The genetic prehistory of southern Africa

TL;DR

This study analyzes the genetic history of southern African populations, revealing ancient lineages, recent admixture events, and links between southern and eastern African groups through genome-wide data.

Contribution

It provides detailed genomic insights into the structure, divergence, and admixture of southern African populations, especially Khoisan groups, using extensive SNP data.

Findings

Khoisan populations split within the last 30,000 years

All individuals show at least 1-2% admixture from non-Khoisan groups

East African Hadza and Sandawe have genetic links to southern Khoisan

Abstract

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