Genome-wide patterns of population structure and admixture in West Africans and African Americans

Abstract

Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans ( n = 365) and individuals with ancestry from West Africa ( n = 203 from 12 populations) and Europe ( n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th–75th percentiles: 11.6–27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

The Genetic Diversity of the Americas

“…These findings are consistent with historical information suggesting that approximately 68% and 32% of African slaves introduced to Brazil originated in westcentral/southeast and West Africa, respectively (84). Subsequent mtDNA and highdensity genotype analyses have confirmed and extended these results, highlighting areas of non-Bantu speakers in northwest and west-central Africa as major sources for the slaves brought to the Americas, with relatively smaller contributions from other regions, such as east African (Bantu-speaking) areas (18,48,57,63,98). Some regional variation has been reported for the relative importance of specific African source regions in the Americas; for instance, the non-Bantu component is more frequent in southern than northern Brazil, in agreement with historical information on the predominant origin of slaves introduced to different parts of this country (48).…”

Genome-wide patterns of population structure and admixture among Hispanic/Latino populations

“…1). We also used the PCA-based methods of Bryc et al (30) to infer ancestry at each locus for the samples genotyped on the Affymetrix 500K, which included more than 100 Mexican samples genotyped by the POPRES project (23) and diverse Native American populations genotyped by Mao et al (26). The local admixture tracks for each individual are in large agreement with the genome-wide average ancestry proportions (Fig.…”

“…A total of 552,025 SNPs were included in the analysis, and configuration parameters were set as follows: mixture proportions (alpha) = 0.2, 0.4, 0.4; number of generations since admixture (g) = 20; recombination rate (r) = 1e-8; fraction of overlap between adjacent windows (offset) = 0.2; and r2 threshold (ldcutoff) = 0.1. Local ancestry estimation for the Mexican individuals was performed using the two-way PCA-based method described in Bryc et al (30) for both the full Illumina 610K and the Affymetrix 500K datasets, in 10 SNP windows. Only Native Americans with <0.01 European ancestry (as estimated from FRAPPE results) were used as the ancestral Native American individuals within their respective datasets.…”

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

“…To refine our assignment within Africa, we compared our samples to another reference panel, consisting of genotype data from 11 West African populations ( Fig. 1B) (17). We intersected 294,651 sites from this reference panel with our sequence data (SI Appendix, Section 14) and conducted PCA to determine whether the individuals showed close affinity to a particular population within the panel.…”