Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages

The phylogeny of the Archaea continues to be revisited and revised as new
groups are discovered and phylogenetic methods improve, but key questions
about their early evolution remain unanswered. It has been suggested that the
root of the Archaea may lie on, or potentially within, any of three major groups
- the Euryarchaeota, TACK+Asgard clade, and DPANN, the last of which
includes many host-associated and genome-reduced lineages. These root
hypotheses make starkly different predictions about the nature of early
archaeal evolution: for example, a root on or within DPANN might suggest a
small-genome and host-associated ancestor, with methanogenesis, the hall-
mark metabolism of the Archaea, evolving later. Here, we investigate the
position of the archaeal root and the nature of the last archaeal common
ancestor using a range of phylogenetic approaches, including the best avail-
able site- and branch-heterogeneous substitution models, and new gene tree-
species tree reconciliation models that capture changes in rates of gene
duplication, loss and transfer across the phylogeny. Our analyses converge on
a narrow archaeal root region at or near the base of the Euryarchaeota, sup-
... mehr
porting hypotheses in which the Last Archaeal Common Ancestor (LACA) was
a complex, free-living (hyper-)thermophilic methanogen. We recover DPANN
as the sister group to TACK and Asgard archaea, and suggest that their genome
evolution has been characterised by episodes of genome streamlining and
expansion, driven by gene loss and transfer.