Methanonatronarchaeia are deep-branching ancestrally methanogenic archaea distant from Halobacteria

Abstract Since their discovery, the phylogenetic placement of the extremely halophilic, methanogenic Methanonatronarchaeia has remained controversial. Different studies have variably placed this lineage as sister to the archaeal class Halobacteria (haloarchaea) or as a deep-branching euryarchaeal group. These conflicting results may reflect methodological artefacts linked to the strong amino acid compositional bias characteristic of halophilic archaea and evolutionary model misspecification. Here, we reanalyse published phylogenomic datasets using site-heterogeneous mixture models that mitigate such biases. Our analyses consistently recover Methanonatronarchaeia as a deep-branching lineage basal to the Methanotecta, independent of the inclusion of the recently described Ordosarchaeia. We further show that Ordosarchaeia do not constitute a distinct lineage but fall within the previously described Halorutilales and Afararchaeaceae. Re-examination of the methyl-coenzyme M reductase phylogeny indicates that the placement of Methanonatronarchaeia mcr genes is best explained by vertical inheritance, without invoking horizontal gene transfer from unknown donors. Together, our results support ancestral methanogenesis within this lineage and its independent adaptation to extreme halophily.