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Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

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dc.contributor.author Parfrey, Laura Wegener
dc.contributor.author Grant, Jessica
dc.contributor.author Tekle, Yonas I.
dc.contributor.author Lasek-Nesselquist, Erica
dc.contributor.author Morrison, Hilary G.
dc.contributor.author Sogin, Mitchell L.
dc.contributor.author Patterson, David J.
dc.contributor.author Katz, Laura A.
dc.date.accessioned 2010-11-15T15:29:05Z
dc.date.available 2011-07-23T08:26:05Z
dc.date.issued 2010-06-01
dc.identifier.uri http://hdl.handle.net/1912/4086
dc.description Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Systematic Biology 59 (2010): 518-533, doi:10.1093/sysbio/syq037. en_US
dc.description.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. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces 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), while the proposed supergroup ‘Chromalveolata’ is rejected. Further, 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, taxonrich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data. en_US
dc.format.mimetype application/pdf
dc.language.iso en_US en_US
dc.relation.uri http://dx.doi.org/10.1093/sysbio/syq037
dc.subject Microbial eukaryotes en_US
dc.subject Supergroups en_US
dc.subject Taxon sampling en_US
dc.subject Rhizaria en_US
dc.subject Systematic error en_US
dc.subject Excavata en_US
dc.title Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life en_US
dc.type Preprint en_US


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