An Alternative Root for the Eukaryote Tree of Life

Abstract

The root of the eukaryote tree of life defines some of the most fundamental relationships among species. It is also critical for defining the last eukaryote common ancestor (LECA), the shared heritage of all extant species. The unikont-bikont root has been the reigning paradigm for eukaryotes for more than 10 years but is becoming increasingly controversial. We developed a carefully vetted data set, consisting of 37 nuclear-encoded proteins of close bacterial ancestry (euBacs) and their closest bacterial relatives, augmented by deep sequencing of the Acrasis kona (Heterolobosea, Discoba) transcriptome. Phylogenetic analysis of these data produces a highly robust, fully resolved global phylogeny of eukaryotes. The tree sorts all examined eukaryotes into three megagroups and identifies the Discoba, and potentially its parent taxon Excavata, as the sister group to the bulk of known eukaryote diversity, the proposed Neozoa (Amorphea + Stramenopila+Alveolata+Rhizaria+Plantae [SARP]). All major alternative hypotheses are rejected with as little as ∼50% of the data, and this resolution is unaffected by the presence of fast-evolving alignment positions or distant outgroup sequences. This "neozoan-excavate" root revises hypotheses of early eukaryote evolution and highlights the importance of the poorly studied Discoba for understanding the evolution of eukaryotic diversity and basic cellular processes.

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

“…However, the majority of eukaryotic lineages of highest taxonomic rank seem to have been identified. 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).…”

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.…”

Exploring the evolutionary history of centrosomes

“…There is a general consensus that the supergroup Amoebozoa is the sister group to Opisthokonta [42,47,[57][58][59]. Amoebozoa constitute a large ensemble of amoebae and flagellates that includes Entamoeba histolytica, a pathogen responsible for amoebic dysentery, and slime moulds such as D. discoideum and P. polycephalum.…”