I recommend acceptance for publication in Life Sciences journal.
The fact that Thermofilum is placed outside Crenarchaeota in Figures 3 and 4 is a little disturbing. I haven’t come across such a placement in other phylogenetic analyses of Archaea, for example in Brochier-Armanet et al 2008 Nat Rev Microb, or Rinke et al. 2013 Nature. I believe this needs to better explained in the manuscript, rather than just saying “this fact is noted”.