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

Qin P, Zhou Y, Lou H, Lu D, Yang X, Wang Y, Jin L, Chung YJ, Xu S - Sci Rep (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

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.

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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.
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f1: 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.

Mentions: We obtained genome-wide data of 34 Eurasian populations from 1000 Genomes Project (1 KG)13, the Human Genome Diversity Panel (HGDP)14 and other studies115. In total, 1,132 Eurasian samples with 186,506 SNPs integrated from different technical platforms were used for analysis (see Methods). To study the signal of gene flow between West and East Eurasian populations (European and Asian populations in Table 1), firstly we performed Principal Component Analysis (PCA)16 both with and without respectively African populations based on 96,538 random SNPs avoiding high linkage disequilibrium. We observed that some clusters of West and East Eurasians are slightly shifted towards each other, indicating potential admixture between them (Fig. 1). There is a clear ‘cline’ between West and East clusters. These shifts of PC patterns are especially obvious for most CSA, some northern EAS including Mongolian, Xibo, Hezhen, Oroqen etc., and eastern EUR including Russian, Finnish and Adygei. We then initiated formal testing for the presence of gene flow.


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

Qin P, Zhou Y, Lou H, Lu D, Yang X, Wang Y, Jin L, Chung YJ, Xu S - Sci Rep (2015)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4382708&req=5

f1: 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.
Mentions: We obtained genome-wide data of 34 Eurasian populations from 1000 Genomes Project (1 KG)13, the Human Genome Diversity Panel (HGDP)14 and other studies115. In total, 1,132 Eurasian samples with 186,506 SNPs integrated from different technical platforms were used for analysis (see Methods). To study the signal of gene flow between West and East Eurasian populations (European and Asian populations in Table 1), firstly we performed Principal Component Analysis (PCA)16 both with and without respectively African populations based on 96,538 random SNPs avoiding high linkage disequilibrium. We observed that some clusters of West and East Eurasians are slightly shifted towards each other, indicating potential admixture between them (Fig. 1). There is a clear ‘cline’ between West and East clusters. These shifts of PC patterns are especially obvious for most CSA, some northern EAS including Mongolian, Xibo, Hezhen, Oroqen etc., and eastern EUR including Russian, Finnish and Adygei. We then initiated formal testing for the presence of gene flow.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

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.

Show MeSH