DNA sequence variation and the recombinational landscape in Drosophila pseudoobscura: A study of the second chromosome

The relationship between rates of recombination and DNA sequence polymorphi sm was analyzed for the second chromosome of Drosophila pseudoobscura. We c onstructed integrated genetic and physical maps of this chromosome using mo lecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromos ome arm (3R) in D. melanogaster. There appears to be very little centromeri c suppression of recombination, and rates of recombination are quite unifor m across most of the chromosome. Levels of sequence variation (theta(w), ba sed on the number of segregating sites) at seven loci (tropomyosin 1, Rhodo psin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consisten t with earlier studies, the average estimate of theta(w) at total sites is 1.5-fold higher than that in D. melanogaster, while average theta(w) at sil ent sites is almost 3-fold higher. These estimates of variation were analyz ed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence va riation in D. pseudoobscura can be explained by differences in regional rat es of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymo us, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima's D statistics for 6 out of th e 7 loci surveyed are negative, suggesting that D. pseudoobscura may have e xperienced a rapid population expansion in the recent past or, alternativel y, that slightly deleterious mutations constitute an important component of standing variation in this species.