Linkage disequilibria and the site frequency spectra in the su(s) and su(w(a)) regions of the Drosophila melanogaster X chromosome

Ch. Langley et al., Linkage disequilibria and the site frequency spectra in the su(s) and su(w(a)) regions of the Drosophila melanogaster X chromosome, GENETICS, 156(4), 2000, pp. 1837-1852
Citations number
Categorie Soggetti
Biology,"Molecular Biology & Genetics
Journal title
ISSN journal
0016-6731 → ACNP
Year of publication
1837 - 1852
SICI code
Over the last decade, surveys of DNA sequence variation in natural populati ons of several Drosophila species and other taxa have established that poly morphism is reduced in genomic regions characterized by low rates of crossi ng over per physical length. Parallel studies have also established that di vergence between species is not reduced in these same genomic regions, thus eliminating explanations that rely on a correlation between the rates of m utation and crossing over. Several theoretical models (directional hitchhik ing, background selection, and random environment) have been proposed as po pulation genetic explanations. In this study samples from an African popula tion (n = 50) and a European population (n = 51) were surveyed at the su(s) (1955 bp) and su(omega) (3213 bp) loci for DNA sequence polymorphism, util izing a stratified SSCP/DNA sequencing protocol. These loci are located nea r the telomere of the X chromosome, in a region of reduced crossing over pe r physical length, and exhibit a significant reduction in DNA sequence poly morphism. Unlike most previously surveyed, these loci reveal substantial sk ews toward rare site frequencies, consistent with the predictions of direct ional hitchhiking and random environment models and inconsistent with the g eneral predictions of the background selection model (or neutral theory). N o evidence for excess geographic differentiation at these loci is observed. Although linkage disequilibrium is observed between closely linked sites w ithin these loci, many recombination events in the genealogy of the sampled alleles can be inferred and the genomic scale of linkage disequilibrium, m easured in base pairs between sites, is the same as that observed for loci in regions of normal crossing over. We conclude that gene conversion must b e high in these regions of low crossing over.