Surveying European and West African Population Structure Using 2,300 Samples with Spatial Information. Y. Wang, K. Noto, J. B. Byrnes, R. E. Curtis, N. M. Myres, M. J. Barber, J. M. Granka, C. A. Ball, K. G. Chahine AncestryDNA, San Francisco, CA.
Population structure arises as a consequence of the interplay between geography, genetic drift, and gene flow. Knowledge of human population structure is fundamental to understanding how demographic history has shaped human genetic diversity. In this work, we investigated the genetic structure of European and West African populations using high-density SNP data. First, we analyzed ~2000 European individuals genotyped at 700,000 SNPs using principal component analysis (PCA), spatial ancestry analysis (SPA), and admixture-model-based method (ADMIXTURE). Despite an overall high level of genetic similarity, we observed significant patterns of genetic variation among European populations, ranging from the regional level (e.g., Northern European vs. Southern European and Eastern European vs. Western European) to the local level (e.g., Iberian vs. Italian and English vs. Irish). We then conducted similar analyses on ~330 individuals sampled from nine West African countries (Senegal, Mali, Ivory Coast, Ghana, Benin, Togo, Nigeria, Cameroon and Congo). Our results revealed strikingly significant structure at the country level, despite geographical proximity. Comparing the three approaches, we found that SPA has better power in predicting the population of single origin individuals, given an accurate reference panel of reasonable size. We further applied SPA to identify SNPs showing large gradients in allele frequency, which can be used to tag candidate regions under natural selection. In addition, we selected two sets of ancestry informative markers (AIMs) that carry substructure information for European and West African populations, respectively. Lastly, we investigated the pattern of genetic variation in African Americans using a large cohort (5,000) of African American individuals and the European and West African reference panels. Our results shed new light on the population and migration history of African Americans.
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