September 8, 2016

Genetic structure in South-Eastern Africa


Another quite interesting paper on Khoesan and Southern African genetics:

Caitlin Uren et al., Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries. Genetics 2016. Freely accessibleLINK [doi:10.1534/genetics.116.187369]


Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.
Figure 2
Five spatially distinct ancestries indicate deep population structure in southern Africa. Using global ancestry proportions inferred from ADMIXTURE k = 10, we plot the mean ancestry for each population in southern Africa. The five most common ancestries in southern Africa, from the Affymetrix HumanOrigins data set, are shown separately in A–E. The x- and y-axes for each map correspond to latitude and longitude, respectively. Black dots represent the sampling location of populations in southern Africa. The third dimension in each map (depth of color) represents the mean ancestry proportion for each group for a given k ancestry, calculated from ADMIXTURE using unrelated individuals, and indicated in the color keys as 0–100% for five specific k ancestries. Surface plots of the ancestry proportions were interpolated across the African continent.

See also:


  1. I doubt khoesan were genetically isolated till 2,000 years ago. That sounds impossible to me.

    1. Depends on what degree of "isolation" you are thinking of. There's some evidence for minor genetic input from East Africa (or maybe is it the Zambia-Katanga-Malawi area, which has some unique mtDNA markers?) prior to Bantu arrival and related to the arrival of pastoralism but otherwise they were pretty much isolated AFAIK.

    2. Please consider that there is a clear jungle belt that separates Southern Africa from the rest, more dynamic and connected, parts of the continent, only less dense in some of the eastern parts (Zambia-Malawi-Mozambique, see map).

      The Bantu expansion (from approx. today's central Cameroon) may have began (per archaeology) as early as 1000 BCE but could not gain momentum until steel tools were common c. 400 BCE. AFAIK it's probable that in the Southern Great Lakes area there was a second center that incorporated local genetics like mtDNA L0k. I'm still awaiting for improved autosomal data on Mozambicans, which in one study appeared quite different from other Bantus and seemingly related to the Twa "Pygmies" of Rwanda and Burundi. It seems that Bantus arrived to the eastern parts of South Africa only as late as c. 300-500 BCE.

  2. This comment has been removed by a blog administrator.

  3. This comment has been removed by a blog administrator.

  4. This comment has been removed by a blog administrator.

    1. I read your attempted comments in my other blog and determined that you are just too Nazi for me to tolerate. Therefore your comments in this blog will also be deleted, Jace. You're banned forever, no appeals.


Please, be reasonably respectful when making comments. I do not tolerate in particular sexism, racism nor homophobia. Personal attacks, manipulation and trolling are also very much unwelcome here.The author reserves the right to delete any abusive comment.

Preliminary comment moderation is... ON (your comment may take some time, maybe days or weeks to appear).