  The inability to resolve deep node relationships of highly divergent/rapidly
evolving protein families is a major factor that stymies evolutionary studies.
In this manuscript, we propose a Multiple Sequence Alignment (MSA) independent
method to infer evolutionary relationships. We previously demonstrated that
phylogenetic profiles built using position specific scoring matrices (PSSMs)
are capable of constructing informative evolutionary histories(1;2). In this
manuscript, we theorize that PSSMs derived specifically from the query
sequences used to construct the phylogenetic tree will improve this method for
the study of rapidly evolving proteins. To test this theory, we performed
phylogenetic analyses of a benchmark protein superfamily (reverse
transcriptases (RT)) as well as simulated datasets. When we compare the results
obtained from our method, PHYlogenetic ReconstructioN (PHYRN), with other MSA
dependent methods, we observe that PHYRN provides a 4- to 100-fold increase in
accurate measurements at deep nodes. As phylogenetic profiles are used as the
information source, rather than MSA, we propose PHYRN as a paradigm shift in
studying evolution when MSA approaches fail. Perhaps most importantly, due to
the improvements in our computational approach and the availability of vast
amount of sequencing data, PHYRN is scalable to thousands of sequences. Taken
together with PHYRNs adaptability to any protein family, this method can serve
as a tool for resolving ambiguities in evolutionary studies of rapidly
evolving/highly divergent protein families.
