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Lesley-Ann Brandt

One of the reasons that the HGDP populations are weighted toward indigenous groups is that there was the understanding that these populations may not be long for the world in their current form. But the Taino genome reconstruction illustrates that even if populations are no longer with us…they are still within us. With that in mind I decided to do some quick “back-of-the-envelope” calculations in relation to the Khoisan people of southern Africa. These are the descendants of the populations which were presumably there before the Bantu, and the basal relationship of the Bushmen to other human lineages is probably a partial testament to their long term residence in this region of Africa.

There are about 300,000 speakers of Khoisan languages left (mostly in South Africa and Namibia). These individuals are not all unmixed in their ancestry. If you look at some of the public genotypes available you can find Bantu African and European ancestry in Bushmen (the European may have come from Griqua). There are about 4 million Cape Coloureds and 8 million Xhosa. Both of these groups have some Khoisan ancestry. Let’s assume that the Cape Coloured are 20% Khoisan, and the Xhosa are 10% Khoisan. This is probably a moderately conservative, but I think it’s close from what I’ve seen. Multiplying that out you get 1.6 million Khoisan represented by the Cape Coloured and the Xhosa. That’s a ratio of over 5:1 in terms of the ancestral components attributed to Khoisan in modern populations being in those groups which don’t identify as Khoisan. This is probably a major underestimate, as other Bantu populations besides the Xhosa likely have some Khoisan ancestry, though less.

This came to mind because I recently watched Spartacus: Blood and Sand with some friends (or at least the first season). We were curious about the background of one of the characters, Lesley-Ann Brandt. From her blog you can find out this about her ethnic background:

You’re probably still asking what makes a “Coloured”, “Coloured”. Well like the name suggests, it is someone of many colours. My heritage consists of German, ( my last name), Indian, British and Spanish. My mother has the Indian, but is very fair and could be mistaken for white if you’ve never met her or you’re not from South Africa.

Her father however was a very dark man with Indian heritage. Her mother had an olive complexion. My father on the other hand has mostly European heritage, (a white German grandfather on his fathers side and a white British Grandfather and Spanish grandmother on his mothers side), but looks much darker than me. On my dad’s side, my grandfather had really dark olive colouring with green eyes and my grandmother was often mistaken as white during Apartheid. She would often sneak into white only grocery stores to buy food because no one really questioned her.

With all due respect to Ms. Brandt, just looking at her face and knowing that she’s Cape Coloured, her Khoisan ancestry seems rather clear to me in her features. From what I have read there’s some stigma associated with this int the Coloured community, or was, so perhaps that is why she seems to be ignorant of it, and attributes her visible non-white features to her Indian ancestry. Her father’s ancestry in particular doesn’t make sense in light of the phenotype she’s attributing to him.

But none of this really matters now. Genotyping would, and will, clear all of these issues up. Well, at least the scientific ones.

Image credits: Ian Beatty and Lesley-Ann Brandt.

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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

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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 population of a large Swedish village into two groups, and calculated their Fst, it should be ~ 0, because if you randomly select from an unstructured population by definition there shouldn’t be noticeable between population differences. In contrast, if you compare a Swedish village to a Japanese village, a large fraction of the genetic variation is going to be distinct to each population. Around ~10% of the genetic variation in fact will be between the two groups. Many of the genes will be extremely informative, so that if you know the allelic state from a given individual you can predict with a high degree of certitude which population that individual was from (e.g., SLC24A5 and EDAR). A small set of ancestrally informative alleles would produce a sequence of conditional probabilities of extremely high certitude (on the order of 10 genes for these two populations should suffice, perhaps three for “government work”).

But to put this in perspective, and show how genetic variation differs from locale to locale, I though I would compare continental-scale Fst values with that in a small region, southern Africa. The Fst values for the first I obtained from Investigation of the fine structure of European populations with applications to disease association studies, and the second, Complete Khoisan and Bantu genomes from southern Africa. The Bantu in this case is Desmond Tutu, who is from the Xhosa tribe, and has substantial admixture from the non-Bantu populations which were resident in South Africa prior to the arrival of the Bantus.

First, in tabular format:

Spain Sweden Russia Japan
France 0.0008 0.0023 0.0037 0.1116
Spain 0.0047 0.0059 0.1118
Sweden 0.0025 0.1095
Russia 0.1057
KB1 NB1 TK1 MD8 Desmond Tutu
KB1 0.021 0.024 0.022 0.08
NB1 -0.007 0.006 0.091
TK1 0.016 0.088
MD8 0.061

Second, two adjacent bar graphs. In the foreground I’ve simply take the Spain vs. other Eurasian population comparisons, while in the background Desmond Tutu is the reference for the four Bushmen.


In some ways this comparison is an exaggeration of the variation in African genes. The Bushmen and Bantu populations are of very distinct origins, as the latter spread over eastern and southern Africa only in the last 2,000 years. The Bushmen-Bantu cultural gap is one of sharp discontinuity, and despite gene flow it is still to some extent a genetic one as well. But there are other factors dampening Fst in this case. First, Tutu is himself of partial Khoisan ancestry (of whom there are other groups besides the Bushmen), so his genetic distance is likely to be smaller than someone from the Zulu tribe, which has presumably had less admixture with the indigenous populations, being a bit farther from the edge of the demographic “wave of advance.” Second, the gene chips are geared toward Eurasian populations, and presumably missed African, and particularly Bushmen, specific variants because they didn’t go looking.

My own confusion on these issues the past week illustrates I suppose the difficulty in mapping these abstruse and yet materially concrete patterns onto human categories. But quite often wrestling with the difficulties in the surest path to illumination.

• Category: Science • Tags: African Genetics, Bushmen, Fst, Genetics, Genomics 
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"