The homeodomain is a DNA binding motif that is usually conserved among diverse taxa. Rapidly evolving homeodomains are thus of interest because their divergence may be associated with speciation. The exact site of the Odysseus (Ods) locus of hybrid male sterility in Drosophila contains such a homeobox gene. In the past half million years, this homeodomain has experienced more amino acid substitutions than it did in the preceding 700 million years; during this period, it has also evolved faster than other parts of the protein or even the introns. Such rapid sequence divergence is driven by positive selection and may contribute to reproductive isolation.

Molecular differentiation between races or closely related species is often incongruent with the reproductive divergence of the taxa of interest. Shared ancient polymorphism and͞or introgression during secondary contact may be responsible for the incongruence. At loci contributing to speciation, these two complications should be minimized (1, 2); hence, their variation may more faithfully reflect the history of the species' reproductive differentiation. In this study, we analyzed DNA polymorphism at the Odysseus (OdsH) locus of hybrid sterility between Drosophila mauritiana and Drosophila simulans and were able to verify such a prediction. Interestingly, DNA variation only a short distance away (1.8 kb) appears not to be influenced by the forces that shape the recent evolution of the OdsH coding region. This locus thus may represent a test case of inferring phylogeny of very closely related species.

The cuticular hydrocarbon (CH) pheromones in Drosophila melanogaster exhibit strong geographic variation. African and Caribbean populations have a high ratio of 5,9 heptacosadiene͞ 7,11 heptacosadiene (the ''High'' CH type), whereas populations from all other areas have a low ratio (''Low'' CH type). Based on previous genetic mapping, DNA markers were developed that localized the genetic basis of this CH polymorphism to within a 13-kb region. We then carried out a hierarchical search for diagnostic nucleotide sites starting with four lines, and increasing to 24 and 43 lines from a worldwide collection. Within the 13-kb region, only one variable site shows a complete concordance with the CH phenotype. This is a 16-bp deletion in the 5 region of a desaturase gene (desat2) that was recently suggested to be responsible for the CH polymorphism on the basis of its expression [Dallerac, R., Labeur, C., Jallon, J. T he molecular-genetic basis of phenotypic variations, either within or between species, is an important topic in genetics, evolution, agriculture, and medicine. Such differences may be morphological, physiological (1, 2), or behavioral (3) and could have either simple (4 -7) or complex (8 -11) genetic bases. Traits pertaining to species or racial differentiation are of special interest as they promise to shed light on the process of speciation (12)(13)(14)(15)(16)(17). Despite a number of methodologies developed for the purpose of complex trait mapping, successes in molecular identification of quantitative trait loci or nucleotides (QTL or QTN, respectively) have been limited to a few cases (7, 18 -20).Naturally occurring polymorphism in the cuticular hydrocarbon (CH) pheromones in Drosophila melanogaster is a promising system for molecular cloning and characterization (21). In different geographical populations of this species, the ratio of the two major isomers of the main female cuticular hydrocarbon, 5,9 heptacosadiene (5,9-HD) and 7,11 heptacosadiene (7,11-HD), varies consistently. Many African and Caribbean populations show a high ratio of 5,9-HD͞7,11-HD, whereas all other populations show a low ratio (1, 21). We shall refer to the former as the ''High'' and the latter as the ''Low'' phenotype. As this geographical variation exists in D. melanogaster, a species highly amenable to molecular genetic analysis, it can thus be a useful system for identifying QTNs for naturally occurring complex traits.An early study (22) suggested that the delta-9 desaturase gene (desat1) is a strong candidate for the CH polymorphism because of its genetic location and the function in the desaturation of the fatty acid. Genetic mapping (1) showed that the phenotypic difference indeed maps to the 1.7-centimorgan (cM) interval where desat1 resides. In this study, we further define the chromosomal segment responsible for the pheromonal difference and then carry out association mapping within the interval among worldwide strains. Specific QTNs for the trait can thus be delineated. Recently, Dallerac et al. (2) reported another d...

The gene for a male ejaculatory protein, Acp26Aa, in four sibling species of the Drosophila melanogaster subgroup has previously been shown to have a nonsynonymous rate (Ka) of nucleotide substitution that is indistinguishable from the synonymous rate (Ks). By examining this gene in two other species of this subgroup, we found that Ka is generally large and can sometimes be more than twice as large as Ks. This suggests that positive selection may be operating at this locus of male reproduction.