Complex Genetic History of East African Human Populations

Abstract

Results from disparate fields indicate that anatomically modern Homo sapiens originated in Africa ~200 thousand years ago (kya), and that East Africa is the likely source of the migration of modern humans out of Africa within the past 100 thousand years. However, the genetic diversity currently found in Africa, and especially East Africa, has not been well studied compared to non-African populations, due in large part to the fact that DNA samples from many remote regions of Africa are currently not available. The goal of this study was, therefore, to characterize genetic variation in previously unstudied East African human populations using mitochondrial and Y chromosome DNA from 1500 individuals. These data were then compared to independently collected data of the same populations from ~1327 nuclear markers (848 microsatellites and 479 insertion/deletion polymorphisms). The data were used to gain insight into patterns of genetic diversity, to construct past relationships of East African populations to each other and to other African populations, to clarify historical demographic events such as population expansion, contraction, and migration that these populations might have experienced. Several independent analyses showed significant relationships between genetic and geographic/linguistic distances among East African populations. Genetic variation is more strongly correlated with geography than is linguistics. Overall, the correlations between genetic versus geographic/ linguistic variation is stronger for autosomal and Y chromosome than for mtDNA lineages. Y chromosome and mtDNA lineage distributions seem to cluster geographically and for some lineages, linguistically. Two major migration events, namely the migration of Bantu-speaking populations from Central/West Africa across sub-Saharan Africa and the migration of pastoralist populations from Sudan and Ethiopia within the past 5000 years have had a major influence on extant genetic patterns in East Africa.