Combination of BLAST and phylogenetic tree analysis provide a more rounded view of molecular phylogeny

Abstract

Probing the phylogeny of species at the molecular level using specific biomarkers has been the de facto approach in understanding the evolutionary relationships between species. Notwithstanding the divergence in evolutionary relationships determined by different molecular markers, molecular phylogeny remains an art form determined by multiple cross-interacting factors. One important determinant in this regard is the type of analysis performed. Modern basic local alignment search tool (BLAST) analysis provides a first-pass and accurate view of the closest relatives of a biomolecule marker such as ribosomal proteins. But, results obtained from BLAST often coaggregate at the species or strain level which translates to a narrow view of phylogeny heavily attached to close sequence homology. While the data informs the species closest in evolutionary relationship to the target species, it nevertheless could not answer the important question of where did the species comes from? One incarnation of the above question could be which genus gave rise to the target biomolecule marker of interest. In this case, a phylogenetic tree using a compendium of well-chosen species could provide an initial guess at the genus which give rise to a particular biomolecule. Specifically, probed at different evolutionary distance from the target biomolecule marker, a phylogenetic tree provides a graded visual description of the evolutionary journey of a particular biomolecule marker. Hence, combining both BLAST and phylogenetic tree analysis would provide one with a well-rounded view of both the short (species) and long (genus) evolutionary distance that one seek to understand at the initiation of the inquest. Specifically, short evolutionary distance at the species level would be probed by BLAST analysis, while long evolutionary distance at the genus level could be revealed by a phylogenetic tree analysis. The latter could always benefit from a well-chosen set of evolutionarily separated species that could lend insights into the closest molecular relative of a particular biomolecule marker of interest. Choice of well separated species in evolutionary distance in this regard is crucial given the goal of identifying the species of closest evolutionary distance.