The Deep(er) Roots of Eukaryotes and Akaryotes

Abstract Locating the root-node of the “tree of life” (ToL) is one of the hardest problems in phylogenetics 1 . The root-node or the universal common ancestor (UCA) divides the descendants into organismal domains 2 . Two notable variants of the two-domains ToL (2D-ToL) have gained support recently 3,4 , though, Williams and colleagues (W&C) 4 claim that one is better supported than the other. Here, we argue that important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data were overlooked 4 . We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. It is well-known that different character-types present different perspectives on evolutionary history that relate to different phylogenetic depths 5–7 . Which of the 2D-ToL 2,4 hypotheses is better supported depends on which kind of molecular features – protein-domains or their component amino-acids – are better for resolving the common ancestors (CA) at the roots of clades. In practice, this involves reconstructing character compositions of the ancestral nodes all the way back to the UCA 2,3 .