Bacterial proteins pinpoint a single eukaryotic root

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. eukaryote phylogeny | phylogenomics | Opimoda | Diphoda | LECA

Integrative modeling of gene and genome evolution roots the archaeal tree of life

“…S14), where the bacterial stem was predicted to have experienced 4.79 substitutions per site, compared with a mean of 0.192 (range, 0.0157-0.546) for within-domain branches. The use of long outgroup branches is a general problem that has contributed to disagreements about the archaeal root as well as about the roots of other major radiations (58)(59)(60)(61), motivating a search for alternative rooting methods.…”

Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life

“…The position of Metamonada, the third major lineage of Excavata, with respect to the root advocated by Derelle et al (138), remains to be established. An important aspect of the recent rooting hypotheses is that all predict that the LECA was a complex, fully fledged eukaryote (96,138,139). The Opimoda-Diphoda rooting further suggests that the LECA was a biflagellated bacteriovorous excavate-like organism (resembling malawimonads and jakobids?)…”

“…The Opimoda-Diphoda rooting further suggests that the LECA was a biflagellated bacteriovorous excavate-like organism (resembling malawimonads and jakobids?) with a complex flagellum-associated cytoskeleton (138,140). Significantly for this paper, sex, including meiosis, gamete fusion mediated by HAP2, and karyogamy mediated by GEX1, can be traced to the LECA under all recently proposed rooting hypotheses, even though evidence for the presence of sex and HAP2 and GEX1 orthologs is presently unavailable for many eukaryotic microkingdoms ( Figs.…”

“…Third, the original evidence for monophyly of unikonts and bikonts (and thus the eukaryotic root position) has been invalidated (131), and alternative rooting hypotheses have been suggested (132)(133)(134)(135)(136). The currently most convincing hypothesis with a well-defined methodology seems to be that of Derelle and Lang (137), recently corroborated by analyses of a larger and taxonomically better-sampled dataset (138). This hypothesis suggests the existence of two principal eukaryotic clades, called Opimoda and Diphoda, and implies that the traditional eukaryotic supergroup Excavata is paraphyletic or polyphyletic, as different lineages of Excavata are grouped with both Opimoda (Malawimonadida) and Diphoda (Discoba) (Fig.…”

Genomic data do not support comb jellies as the sister group to all other animals

“…In particular, the inclusion of outgroups very distant from the ingroup can cause reconstruction artifacts by attracting fast-evolving (long-branched) ingroup species toward the root (25,(27)(28)(29)(30)(31). A typical solution is to introduce more closely related outgroups to "break up" the long branch leading to the ingroup, but long-branch attraction artifacts can be further minimized by also removing the distant outgroups.…”