The idea to use whole genome data for archaeal phylogenies is interesting, as the 16S rRNA phylogenies can be poor in resolving relationships among archaeal lineage due to GC content bias in hyperthermophilic Archaea.
Why at higher ranks, genomic approaches are more effective? That needs more explanation. And authors should also consider the large benefits of 16S data availability, specially at high ranks (genus and above) where the 16S has good resolution.