The genetic structure and history of Africans and African Americans

Abstract

Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, four African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties. We observed high levels of mixed ancestry in most populations, reflecting historical migration events across the continent. Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan speakers and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (approximately 71%), European (approximately 13%), and other African (approximately 8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies.

Figure 1

Neighbor-joining tree from pairwise D² genetic distances between populations (65). African population branches are color-coded according to language family classification. Population clusters by major geographic region are noted; bootstrap values above 700 out of 1000 are indicated by thicker lines and bootstrap number.

Figure 2

Principal components analysis (22) created on the basis of individual genotypes. (A) Global data set and (B) African data set.

Figure 3

STRUCTURE analysis of the global data set with 1327 markers genotyped in 3945 individuals. Each vertical line represents an individual. Individuals were grouped by self-identified ethnic group (at bottom) and ethnic groups are clustered by major geographic region (at top). Colors represent the inferred ancestry from K ancestral populations. STRUCTURE results for K = 2 to 14 (left) are shown with the number of similar runs (F) for the primary mode of 25 STRUCTURE runs at each K value (right).

Figure 4

Expanded view of STRUCTURE results at K = 14. Populations from the CEPH diversity panel are identified by asterisks. Languages spoken by populations are classified as Niger-Kordofanian (NK), Nilo-Saharan (NS), Afroasiatic (AA), Khoesan (KS), or Indo-European (IE).

Figure 5

Geographic and genetic structure of populations within Africa. (A) Geographic discontinuities among African populations using TESS, assuming a model of no population admixture (25). Circles indicate location of populations included in the study. (B) Inferred proportions of ancestral clusters from STRUCTURE analysis at K = 14 for individuals grouped by geographic region and language classification. Classifications of languages spoken by self-identified ethnic affiliation in the Africans are as in Fig. 1. (C) Inferred proportion of ancestral clusters in individuals from STRUCTURE analysis at K = 14.

Figure 6

Analyses of Cape Mixed Ancestry (CMA) and African American populations. Frequencies of inferred ancestral clusters are shown for K = 14 with the global data set for individuals (top row) and proportion of AACs in self-identified populations (bottom row). The proportions of AACs in the CMA and African American populations are highlighted in the center bottom row; proportions of AACs in individuals, sorted by Niger-Kordofanian, European, SAK, and/or Indian ancestry, are shown to the left and right, bottom row.