Construction of a Phylogenetic Tree Based on the Average Amino Acid Composition of Exomes

Abstract

All extant cellular organisms are believed to have descended from a common ancestor, and numerous phylogenetic trees have been constructed using various genetic and molecular data. In this study, I hypothesized that the average amino acid composition of an exome—computed across all exons—could serve as an index reflecting an organism’s characteristic amino acid usage and could be used to construct a phylogenetic tree. To test this hypothesis, I analyzed publicly available exome data from 81 species. For each species, I counted the fractional composition of each amino acid in each exon, and then calculated the average amino acid composition. I measured the pairwise distances between species using the angular distance based on these average compositions. Hierarchical clustering with Ward’s method was applied to construct a phylogenetic tree. The resulting tree showed a reasonable degree of similarity to previously established phylogenies, suggesting that this exome-based amino acid composition approach may offer some utility for inferring evolutionary relationships. To my knowledge, this is the first demonstration of constructing a phylogenetic tree solely from average exome-wide amino acid composition.