Recent selection on synonymous codon usage in Drosophila

Evidence from a variety of sources indicates that selection has influenced synonymous codon usage in Drosophila. It has generally been difficult, howe ver, to distinguish selection that acted in the distant past from ongoing s election. However, under a neutral model, polymorphisms usually reflect mor e recent mutations than fixed differences between species and may, therefor e, be useful for inferring recent selection. If the ancestral state is pref erred, selection should shift the frequency distribution of derived states/ site toward lower values; if the ancestral is unpreferred, selection should increase the number of derived states/site. Polymorphisms were classified as ancestrally preferred or unpreferred for several genes of D. simulans an d D. melanogaster. A computer simulation of coalescence was employed to der ive the expected frequency distributions of derived states/site under vario us modifications of the Wright-Fisher neutral model, and distributions of t est statistics (t and Mann-Whitney U) were derived by appropriate sampling. One-tailed tests were applied to transformed frequency data to assess whet her the two frequency distributions deviated from neutral expectations in t he direction predicted by selection on codon usage. Several genes from D. s imulans appear to be subject to recent selection on synonymous codons, incl uding one gene with low codon bias, esterase-6. Selection may also be actin g in D. melanogaster.