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study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

Fig. 1.

Population structure within West Africa and relation to language and geography. (A) FRAPPE analysis of the West African populations. Individuals are represented as thin vertical lines partitioned into segments corresponding to the inferred membership in K = 2 through K = 5 genetic clusters as indicated by the colors (see Figs. S2–S5 for additional results). (B) Principal components 1 and 2 of the African individuals. (C) Principal components 1 and 2 of the African individuals, excluding the Fulani population, wherein the components have been rotated to emphasize further similarity with geography. (D) Approximate locations of sampled populations in Africa. (E and F) FRAPPE clustering of Europeans, African Americans, and West Africans. Individuals are represented as thin vertical lines partitioned into K segments corresponding to the inferred membership of the genetic clusters indicated by the colors. Values for K = 2 (E) and K = 4 (F) are shown for comparison between the two analyses.

Fig. 2.

Results of our PCA-based ancestry estimation method. (A) Graphical illustration of approach: Euclidean distances from a given individual's coordinates in PCA space (i.e., “loadings”) and the West African centroid (“a”) and the European centroid (“b”) along PC1 for PCA space that includes Europeans, African Americans, and West Africans. (B) Local ancestry estimation using the PCA sliding window approach and associated HMM for number of chromosomes for a given individual (i.e., “0,” “1,” or “2”) with African ancestry. (C–F) Individual ancestry estimates of 4 representative African-American individuals (denoted 1, 2, 3, and 4 in Fig. 2A) in our dataset of 365 individuals. The colors represent two chromosomes of West African ancestry (blue), two chromosomes of European ancestry (red), or one chromosome of West African and one chromosome of European ancestry (green). (G) Mean ancestry of 365 African-American individuals at each window across chromosome (chrom) 1, chrom 11, chrom 12, and chromosome X (X Chr). The black line shows the overall mean estimated ancestry. Red bands indicate +3 and −3 SDs from the mean ancestry. (All chromosomes are reported in Fig. S10).