The evolutionary origins of extreme halophilic Archaea

Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also referred to as Haloarchaea) resulted in hypotheses that imply the new groups share a common ancestor with the Haloarchaea. However, more recent analyses have led to a shift: the Nanohaloarchaea have been largely accepted as being a member of the DPANN superphylum, outside of the euryarchaeota; while the Methanonatronarchaeia have been placed near the base of the Methanotecta (composed of the class II methanogens, the Halobacteriales, and Archaeoglobales). These opposing hypotheses have far-reaching implications on the concepts of convergent evolution (unrelated groups evolve similar strategies for survival), genome reduction, and gene transfer. In this work, we attempt to resolve these conflicts with phylogenetic and phylogenomic data. We provide a robust taxonomic sampling of Archaeal genomes that spans the Asgardarchaea, TACK Group, euryarchaeota, and the DPANN superphylum. In addition, we assembled draft genomes from seven new representatives of the Nanohaloarchaea from distinct geographic locations. Phylogenies derived from these data imply that the highly conserved ATP synthase catalytic/non-catalytic subunits of Nanohaloarchaea share a sisterhood relationship with the Haloarchaea. We also employ a novel gene family distance clustering strategy which shows this sisterhood relationship is not likely the result of a recent gene transfer. In addition, we present and evaluate data that argue for and against the monophyly of the DPANN superphylum, in particular, the inclusion of the Nanohaloarchaea in DPANN. Significance StatementMany recent analyses have considered large groups of Bacteria and Archaea composed exclusively of environmentally assembled genomes as deep branching taxonomic groups in their respective domains. These groups display characteristics distinct from other members of their domain, which can attract unrelated lineages into those groups. This manuscript evaluates the case of the Nanohaloarchaea, and their inclusion in the DPANN Archaea, through careful analysis of the genes that compose the core of the Nanohaloarchaea. Analyses without inspection of the genes that compose a phylogenomic marker set increases the potential for the inclusion of artifacts and confuses the tree/web of life. Due to horizontal gene transfer and phylogenetic reconstruction artifacts, the placement of divergent archaeal classes into larger groups remains uncertain.