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SNPs across the Sub-Sahara

Lauren Ware

A new study of human genetic variation across sub-Saharan populations complicates the history of African populations and the origins of modern man.  

The most comprehensive study of genome-wide single nucleotide polymorphisms (SNPs) across sub-Saharan Africa populations to date has yielded insights into the rich, complex history of Africans, as well as the origins of modern humans.

San rock art from a cave in the Soutpansberg mountain range in the Limpopo province, South Africa. Source: Carina Schlebusch

As reported in the September 21 issue of Science (1), an international research team analyzed the DNA from 220 individuals from 11 different populations in southern Africa. They looked at more than 2 million SNPs, places in the genome where just one nucleotide is changed. According to lead study author Mattias Jakobsson, an assistant professor of evolutionary biology at Uppsala University in Uppsala, Sweden, the most striking result may be the deep population structure that the group discovered.

This larger data set confirmed previous studies that described a split about 100,000 years ago between click-speaking Khoe-San individuals and all African as well as non-African groups. Later, a second split occurred between two Khoe-San groups. “The northern Khoe-San group split from the southern group about 35,000 years ago,” said Carina Schlebusch, lead study author and a postdoc at Uppsala University.

One of the group’s goals was to more precisely pinpoint the origin of modern humans. Archeological records suggest that modern humans emerged from East Africa, but recent genetic studies have suggested that Southern Africa origins are more likely. In the end, the team couldn’t determine the actual place of origin. “Using our data and a number of different summary statistics, we don’t find a coherent picture,” said Jakobsson. However, their data did led them to postulate that modern humans possibly arose from a non-homogeneous group, one to which multiple, different groups of humans contributed genes.

To trace the origins of modern man, the team specifically focused their analysis on gene variants that are shared among all humans living today. “Those regions should pinpoint genes that have been modified or changed prior to the deepest split among modern humans 100,000 years ago. We think those genes are the ones that were coupled with the emergence of anatomically modern humans,” said Jakobsson. For example, looking at those specific genes, the scientists found three that are involved in skeletal development.

In addition, the analysis revealed the rich, ethnic diversity within the Khoe-San people. Besides the split between northern and southern groups, the team found that genes involved in muscle function, immune response, and UV-light protection were likely selected within local groups.

Himla Soodyall, a geneticist with the University of Witwatersrand in Johannesburg, South Africa, and a study coauthor, has been working with the Khoe-San people for many years. “I think this collaboration has brought home the message that yes, indeed, a lot has come out of Africa. I hope that we could say that Southern Africa has contributed remarkably to the history of the peoples of the world,” she said.


1. Schlebusch, C.M., P. Skoglund, P. Sjödin, L.M. Gattepaille, D. Hernandez, F. Jay, S. Li, M.D. Jongh, A. Singleton, M.G.B. Blum, et al. “Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science. [Published online September 20, 2012]