  The history of southern Africa involved interactions between indigenous
hunter-gatherers and a range of populations that moved into the region. Here we
use genome-wide genetic data to show that there are at least two admixture
events in the history of Khoisan populations (southern African hunter-gatherers
and pastoralists who speak non-Bantu languages with click consonants). One
involved populations related to Niger-Congo-speaking African populations, and
the other introduced ancestry most closely related to west Eurasian (European
or Middle Eastern) populations. We date this latter admixture event to
approximately 900-1,800 years ago, and show that it had the largest demographic
impact in Khoisan populations that speak Khoe-Kwadi languages. A similar signal
of west Eurasian ancestry is present throughout eastern Africa. In particular,
we also find evidence for two admixture events in the history of Kenyan,
Tanzanian, and Ethiopian populations, the earlier of which involved populations
related to west Eurasians and which we date to approximately 2,700 - 3,300
years ago. We reconstruct the allele frequencies of the putative west Eurasian
population in eastern Africa, and show that this population is a good proxy for
the west Eurasian ancestry in southern Africa. The most parsimonious
explanation for these findings is that west Eurasian ancestry entered southern
Africa indirectly through eastern Africa.
