Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Non-Parametric Bootstrap Support

Whole genome comparisons based on Average Nucleotide Identities (ANI) and
the Genome-to-genome distance calculator have risen to prominence in
rapidly classifying prokaryotic taxa using whole genome sequences. Some
implementations have even been proposed as a new standard in species
classification and have become a common technique for papers describing
newly sequenced genomes. However, attempts to apply whole genome
divergence data to delineation of higher taxonomic units and to
phylogenetic inference have had difficulty matching those produced by more
complex phylogenetic methods. We present a novel method for generating
statistically supported phylogenies of archaeal and bacterial groups using
a combined ANI and alignment fraction-based metric. For the test cases to
which we applied the developed approach we obtained results comparable
with other methodologies up to at least the family-level.  The
developed method uses non-parametric bootstrapping to gauge support for
inferred groups.  This method offers the opportunity to make use
of whole-genome comparison data, that are already being generated, to
quickly produce phylogenies including support for inferred groups.
Additionally, the developed ANI methodology can assist classification of
higher taxonomic groups. Included herein are supplemental materials, and
all whole genome datasets used throughout the construction of this work.