  Southern and eastern African populations that speak non-Bantu languages with
click consonants are known to harbour some of the most ancient genetic lineages
in humans, but their relationships are poorly understood. Here, we report data
from 23 populations analyzed at over half a million single nucleotide
polymorphisms, using a genome-wide array designed for studying human history.
The southern African Khoisan fall into two genetic groups, loosely
corresponding to the northwestern and southeastern Kalahari, which we show
separated within the last 30,000 years. We find that all individuals derive at
least a few percent of their genomes from admixture with non-Khoisan
populations that began approximately 1,200 years ago. In addition, the east
African Hadza and Sandawe derive a fraction of their ancestry from admixture
with a population related to the Khoisan, supporting the hypothesis of an
ancient link between southern and eastern Africa
