Evaluating rare amino acid substitutions (RGC-CAMs) in a yeast model Clade

Abstract

When inferring phylogenetic relationships, not all sites in a sequence alignment are equally informative. One recently proposed approach that takes advantage of this inequality relies on sites that contain amino acids whose replacement requires multiple substitutions. Identifying these so-called RGC-CAM substitutions (after Rare Genomic Changes as Conserved Amino acids-Multiple substitutions) requires that, first, at any given site in the amino acid sequence alignment, there must be a minimum of two different amino acids; second, each amino acid must be present in at least two taxa; and third, the amino acids must require a minimum of two nucleotide substitutions to replace each other. Although theory suggests that RGC-CAM substitutions are expected to be rare and less likely to be homoplastic, the informativeness of RGC-CAM substitutions has not been extensively evaluated in biological data sets. We investigated the quality of RGC-CAM substitutions by examining their degree of homoplasy and internode certainty in nearly 2.7 million aligned amino acid sites from 5,261 proteins from five species belonging to the yeast Saccharomyces sensu stricto clade whose phylogeny is wellestablished. We identified 2,647 sites containing RGC-CAM substitutions, a number that contrasts sharply with the 100,887 sites containing RGC-non-CAM substitutions (i.e., changes between amino acids that require only a single nucleotide substitution). We found that RGC-CAM substitutions had significantly lower homoplasy than RGC-non-CAM ones; specifically RGC-CAM substitutions showed a per-site average homoplasy index of 0.100, whereas RGC-non-CAM substitutions had a homoplasy index of 0.215. Internode certainty values were also higher for sites containing RGC-CAM substitutions than for RGC-non-CAM ones. These results suggest that RGC-CAM substitutions possess a strong phylogenetic signal and are useful markers for phylogenetic inference despite their rarity. Copyright: © 2014.