Molecular adaptation reflects taxon-specific mutational biases

Abstract

A fundamental question in molecular evolution is the extent to which patterns of adaptive change are shaped by mutational biases that make some variants more likely than others to arise. Past studies provide support for important effects of mutation bias on adaptive change, but leave open the empirical question of how strongly and how broadly evolutionary patterns depend on taxon-specific mutational tendencies. To characterize this effect quantitatively, we aggregated nucleotide substitution spectra for adaptive amino acid changes from 14 species, primarily from adaptive laboratory evolution studies. We then paired each species-specific spectrum of adaptive changes with independently sourced measurements of the mutation spectrum of that same species. Across the 14 species, we find considerable heterogeneity in the relative rates of the six possible types of single-nucleotide changes, for both the mutational and adaptive spectra. Comparing these spectra across species, we find that, the stronger the bias toward a given mutation type in the mutation spectrum of a species, the more that mutation type contributes to adaptive substitutions in that species. We conclude that, for the adaptation of proteins via amino acid changes, taxon-specific patterns of adaptive substitution are strongly responsive to taxon-specific mutational biases across mutation types.