Over-represented pairwise 16S rRNA gene sequence distance levels among prokaryotes

Abstract

We still do not know the main patterns of prokaryote evolution. This is due to the antiquity of these events, as well as major non-linear differences in evolutionary rates among lineages and within different sequence positions, in addition to horizontal gene transfer. Here, we addressed prokaryotic evolutionary patterns using the simple approach of determining whether there are pairwise 16S rRNA gene sequence distances that are over-represented on average in current reference databases. Our rationale was that, despite major differences in evolutionary rates, the average rate among all lineages would reflect the history of speciation events. Using an alignment-independent approach, we identified three Euclidean distances being over-represented in the Greengenes 97 % identity database. Taxonomic assignments of these distances showed that they corresponded to the family, phylum and kingdom levels, respectively. Therefore, we propose that these taxonomic levels correspond to ancient speciation events.