An estimate of the deepest branches of the tree of life from ancient vertically evolving genes

• DOI: 10.7554/elife.66695
• Publication Date: 2022-02-22T00:00:20Z
• Authors: Edmund RR Moody; Tara A Mahendrarajah; Nina Dombrowski; James W Clark; Celine Petitjean; Pierre Offre; Gergely J Szöllősi; Anja Spang; Tom A Williams
• Keywords: Ribosomal protein; Three-domain system

Core gene phylogenies provide a window into early evolution, but different sets and analytical methods have yielded substantially views of the tree life. Trees inferred from small set universal core genes typically supported long branch separating archaeal bacterial domains. By contrast, recent analyses broader non-ribosomal suggested that Archaea may be less divergent Bacteria, estimates inter-domain distance are inflated due to accelerated evolution ribosomal proteins along branch. Resolving this debate is key determining diversity domains, shape life, our understanding course cellular evolution. Here, we investigate evolutionary history marker debate. We show reduced Archaea-Bacteria (AB) length result transfers hidden paralogy in expanded set. analysis broad range manually curated datasets an evenly sampled 700 Bacteria reveals current likely underestimate AB substitutional saturation poor model fit; best-performing phylogenetic markers tend support longer lengths; lengths statistically indistinguishable. Furthermore, phylogeny 27 highest-ranked recovers clade DPANN at base places Candidate Phyla Radiation (CPR) within as sister group Chloroflexota.