Category Archives: African Genetics

Echoes from the last Green Sahara: whole genome analysis of Fulani, a key population to unveil the genetic evolutionary history of Africa: Background The Sahelian Fulani are the largest nomadic […]

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Two interesting papers in Genome Biology that are open access, Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations and African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Since they are open access […]

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PNAs has a new paper out, Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation. From what I can tell this was never a preprint, so it’s all new…. Or is it? Looking closely at some of the populations sampled, I’m about 85% sure that I saw a […]

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In a deep sense, we know a lot more about the population genetic history of England at the fine-grain than we do about the whole continent of Africa. That’s going to change in the near future, as researchers now realize that the history and emergence of modern humans within the continent was a more complex, […]

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Very readable review, Gene Discovery for Complex Traits: Lessons from Africa. It’s open access, so I recommend it. The summary: The genetics of African populations reveals an otherwise “missing layer” of human variation that arose between 100,000 and 5 million years ago. Both the vast number of these ancient variants and the selective pressures they […]

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Martin Meredith’s The Fortunes of Africa glosses very quickly over one of the major reasons that the “great scramble” for the continent occurred in the late 19th century, the discovery of the usefulness of quinine as an anti-malarial agent. Perhaps because I’ve read Plagues and Peoples and The Retreat of the Elephants: An Environmental History […]

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The major frontier in the understanding of human population genetic structure in the next five years is going to be Africa. There are several reasons for this. The ‘standard model’ of late has been that a group of humans left eastern Africa ~50,000 years ago, and swept across the world in one go. Though Africa […]

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I mentioned this in passing on my post on ASHG 2012, but it seems useful to make explicit. For the past few years there has been word of research pointing to connections between the Khoisan and the Cushitic people of Ethiopia. To a great extent in the paper which is forthcoming there is the likely […]

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There’s two papers in Nature Genetics on the 17q21.31, and variation of haplotypes of inversions in world wide populations. Here’s a part of the discussion from the first paper:
In conclusion, we propose that the ancestral H2′ haplotype a…

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After the second Henn et al. paper I did download the data. Unfortunately there are only 62,000 SNPs intersecting with the HGDP. This is somewhat marginal for fine-grained ADMIXTURE analyses, though sufficient for PCA from what I recall. That being said, the intersection with the HapMap data sets runs from ~190,000 SNPs, to the full […]

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Zinedine Zidane, a Kabyle There is a new paper in PLoS Genetics out which purports to characterize the ancestry of the populations of northern Africa in greater detail. This is important. The HGDP data set does have a North African population, the Mozabites, but it’s not ideal to represent hundreds of millions of people with […]

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In my post below, Tutsi probably differ genetically from the Hutu, there were many comments. Some I did not post because they were rude, though they did ask valid questions. I will address those issues, but let me quote one comment:
That’s an interes…

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A Cape Coloured family

I’ve mentioned the Cape Coloureds of South Africa on this weblog before. Culturally they’re Afrikaans in language and Dutch Reformed in religion (the possibly related Cape Malay group is Muslim, though also Afrikaan…

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Aka Pygmies
The Pith: There has been a long running argument whether Pygmies in Africa are short due to “nurture” or “nature.” It turns out that non-Pygmies with more Pygmy ancestry are shorter and Pygmies with more non-Pygmy …

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Over the past few days I’ve been trying to read a bit on the Sandawe. Most of the stuff I’ve been able to find is in the domain of linguistics, and is basically unintelligible to me in any substantive manner. The crux of the curiosity here …

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Khoikhoi on the move….

Dienekes mentioned today a new paper, Signatures of the pre-agricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages. Because of the recent comments in this s…

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The Pith: I review a recent paper which argues for a southern African origin of modern humanity. I argue that the statistical inference shouldn’t be trusted as the final word. This paper reinforces previously known facts, but does not add much th…

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In the open thread someone asked: “Any recent stuff on the genetics of Ethiopians.” That prompted me to look around, because I’m curious too. Poking around Wikipedia I couldn’t find anything recent. A lot of the studies are older uniparental lineage based works (NRY and mtDNA). Ethiopia is interesting because unlike almost all other Sub-Saharan […]

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Last year a paper came out in Science which made a rather large splash, The Genetic Structure and History of Africans and African Americans by Tishkoff et al. Since it’s more than a year old I recommend that those of you curious about the details of the paper and don’t have academic access go through […]

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Since we’ve been talking about Fst a fair amount, I thought it might be nice to put it in some concrete graphical perspective. First, to review Fst in the genetic context measures the proportion of genetic variation which can be attributed to between population differences. To give a “toy” example if you randomly divided the […]

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Razib Khan