Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?

We tested the placement of N. equitans in the archaeal phylogeny using a large dataset of concatenated ribosomal proteins from 25 archaeal genomes. We indicate that the placement of N. equitans in archaeal phylogenies on the basis of ribosomal protein concatenation may be strongly biased by the coupled effect of its above-average evolutionary rate and lateral gene transfers. Indeed, we show that different subsets of ribosomal proteins harbor a conflicting phylogenetic signal for the placement of N. equitans. A BLASTP-based survey of the phylogenetic pattern of all open reading frames (ORFs) in the genome of N. equitans revealed a surprisingly high fraction of close hits with Euryarchaeota, notably Thermococcales. Strikingly, a specific affinity of N. equitans and Thermococcales was strongly supported by phylogenies based on a subset of ribosomal proteins, and on a number of unrelated molecular markers.We suggest that N. equitans may more probably be the representative of a fast-evolving euryarchaeal lineage (possibly related to Thermococcales) than the representative of a novel and early diverging archaeal phylum.Despite a ubiquitous distribution [1] and a diversity that may parallel that of the Bacteria (for a recent review see [2]), the Archaea still remain the most unexplored of life's domains. Whereas 21 different phyla are identified in the Bacteria (National Center for Biotechnology Information (NCBI) Taxonomy Database, as of October 2004 [3]), known cultivable archaeal species fall into only two distinct phyla - the Crenarchaeota and the Euryarchaeota [4] - on the basis of small subunit rRNA (SSU rRNA) (NCBI Taxonomy Database, as of October 2004 [3]). A number of non-cultivated species that do not group with either Crenarchaeota or Euryarchaeota have been tentatively assigned to a third phylum, the Korarchaeota [5]. However, this group may be artefactual, as well as that formed by other environmental 16S rRNA sequences [2].The Crenarchaeota/Euryarchaeota divi