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220px-Africa_satellite_orthographicJoe Pickrell‘s paper, Ancient west Eurasian ancestry in southern and eastern Africa, is finally out. Readers of this weblog will be aware of its broad outlines, as it is been circulated as a preprint. He’s graciously acknowledged the response on this weblog and Haldane’s Sieve as informative feedback in the final paper. Why? I think it’s “because intersectionality,” as they say. The topic that is being explored by statistical historical genetics is by its nature multidisciplinary, and biologists bringing powerful and abstruse techniques to the field need the input of those with “thick” area knowledge to truly open all the windows which can shed light upon a topic. Startling scientific insights become much richer, and inform our picture of the past, when integrated into the full body of previous historical scholarship.

After reading Peter Bellwood’s First Migrants, I am now tempted to coin a phrase: “Nothing in history makes sense except in light of demography.” This is obviously too strong a phraseology, but if the methods of modern statistical genetics are correct in the peculiar inferences they’re making, then we do need to rewrite the history books to a great extent. Or at least expand the purview of what we consider history, and how we understand what archaeology is telling us. For example, Africa is often represented in the public imagination as the ur-continent: unchanging, everlasting, primal. But the results we see from genetics, the relative similarity of populations from Nigeria to the South Africa’s Eastern Cape, and the minimal impact of the ancient hunter-gatherers on the ancestral variation of these people, attest to recent and revolutionary changes in the character of the population of the African continent, which belies its static perception. This recent paper, as well as Luca Pagani’s result on admixture within Ethiopia, implies that demography has wrought drastic change among the non-Bantu people of eastern and southern Africa, pushing them to the margins of history. To put it more starkly: when the pyramids of Egypt were being built the vast continent to the south would have been unrecognizable in terms of its human geography to a physical anthropologist.

9781405189095_p0_v1_s260x420 And this is not just a feature of Africa. In First Migrants the author recounts a personal communication from a scholar who has assembled unpublished data on the skeletal remains and ancient DNA from a community in northern Vietnam ~4,000 years ago. This seems to have have a frontier agricultural settlement, on the edge of rice culture. While the majority of individuals exhibited the body type and skull form of modern Asians, a minority manifested what the author terms “Austro-Melanesian” physical attributes. And critically, the ancient mtDNA haplogroups break down in the exact same ratios as the morphological remains, with a majority shared with modern Northeast Asians, but a minority of a type limited to Southeast Asia, and usually inferred to suggest common heritage with the peoples of Australasia and South Asia.

What the researcher above captured was a snapshot in time, freezing a moment which was transitory, as the ancient substrate of Southeast Asia was absorbed into the advancing wave of farmers. One could go on in this vein. We know so much more than we did in the past, and not to be hyperbolic, but some of what we know suspect resembles Conan the Barbarian more than the wildest imaginings of prehistorians of the past generation. But that’s one of the great things about scholarship: it can confound pedestrian expectations. And on occasion which captures the ineffable aspects of truth obscured should astound us.

Citation: doi:10.1073/pnas.1313787111


• Category: History, Science • Tags: Khoikhoi 
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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 space on the genetic history of Africa I was curious, but after reading it I have to say I can’t make much sense of the alphabet soup of haplogroups. Remember, there are different ways to capture and analyze the variation in one’s genes. A common activity is to sweep over the whole genome and focus on single nucleotide polymorphisms, variation at the base pair level. So my own analyses using ADMIXTURE focus on tens or hundreds of thousands of such markers. But there are other types of genomic variation, such as copy number, microsatellites, and minsatellites.

Additionally, much of the older human phylogeographic literature focused on mtDNA and Y chromosomal variance. For mtDNA it was partly a function of how easy it was to extract the genetic material (it’s copious on the cellular level). But perhaps more importantly these two types of variance aren’t subject to recombination. This means they are defined by clean phylogenetic trees which do not exhibit reticulation (recombination chops apart correlated markers and mixes & matches them) and presumably are not subject to natural selection, and so perfect for coalescent theory. So you can posit lineages related to each other by steps of sets of mutations, and also easily calculate the time until the last common ancestor for two different branches of the tree using a “molecular clock” model.

Here’s the abstract:

The study of Y chromosome variation has helped reconstruct demographic events associated with the spread of languages, agriculture and pastoralism in sub-Saharan Africa, but little attention has been given to the early history of the continent. In order to overcome this lack of knowledge, we carried out a phylogeographic analysis of haplogroups A and B in a broad dataset of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. The combined high resolution SNP analysis with STR variation of their sub-clades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional pre-agricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies, and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent. These results open new perspectives on the early history of Homo sapiens in Africa, with particular attention to areas of the continent where human fossil remains and archaeological data are scant.

The authors posit that the connections between southern African Bushmen and the Pygmies of central Africa which they find in the Y chromosomal lineages might have been mediated by the peregrinations of Khoikhoi pastoralists, who possibly diffused from a central-southern African ur-heimat in advance of the Bantu expansion. This seems plausible to me.

The main issue which I’m curious about in regards to all these results are the connections between Pygmies and Bushmen set against the Bantus. I certainly had no expected it, and it has been repeated several times. There is now a lot of weird evidence that demands a hypothesis.

Image credit: Wikipedia

(Republished from Discover/GNXP by permission of author or representative)
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"