Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life
Parfrey, Laura Wegener
Tekle, Yonas I.
Morrison, Hilary G.
Sogin, Mitchell L.
Patterson, David J.
Katz, Laura A.
MetadataShow full item record
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.
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.
Showing items related by title, author, creator and subject.
Yoon, Hwan Su; Grant, Jessica; Tekle, Yonas I.; Wu, Min; Chaon, Benjamin C.; Cole, Jeffrey C.; Logsdon, John M.; Patterson, David J.; Bhattacharya, Debashish; Katz, Laura A. (BioMed Central, 2008-01-18)Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, ...
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing Keeling, Patrick J.; Burki, Fabien; Wilcox, Heather M.; Allam, Bassem; Allen, Eric E.; Amaral-Zettler, Linda A.; Armbrust, E. Virginia; Archibald, John M.; Bharti, Arvind K.; Bell, Callum J.; Beszteri, Bank; Bidle, Kay D.; Cameron, Connor T.; Campbell, Lisa; Caron, David A.; Cattolico, Rose Ann; Collier, Jackie L.; Coyne, Kathryn J.; Davy, Simon K.; Deschamps, Phillipe; Dyhrman, Sonya T.; Edvardsen, Bente; Gates, Ruth D.; Gobler, Christopher J.; Greenwood, Spencer J.; Guida, Stephanie M.; Jacobi, Jennifer L.; Jakobsen, Kjetill S.; James, Erick R.; Jenkins, Bethany D.; John, Uwe; Johnson, Matthew D.; Juhl, Andrew R.; Kamp, Anja; Katz, Laura A.; Kiene, Ronald P.; Kudryavtsev, Alexander N.; Leander, Brian S.; Lin, Senjie; Lovejoy, Connie; Lynn, Denis; Marchetti, Adrian; McManus, George; Nedelcu, Aurora M.; Menden-Deuer, Susanne; Miceli, Cristina; Mock, Thomas; Montresor, Marina; Moran, Mary Ann; Murray, Shauna A.; Nadathur, Govind; Nagai, Satoshi; Ngam, Peter B.; Palenik, Brian; Pawlowski, Jan; Petroni, Giulio; Piganeau, Gwenael; Posewitz, Matthew C.; Rengefors, Karin; Romano, Giovanna; Rumpho, Mary E.; Rynearson, Tatiana A.; Schilling, Kelly B.; Schroeder, Declan C.; Simpson, Alastair G. B.; Slamovits, Claudio H.; Smith, David R.; Smith, G. Jason; Smith, Sarah R.; Sosik, Heidi M.; Stief, Peter; Theriot, Edward; Twary, Scott N.; Umale, Pooja E.; Vaulot, Daniel; Wawrik, Boris; Wheeler, Glen L.; Wilson, William H.; Xu, Yan; Zingone, Adriana; Worden, Alexandra Z. (Public Library of Science, 2014-06-24)Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their ...
Parfrey, Laura Wegener; Barbero, Erika; Lasser, Elyse; Dunthorn, Micah; Bhattacharya, Debashish; Patterson, David J.; Katz, Laura A. (Public Library of Science (PLoS), 2006-12-22)Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification—plants, animals, fungi, and protists—have been transformed ...