Tag: African Genomics

Africa’s hidden people hold the keys to the past

By Razib Khan | December 2, 2012 12:42 am

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 answer to the question of who lived in East Africa before the Bantu, and before the most recent back-migration of West Eurasians. On one level I’m confused as to why this has to be something of a mystery, because the most recent genetic evidence suggests a admixture on the order of 2-3,000 years before the past.* If the admixture was so recent we should find many of the “first people,” no? As it is, we don’t. I think these groups, and perhaps the Sandawe, are the closest we’ll get.

Publication is imminent at this point (of this, I was assured), so I’m going to just state the likely candidate population (or at least one of them): the Sanye, who speak a Cushitic language with possible Khoisan influences. There really isn’t that much information on these people, which is why when I first heard about the preliminary results a few years back and looked around for Khoisan-like populations in Kenya I wasn’t sure I’d hit upon the right group. But at ASHG I saw some STRUCTURE plots with the correct populations, and the Sanye were one of them. I would have liked to see something like TreeMix, but the STRUCTURE results were of a quality that I could accept that these populations were not being well modeled by the variation which dominated their data set. Though Cushitic in language the Sanye had far less of the West Eurasian element present among other Cushitic speaking populations of the Horn of Africa. Neither were their African ancestral components quite like that of the Nilotic or Bantu populations. The clustering algorithm was having a “hard time” making sense of them (it seemed to wanted to model them as linear combinations of more familiar groups, but was doing a bad job of it).

Here is an interesting article on these groups: Little known tribe that census forgot. Like the Sandawe this is a population which seems to have been hunter-gatherers very recently, and to some extent still engage in this lifestyle. In this way I think they are fundamentally different from Indian tribal populations, who are often held up to be the “first people” of the subcontinent.  More and more it seems that the tribes of India are less the descendants of the original inhabitants of the subcontinent, at least when compared to the typical Indian peasant, and more simply those segments of the Indian population which were marginalized and pushed into less productive territory. Over time they naturally diverged culturally because of their isolation, but the difference was not primal. In contrast, groups like the Sanye and Sandawe may have mixed to a great extent with their neighbors (and lost their language like the Pygmies), but evidence of full featured hunting & gathering lifestyles implies a sort of direct cultural continuity with the landscape of eastern Africa before the arrival of farmers and pastoralists from the west and north.

* I understand some readers refuse to accept the likelihood of these results because of other lines of information. I am just relaying the results of the geneticists. I am not interested in re-litigating prior discussions on this. We’ll probably have a resolution soon enough.

The Fulani have an old "Berber" (?) element

By Razib Khan | January 16, 2012 10:26 am


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 250,000 SNPs (this makes sense since the Henn et al. #2 data set has some HapMap populations in it). So I’ve been experimenting a fair amount in the past few days, and I thought I would post on one issue which was clear in the original paper, but which I have replicated.

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Tutsi genetics, ii

By Razib Khan | August 31, 2011 12:21 am

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 interesting possibility, but this admixture run didn’t split the non-hunter-gatherer Africans that well. In one of your previous analyses on East Africa you managed to get a pretty accurate ‘Afro-Asiatic/Cushitic’ and ‘Nilotic’ cluster. Is it possible that you could run this Tutsi sample using the same admixture settings as in the ‘Flavors of Afro-Asiatic’ blog post to see if he carries a significant Nilotic component or is mainly Bantu & Cushitic derived?

So I replicated ADMIXTURE runs for many of the same populations as I did in my post, Flavors of Afro-Asiatic. I also pared down the population set and generated a PCA with EIGENSOFT. Before I get to those results, let me tackle the questions.

1) “Are the Luhya suitable proxies for the Hutus?”

Probably. The reason is that Bantu-speaking populations, from the Congo to South Africa, are surprisingly similar. Not only that, but these populations are very distinctive from groups which are close them geographically, but linguistically different (e.g., Khoe, Sandawe, Masai). The Luhya  are not exceptional. I’ve run the Henn et al. data sets enough to be convinced that they’re exactly as they should be. They are pretty much what you’d expect from Kenyan Bantu. A predominant element which ties them back to an East-Central African point of origin, with some admixture with other East African elements (similarly, South African Bantu exhibit Khoisan admixture). The Hutu may be peculiar, but we don’t know, and my null is that they’re mostly Bantu with some admixture, as is the case with most Bantu speaking populations (this one Tutsi seems to be an exception in that context, as they are presumably Bantu speaking). If you think that the the Luhya are not suitable, I invite you to download the HapMap Luhya, and merge them with some of the Henn et al. data sets (or HGDP or Behar data sets). I think that should convince you.

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The Sandawe: after the demographic flood

By Razib Khan | April 9, 2011 10:21 pm

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 is that the Sandawe, like their Hadza neighbors, have clicks in their language, and so have been classified with the Khoisan. Here’s some background:

The most promising candidate as a relative of Sandawe are the Khoe languages of Botswana and Namibia. Most of the putative cognates Greenberg (1976) gives as evidence for Sandawe being a Khoesan language in fact tie Sandawe to Khoe. Recently Gueldemann and Elderkin have strengthened that connection, with several dozen likely cognates, while casting doubts on other Khoisan connections. Although there are not enough similarities to reconstruct a Proto-Khoe-Sandawe language, there are enough to suggest that the connection is real.

I can’t speak to the validity of this at all, obviously. Some scholars do argue that the clicks in the Sandawe language were only acquired through interaction with peoples such as the Hadza, making an analogy to Xhosa, a Bantu language which has been strongly influenced by Khoi dialects. In any case, after having run ADMIXTURE a bunch of times on African population sets, and checked the genetic distances of the inferred ancestral ones, one thing that is clear is that the Sandawe don’t show a particularly close genetic relationship to the Bushmen, nor do they show a close relationship to the Hadza. In fact, the Hadza, Pygmies, and Bushmen show a closer relationship to each other, distant as it is, than to the Sandawe. The Sandawe themselves are distinctive from their Bantu neighbors, but, their connections seem more clear to the Masai and other peoples to the north.

Some of the anthropological stuff that I did find on the Sandawe not having to do with linguistics considered the issue of their status as hunter-gatherers, and their shift toward a form of agriculture within the past few centuries. Not surprisingly much of this literature consisted of ideologically shrill posturing, denouncing past scholarship for insensitivity and bigotry, while taking their own maximalist position. For example there has been the hypothesis that hunter-gatherer populations tend to be genetically and culturally isolated from agriculturalists, with several African groups used as exemplars. A group of anthropologists argue strenuously that this model may just be a construction of the biases of previous generations of scholars. But they offer little in the way of counterargument, more keen on uncovering the faults in the motives and methods of their predecessors than in building anything anew.

Genetics can help us a little here. Below are the results of ADMIXTURE and PCA I ran for a selection of populations. I pulled in some Behar et al. samples and merged it with the Henn et al. data set. The marker list was pruned down to ~160,000 SNPs. The limited selection of populations was conscious, insofar as I was exploring specific questions about the relationship of East African populations to Eurasian ones. At K = 8 the populations in my data set separated rather well. Do not take this separation as evidence that this K is a reflection of absolute concrete ancestral populations. Here’s the bar plot:

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CATEGORIZED UNDER: Genetics, Genomics, History

The men of Africa

By Razib Khan | April 6, 2011 4:09 pm


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:

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CATEGORIZED UNDER: Genetics, Genomics

Genetic variation within Africa (and the world)

By Razib Khan | August 22, 2010 1:16 pm

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 the free registration, as you can then read it in full. Unlike Reich et al. the Science paper didn’t unveil a new method of analysis. It was the standard bread & butter, with PCA’s & STRUCTURE plots & phylogenetic trees. But the coverage of populations within Africa was massive. They had a lot of results and relationships to cover, and ended up with a 100 page supplement.

I commend the whole paper to you. But there are two elements I want to highlight. First, a three dimensional PCA plot. It has the first, second and third principal components of variation. In other words, the three largest independent dimensions in terms of explanatory power of genetic variation. Panel A includes all world populations, and panel B just Africans.

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CATEGORIZED UNDER: Genetics, Genomics
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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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