Patterns of genetic diversity depend on genomic architecture. (A) Nucleotide polymorphism of silent sites in 20-kb windows is depressed in chromosome centers (and tips) compared to arm domains for Tropical strains (median of 20-kb windows on arms πsil = 0.165%; centers πsil = 0.041%; Wilcoxon χ2 = 1996.3; P < 0.0001). However, absolute divergence (Dxy) between Tropical and the distant Kerala group strains is largely insensitive to chromosomal domain. The recombination-associated domain structure of the X chromosome is less pronounced than for autosomes (Cutter and Choi 2010; Ross et al. 2011). (B) Chromosome centers also show more skew in the site frequency spectrum, indicative of an excess of rare alleles, which is expected to result from the interaction of selection and linkage. These qualitative patterns are consistent with analysis restricted to synonymous sites (Supplemental Fig. 10), indicating that differential constraint in noncoding regions does not drive the observed genomic patterns of polymorphism.
