Abstract
The tree of life is generally estimated from a core set of 16-56 genes coding for proteins predominantly involved in translation and other conserved informational and cellular processes. These markers represent only a fraction of the genes that were likely present in the last universal common ancestor (LUCA), but are useful for deep phylogenetic reconstructions because their mode of inheritance appears to be mainly vertical, which satisfies the assumptions of gene concatenation and supertree methods. Previous phylogenetic analyses of these genes recovered a long branch between Archaea and Bacteria. By contrast, a recent study made use of a greatly expanded set of 381 marker genes and recovered a much shorter branch length between Archaea and Bacteria, comparable to some divergences within the domains. These analyses suggest that the apparent deep split between Archaea and Bacteria may be the result of accelerated evolution of ribosomal genes. Here we re-evaluate the evolutionary history of the expanded marker gene set and show that substitutional saturation, inter-domain gene transfer, hidden paralogy, and poor model fit contribute to the inference of an artificially shortened inter-domain branch. Our results do not exclude a moderately faster rate of ribosomal gene evolution during the divergence of Archaea and Bacteria, but indicate that vertically-evolving marker genes across all functional categories support a major genetic divergence between the two primary domains of life.
Competing Interest Statement
The authors have declared no competing interest.
