Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors.

The episymbiotic DPANN archaea are thought to be one of the four major archaeal clades. However, the monophyly and placement of DPANN within the archaeal tree remain debated, and their fast-evolving reduced genomes render phylogenetic reconstructions challenging. Here we used 126 highly conserved protein markers, extensive taxon sampling representing the 11 known DPANN phyla and in-depth phylogenomic analyses to reassess DPANN monophyly and their relationships to other archaea. Our analyses robustly support the monophyly and placement within Euryarchaeota, and we identify the probably free-living Altiarchaeota as the earliest diverging DPANN branch. Our phylogenies suggest DPANN probably acquired several hallmark proteins through ancient horizontal gene transfer events from different bacterial donors, notably Patescibacteria and Omnitrophota, two bacterial phyla that also exhibit episymbiotic lifestyles. Overall, the monophyletic DPANN archaea probably evolved from a free-living, euryarchaeal-like ancestor, with proteins of bacterial origin playing a role in the emergence of their episymbiotic lifestyle.