Nucleotide Substitution Bias within the Genus Drosophila Affects the Pattern of Proteome Evolution

The availability of complete genome sequences for 12 Drosophila species provides an unprecedented resource for large-scale studies of genome evolution. In this study, we looked for correlated shifts in the patterns of genome and proteome evolution within the genus Drosophila. Specifically, we asked if the nucleotide composition of the Drosophila willistoni genome—which is significantly less GC rich than the other 11 sequenced Drosophila genomes—is reflected in an altered pattern of amino acid substitutions in the encoded proteins. Our results show that this is indeed the case: There are large and highly significant asymmetries in the patterns of amino acid substitution between D. willistoni and Drosophila melanogaster, and they are in the direction predicted by the nucleotide biases. The implication of this result, combined with previous studies on long-term proteome evolution, is that substitutional biases at the DNA level can be a major factor in determining both the long-term and the short-term directions of proteome evolution.