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Background  Several lines of evidence suggest that codon usage in the  Drosophila saltans  and  D. willistoni  lineages has shifted towards a less frequent use of GC-ending codons. Introns in these lineages show a parallel shift toward a lower GC content. These patterns have been alternatively ascribed to either a shift in mutational patterns or changes in the definition of preferred and unpreferred codons in these lineages.    Results and discussion  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.    Conclusion  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.

bmc biology

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