Divergence time estimations of Class II methanogens and other Halobacteriota lineages under different root settings. Phylogenomic trees were reconstructed using IQ-TREE 2 (62–64) under parameters -alrt 1000 -bb 1000 -m LG + R10 + C60, based on the concatenated alignments of SMC and 37 conserved proteins (2, 65, 87, 91). Node dates were inferred using MCMCTree in paml v4.8 (89, 90). The substitution rate was calculated using 3.46 Ga (92) as the root node age. The root node, representing the beginning of the archaeal domain radiation, was calibrated to 3.46–4.29 Ga (92, 93). The MRCA of the crown-group oxygenic Cyanobacteria was calibrated to 2.50–3.00 Ga (40, 44). The divergence between families Nostocaceae and Chroococcidiopsidaceae was calibrated to 0.80–2.00 Ga (94–96). The 95% highest posterior density intervals were indicated by flanking horizontal bars. The last common ancestor of Class II methanogens is marked with a star. The geological timescale follows the ICS International Chronostratigraphic Chart (v 2023/06) (97). The visualization was accomplished using the R package ggtree (98). A) The root was set between the superphylum DPANN and the rest of archaeal lineages. B) The root was set between the superphyla DPANN, TACK, Asgard and the rest archaeal lineages. C) The root was set between the superphylum TACK and other archaeal lineages, after excluding DPANN species.