Figure 3
Positive selection signatures for variants that correlate with Δphotoperiod. (A) DIND test results: the dashed line represents the 95th percentile of a distribution of 20,000 randomly selected HGDP-CEPH single nucleotide polymorphisms (SNPs). The gray shaded areas indicate frequency ranges where the ratio could not be calculated (see Methods). SNPs above the 95th percentile are shown as black circles (open: top variants from the five gene sets; solid: disease-associated SNPs). (B) Schematic representation of CEPH haplotypes in the region surrounding rs752579 (in RAI1), selected as an example. Each line represents a haplotype, columns indicate polymorphic positions. Dark gray, derived alleles; light gray, ancestral alleles. (C) Extended haplotype homozygosity decay plot for rs752579. (D) Correlation between Δphotoperiod and allele frequency for rs752579. Populations from different broad geographic areas are coded by different colors. CEPH, 1000 Genomes Phase I data for Utah Residents with Northern and Western European ancestry; CHB + JPT, 1000 Genomes Phase I data for Han Chinese in Beijing plus Japanese in Tokyo; DIND, Derived Intra-allelic Nucleotide Diversity; EHHS, extended haplotype homozygosity of an individual SNP site.