton, MA 01003, USA; E-mail: <email>lkatz@smith.edu</email>
</corresp>
<fn><p>Laura Wegener Parfrey and Jessica Grant have contributed equally to this work.</p>
</fn>
<fn><p>Associate Editor: Cécile Ané</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>10</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="epub"><day>23</day>
<month>7</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>1</day>
<month>10</month>
<year>2011</year>
</pub-date>
<pmc-comment> PMC Release delay is 12 months and 0 days and was based on the
. </pmc-comment>
<volume>59</volume>
<issue>5</issue>
<fpage>518</fpage>
<lpage>533</lpage>
<history><date date-type="received"><day>30</day>
<month>9</month>
<year>2009</year>
</date>
<date date-type="rev-recd"><day>1</day>
<month>12</month>
<year>2009</year>
</date>
<date date-type="accepted"><day>25</day>
<month>5</month>
<year>2010</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org</copyright-statement>
<copyright-year>2010</copyright-year>
</permissions>
<abstract><p>An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level “supergroups,” many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88–451) and levels of missing data (17–69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup “Chromalveolata” is rejected. Furthermore, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support (BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.</p>
</abstract>
<kwd-group><kwd>Excavata</kwd>
<kwd>microbial eukaryotes</kwd>
<kwd>Rhizaria</kwd>
<kwd>supergroups</kwd>
<kwd>systematic error</kwd>
<kwd>taxon sampling</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
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<li>Massachusetts</li>
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<name sortKey="Katz, Laura A" sort="Katz, Laura A" uniqKey="Katz L" first="Laura A." last="Katz">Laura A. Katz</name>
<name sortKey="Lasek Nesselquist, Erica" sort="Lasek Nesselquist, Erica" uniqKey="Lasek Nesselquist E" first="Erica" last="Lasek-Nesselquist">Erica Lasek-Nesselquist</name>
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