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.2015 Feb 17;112(7):E693-9.
doi: 10.1073/pnas.1420657112. Epub 2015 Feb 2.

Bacterial proteins pinpoint a single eukaryotic root

Affiliations

Bacterial proteins pinpoint a single eukaryotic root

Romain Derelle et al. Proc Natl Acad Sci U S A..

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.

Keywords: Diphoda; LECA; Opimoda; eukaryote phylogeny; phylogenomics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

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).
Fig. 2.
Fig. 2.
Summary of phylogenetic results. (A) Node supports for the alternative rooting hypothesis. Shaded boxes indicate the topology obtained in the best ML tree or the Bayesian consensus tree. “EUBAC reduced” refers to the EUBAC dataset without the 10 distant markers identified in He et al. (28). (B) Relative distances outgroup-eukaryotes. Shaded boxes indicate the lowest distances outgroup-eukaryotes for each of the three evolutionary models. (C) Unrooted Bayesian consensus trees obtained from the ALPHA-PROT and EUBAC datasets under the CAT-GTR + Γ4 model (eukaryotic relationships shown in Fig.1) with their outgroup highlighted in red.
See this image and copyright information in PMC

References

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