Phylogenomics reshuffles the eukaryotic supergroups

Abstract

Background: Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial.

Methodology/principle findings: Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history.

Conclusions: This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name 'SAR' (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes.

Figure 1. Best maximum likelihood tree of eukaryotes found using TREEFINDER, with 10 starting trees obtained with the global tree searching procedure.

Numbers at nodes represent the result of the bootstrap analysis (underlined numbers; hundred bootstrap pseudoreplicates were performed) and Bayesian posterior probabilities. Black dots represent values of 100% bootstrap support (BP) and Bayesian posterior probabilities (BiPP) of 1.0. Nodes without numbers correspond to supports weaker than 50% BP and 0.8 BiPP.