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.