Changes in the recombinational environment affect divergence in the yellowgene of drosophila

The complete coding region of the yellow (y) gene was sequenced in differen t Drosophila species. In the species of the melanogaster subgroup (D. melan ogaster, D. simulans, D. mauritiana, D. yakuba, and D. erecta), this gene i s located at the tip of the X chromosome in a region with a strong reductio n in recombination rate. In contrast, in D. ananassae (included in the anan assae subgroup of the melanogaster group) and in the obscura group species (D. subobscura, D. madeirensis, D. guanche, and D. pseudoobscura), the y ge ne is located in regions with normal recombination rates. As predicted by t he hitchhiking and background selection models, this change in the recombin ational environment affected synonymous divergence in the y-gene-coding reg ion. Estimates of the number of synonymous substitutions per site were much loa er between the obscura group species and D. ananassae than between the species of the obscura group and the melanogaster subgroup. In fact, a hig hly significant increase in the rate of synonymous substitution was detecte d in all lineages leading to the species of the melanogaster subgroup relat ive to the D. ananassae lineage. This increase can be explained by a higher fixation rate of mutations from preferred to unpreferred codons (slightly deleterious mutations). The lower codon bias detected in all species of the melanogaster subgroup relative to D. ananassae (or to the obscura group sp ecies) would be consistent with this proposal. Therefore, at least in Droso phila, changes in the recombination rate in different lineages might cause deviations of the molecular-clock hypothesis and contribute to the overdisp ersion of the rate of synonymous substitution. In contrast, the change in t he recombinational environment of the y gene has no detectable effect on th e rate of amino acid replacement in the Yellow protein.