Highly degenerated genomes of many symbiont organisms tend to move around, in particular, to the baseline of a tree and thus distorts the overall structure of the tree. Therefore, it is better not to mix them with free-living organisms in a study. We rephrased the corresponding paragraph in the manuscript: “The nanosized archaean symbiont Nanoarchaeum equitans has a highly reduced genome (490,885 bp). It is the only described representative of a newly proposed phylum Nanoarchaeota and it cuts into the otherwise monophyletic phylum Euryarchaeota. We note that the monophyly of Euryarchaeota was also violated by Nanoarchaeum in some 16S rRNA trees, see, e.g., Figure 4 in a 2009 microbial survey as well as (c) and (d) in our Figure 3. It has been known that tiny genomes of endosymbiont microbes often tend to move towards baseline of a tree and distort the overall picture. In fact, we have suggested skipping such tiny genomes when studying bacterial phylogeny, see, e.g., (citing our 2010 paper) and a note in the home page of the CVTree Web Server. In the present case we may at most say that Nanoarchaeota probably makes a separate phylum, but its cutting into Euryarchaeota might be a side effect due to the tiny size of the highly reduced genome”.
present a comparative analysis of the taxonomic classification of the Archaea domain.