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Bacterial proteins pinpoint a single eukaryotic root

The root of eukaryote phylogeny formally represents the last eukaryotic common ancestor (LECA), but its position has remained controversial. Using new genome sequences, we revised and expanded two datasets of eukaryotic proteins of bacterial origin, which previously yielded conflicting views on the eukaryotic root. Analyses using state-of-the-art phylogenomic methodology revealed that both expanded datasets now support the same root position.

Romain Derellea,b,1, Guifré Torruellac, Vladimír Klimešd, Henner Brinkmanne, Eunsoo Kimf, Čestmír Vlčekg, B. Franz Langh, and Marek Eliášd

Subject: EVOLUTION

Significance

The root of eukaryote phylogeny formally represents the last eukaryotic common ancestor (LECA), but its position has remained controversial. Using new genome sequences, we revised and expanded two datasets of eukaryotic proteins of bacterial origin, which previously yielded conflicting views on the eukaryotic root. Analyses using state-of-the-art phylogenomic methodology revealed that both expanded datasets now support the same root position. Our results justify a new nomenclature for the two main eukaryotic groups and provide a robust phylogenetic framework to investigate the early evolution of the eukaryotic cell.

Abstract

The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between “Unikonta” and “Bikonta,” with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.

 

See: http://www.pnas.org/content/112/7/E693.abstract.html?etoc

PNAS February 17, 2015 vol. 112 no. 7 E693-E699

 

Fig. 1.

Fig. 1. Bayesian consensus trees. Bayesian consensus trees obtained from the ALPHA-PROT (left trees) and EUBAC (right trees) datasets under the CAT-GTR + Γ4 model. Posterior probabilities equal to 1 are not displayed. The two outgroups (Alpha-Proteobacteria and Eubacteria, respectively) are not shown for design reasons (gain of space).

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