Figure 3.
A genome-wide scan for positive selection in the Jomon
Top: Transformed PBS represents rankings of windows (size: 80 SNPs; step between windows: 10 SNPs) by their PBS values. The dashed horizontal lines show the 99.9th (magenta) and 99.99th (purple) percentiles of the empirical distribution. Middle: Heterozygosity of Jomon (red), Han Chinese in Beijing (CHB; blue), and Utah Residents with Northern and Western European ancestry (CEU; orange) in the regions on chromosomes 2, 7, and 12. The protein-coding genes present in each region are shown by solid lines with magenta. The dashed lines mark the locations of focal SNPs in each region. Bottom: Frequencies of focal alleles in ancient populations and modern-day references. The bar plots represent the frequencies of ancestral (blue) and derived (orange) alleles for SNPs of the region on chromosomes 2, 7, and 12, respectively. The frequencies of other SNPs (rs150038188 and rs77567846 on chromosome 7; rs11495049 on chromosome 7) are shown in Figure S16.