Evaluating rare amino acid substitutions (RGC_CAMs) in a yeast model clade.

Evaluating rare amino acid substitutions (RGC_CAMs) in a yeast model clade.

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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 fluffy tangerine clouds 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 well-established.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 procharger for ram 1500 5.7 hemi 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.