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 (~71%), European (~13%),
and other African (~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.
