Human Population Differentiation Is Strongly Correlated with Local Recombination Rate
Figure 4
The relationship between population differentiation and recombination rate in the larger set of HapMap 3 populations.
We placed 1,326,404 autosomal HapMap 3 SNPs (release 2) [57] into 10 bins according to recombination rate and estimated for each bin (A) global population differentiation between all 11 populations, and (B–E) population differentiation between pairs of populations. To avoid clutter, (B–E) depict only the linear (dashed lines) and quadratic (solid lines) regression of FST estimates as a function of the median recombination rate in each bin and partition the populations-pairs as follows: (B) FST between an African and a non-African population, where a negative correlation is observed with recombination rate, and where the quadratic regression is convex, (C) FST between a population of European, East Asian, or South Asian ancestry and a second population of a different one of these three ancestries, which shows a concave quadratic regression for all pairs of populations, and which recapitulates the result observed between North Europeans and East Asians in the uniformly-ascertained datasets (Figure 1D and Figure 3D). (A weaker phenomenon is observed for the South Asian GIH sample, which may be due to this population being somewhat related to both Europeans and East Asians [70], thereby confounding the North European–East Asian signal), (D) FST between two African populations, which shows a much steeper linear regression compared to intercontinental FST, as well as a convex quadratic regression, and (E) FST between closely-related non-African populations (within either Europe or East Asia; genome-wide FST<0.008), showing a very steep linear regression and a convex quadratic regression. FST based on all SNPs in all bins combined is presented as a horizontal dotted line and is equal to 1 in panels B–E since these present normalized FST values obtained by dividing each value by the genome-wide FST for the same pair of populations. Population codes are as follows: WAF (“West African”) is a combined sample of YRI (Yoruba in Ibadan, Nigeria) and LWK (Luhya in Webuye, Kenya); EAS (“East Asia”) is a combined sample of CHB (Han Chinese in Beijing, China), CHD (Chinese in Metropolitan Denver, CO, USA), and JPT (Japanese in Tokyo, Japan); EUR (“Europe”) is a combined sample of CEU (ancestry from Northern and Western Europe) and TSI (Toscani in Italia); GIH is a sample of Gujarati Indians in Houston, TX, USA; MKK is a sample of Maasai in Kinyawa, Kenya; and CHI (Chinese) is a combined sample of CHB and CHD.