Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life Journal Article


Authors: Parfrey, Laura Wegener; Grant, Jessica; Tekle, Yonas I.; Lasek-Nesselquist, Erica; Morrison, Hilary G.; Sogin, Mitchell L.; Patterson, David J.; Katz, Laura A.
Article Title: Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
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.
Keywords: Evolutionary Biology; LONG-BRANCH ATTRACTION; protein evolution; GENE-TRANSFER; PHYLOGENETIC; INFERENCE; MULTIPLE SEQUENCE ALIGNMENT; MICROBIAL EUKARYOTES; molecular phylogenetics; EXCAVATA; PHOTOSYNTHETIC EUKARYOTES; MISSING DATA; secondary endosymbiosis; supergroups; Rhizaria; systematic error; taxon sampling; PLASTID EVOLUTION
Journal Title: Systematic Biology
Volume: 59
Issue: 5
ISSN: 1063-5157
Publisher: Oxford University Press  
Publication Place: OXFORD; GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND
Date Published: 2010-01-01
Start Page: 518
End Page: 533
Language: English
DOI/URL:
Notes: PT: J; NR: 105; TC: 0; J9: SYST BIOL; PG: 16; GA: 662OI