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Genetics Reveal Shared History of Southern and Eastern African Ethnic Groups

New genetic study reveals that populations in southern Africa that speak non-Bantu languages characterized by click consonants fall into two major groups. HU-scientist Tom Güldemann co-authored publication in Nature Communications.

Scientists have long debated whether populations in eastern and southern Africa that speak non-Bantu languages with click consonants descend from a common ancestor. The most comprehensive survey of genetic diversity in these populations to date provides strong evidence for a genetic link between eastern and southern Africa. The research also documents genetic differentiation between forager populations living in the northwestern and southeastern Kalahari that began up to 30,000 years ago. Furthermore, there is a genetic signature of population mixture between these indigenous populations and migrants from the north beginning 1,200 years ago.

Scientists have found a deep genetic link between populations in eastern and southern Africa that speak non-Bantu languages characterized by click consonants. These populations—which are known to carry the most ancient lineages present in humans today—were largely hunter-gatherers until recently when some of them began practicing agriculture.

By studying DNA variation, the international team found that the Khoisan populations in southern Africa comprise two major genetic groups, and that both of these groups share a genetic link to populations in eastern Africa. The paper is being published in Nature Communications.

“For years the hunter-gatherer populations of southern Africa have been treated as genetically equivalent,” said Brigitte Pakendorf, senior scientist at the CNRS lab Dynamique du Langage in Lyon, who coordinated the study. “But our work indicates that these populations each have their own complex history.”

“It is very interesting that the increasing linguistic evidence that  Khoisan is not a family of related languages, but a group that emerged largely due to contact processes, appears corroborated by the genetic data,” adds Tom Güldemann, co-author and professor at the Institute for Asian and African Studies at Humboldt University, Berlin.

In the most comprehensive survey of genetic diversity in southern Africa to date, the team obtained data from 21 southern African and two eastern African groups, studying more than 500,000 specific DNA variants to examine patterns of genetic similarities and differences between the population groups.

The first set of results concern the southern African Khoisan. The study shows that the two major genetic groups of Khoisan, who live in different parts of the Kalahari semi-desert in southern Africa, diverged within the last 30,000 years. However, the analysis also shows that since that time, the Khoisan have mixed with other African populations who had migrated to southern Africa beginning about 1,200 years ago.

 “All the Khoisan have varying amounts of mixture,” said Joseph Pickrell, a research fellow at Harvard Medical School who is the lead author of the study. “Some have only small amounts and have been largely isolated, while others have mixed extensively.”

 “This study was only made possible by a confluence of unique resources, including a comprehensive sample collection and new statistical and genetic tools, which have allowed us to peel back the recent history of mixture to learn about the relationships among Khoisan populations that existed thousands of years ago,” said co-author Mark Stoneking, professor at the Max Planck Institute for Evolutionary Anthropology.

According to David Reich, a professor of genetics at Harvard Medical School and another co-author, “The deep link we find between southern and eastern African hunter gatherers is exciting. Our results suggest that prior to migrations from the north, such populations may have been spread continuously over a huge geographic range including Tanzania and southern Africa.”


-Joe Pickrell and David Reich, Harvard Medical School and the Broad Institute of Harvard and MIT and

-Brigitte Pakendorf, Laboratoire Dynamique du Langage, UMR5596, CNRS & Université Lyon Lumière 2

-Mark Stoneking, Max Planck Institute for Evolutionary Anthropology,

-Tom Güldemann, Institute of Asian and African Studies, Humboldt University, Berlin & Max Planck Institute for Evolutionary Anthropology

Original publication:

Joseph K. Pickrell, Nick Patterson, Chiara Barbieri, Falko Berthold, Linda Gerlach, Tom Güldemann, Blesswell Kure, Sununguko Wata Mpoloka, Hirosi Nakagawa, Christfried Naumann, Mark Lipson, Po-Ru Loh, Joseph Lachance, Joanna Mountain, Carlos Bustamante, Bonnie Berger, Sarah Tishkoff, Brenna Henn, Mark Stoneking, David Reich, Brigitte Pakendorf
The genetic prehistory of southern Africa
Nature Communications, October 2012



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