Quantitating and dating recent gene flow between European and East Asian populations

Abstract

Historical records indicate that extensive cultural, commercial and technological interaction occurred between European and Asian populations. What have been the biological consequences of these contacts in terms of gene flow? We systematically estimated gene flow between Eurasian groups using genome-wide polymorphisms from 34 populations representing Europeans, East Asians, and Central/South Asians. We identified recent gene flow between Europeans and Asians in most populations we studied, including East Asians and Northwestern Europeans, which are normally considered to be non-admixed populations. In addition we quantitatively estimated the extent of this gene flow using two statistical approaches, and dated admixture events based on admixture linkage disequilibrium. Our results indicate that most genetic admixtures occurred between 2,400 and 310 years ago and show the admixture proportions to be highly correlated with geographic locations, with the highest admixture proportions observed in Central Asia and the lowest in East Asia and Northwestern Europe. Interestingly, we observed a North-to-South decline of European gene flow in East Asians, suggesting a northern path of European gene flow diffusing into East Asian populations. Our findings contribute to an improved understanding of the history of human migration and the evolutionary mechanisms that have shaped the genetic structure of populations in Eurasia.

Figure 1. PC plots indicate potential gene flow between EUR and EAS.

(a) PC plot of 1,219 samples from 35 populations that were clustered into EAS, EUR, CSA, and African. (b) Fine resolution of the PC plot after removing YRI. Both plots were based on 96,538 pruned SNPs to reduce linkage disequilibrium relationships.

Figure 2. Determining surrogates of ancestral populations.

f₄(YRI, EUR; EAS_i, EAS_j) and f₄(YRI, EAS; EUR_i, EUR_j) were used to identify least-admixed populations as ancestral surrogates of (a) EAS and (b) EUR, respectively. Positive values in (a) indicate there is less EUR ancestry in EAS_i than in EAS_j, and positive values in (b) indicate there is less EAS ancestry in EUR_i than in EUR_j.

Figure 3. Correlation of gene flow and geographical locations of populations.

(a) West-to-East descent of EUR ancestry in 33 populations (except for Makrani who significantly admixed with Africans) (r² = 0.74). (b) North-to-South descent of EUR ancestry in 17 populations of EAS (r² = 0.71).