Fluctuating mutation bias and the evolution of base composition in Drosophila

The idea that the pattern of point mutation in Drosophila has remained cons tant during the evolution of the genus has recently been challenged. A stud y of the nucleotide composition focused on the Drosophila saltans group has evidenced unsuspected nucleotide composition differences among lineages. C ompositional differences are associated with an accelerated rate of amino a cid replacement in functionally less constrained regions. Here we reassess this issue from a different per spective. Adopting a maximum-likelihood est imation approach, we focus on the different predictions that mutation and s election make about the nonsynonymous-to-synonymous rate ratio. We investig ate two gene regions, alcohol dehydrogenase (Adh) and xanthine dehydrogenas e (Xdh), using a balanced data set that comprises representatives from the melangaster, obscura, saltans, and willistoni groups. We also consider repr esentatives of the Hawaiian picture-winged group. These Hawaiian species ar e known to have experienced repeated bottlenecks and are included as a refe rence for comparison. Our results confirm patterns previously detected. The branch ancestral to the fast-evolving willistoni/saltans lineage, where mo st of the change in GC content has occurred, exhibits an excess of synonymo us substitutions. The shift in mutation bias has affected the extent of the rate variation among sites in Xdh.