Phylogenomics provides robust support for a two-domains tree of life.

Abstract

Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal "tree of life" based upon conserved core genes. Vigorous ongoing debate about eukaryote origins is based upon assertions that the topology of the tree of life depends on the taxa included and the choice and quality of genomic data analysed. Here we have reanalysed the evidence underpinning those claims and bring more data to bear on the question by using supertree and coalescent methods to interrogate >3000 gene families in Archaea and eukaryotes. We find that eukaryotes consistently originate from within the Archaea in a two-domains tree when due consideration is given to the fit between model and data. Our analyses support a close relationship between eukaryotes and Asgard Archaea and identify the Heimdallarchaeota as the current best candidate for the closest archaeal relatives of the eukaryotic nuclear lineage.