Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences

To gain additional insight into this question, we quantified background substitutional patterns in the saltans/willistoni group using inactive copies of a novel, Q-like retrotransposable element. We demonstrate that the pattern of background substitutions in the saltans/willistoni lineage has shifted to a significant degree, primarily due to changes in mutational biases. These differences predict a lower equilibrium GC content in the genomes of the saltans/willistoni species compared with that in the D. melanogaster species group. The magnitude of the difference can readily account for changes in intronic GC content, but it appears insufficient to explain changes in codon usage within the saltans/willistoni lineage.We suggest that the observed changes in codon usage in the saltans/willistoni clade reflects either lineage-specific changes in the definitions of preferred and unpreferred codons, or a weaker selective pressure on codon bias in this lineage.Codon bias refers to the unequal usage of synonymous codons in protein coding sequences. Preferred codons are believed to correspond to more abundant transfer (t)RNAs [1]. In genes with high codon bias, the frequent presence of preferred codons is believed to increase the efficiency and/or fidelity of translation [2-4]. In Drosophila, empirical evidence suggests that the degree of codon bias can have substantial effects on active protein level; replacements of preferred codons with unpreferred ones in the alcohol dehydrogenase (Adh) gene result in significant decreases in levels of protein activity [5].Within the genome of a particular species, the level of codon bias for any given gene is thought to be governed by the dynamic interplay among natural selection, mutation, and drift. Accordingly, codon bias levels will be affected by the rate and dominance of mutations affecting codon bias, the stochasticity associated with the population processes affecting these mutations (mediated through factors such as effective po