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Khoisan

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Adapted from Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

It is common for strong results from population genetics to be confused when it is translated for public consumption. The best example is that of “mtDNA Eve.” Despite the big warning label that mtDNA Eve is one of many female ancestors, the public has gained the impression that she is the female ancestor. A similar problem is cropping up with the Khoisan paper which reports that they went through a relatively mild bottleneck in comparison to other modern human populations. There’s a reason I titled the post The Least Bottlenecked Humans of All. It’s a defensible reduction of the results. In contrast many popular treatments are translating the results into the conclusion that “the Khoisan had the largest population of all human groups at some point in the past.” The reason I avoided this formulation is that plainly stated I doubt that at any time the Khoisan as we understand them, a genetically-culturally coherent group in southern Africa, had the largest population of all. Humans of various sorts have been common across Afro-Eurasia for over a million years. Is it plausible that ancestors of the Khoisan had the largest populations of all? Anne Gibbon’s somewhat cautiously stated piece in Science, Dwindling African tribe may have been most populous group on planet, relays the sentiment which I share:

Other researchers agree that it’s likely that the Khoisan descend from a large population. But because sampling of African genomes is still so spotty, not everyone is yet convinced that the Khoisan “was the largest population on Earth at some point,” says evolutionary geneticist Pontus Skoglund of Harvard University. “Many African populations are not included for comparison,” he says, so it is possible that some of the diversity seen in the Khoisan was inherited from recent interbreeding that cannot yet be detected.

Either way, the study makes it clear that even though the Khoisan are genetically diverse by today’s standards, even they carry just a fraction of our ancestors’ genetic legacy over the past 120,000 years. “It is quite staggering how much extraordinary genetic variation and ethnic diversity was present but is now lost,” Skoglund says. The Khoisan, retaining more than the rest of us, offer a rare window to look back in time at some of that diversity.

The biggest gap in the current study is that many extinct lineages were not included. Obviously they couldn’t be included, because they’re extinct, though at some point in the future ancient DNA or (more likely in the African context) reconstruction of ancient genomes from extant populations which have absorbed them, might allow for a better understanding of Pleistocene human population sizes. Population genomics is powerful, but it has limits. We need to be cautious about assuming that what we can illuminate with current methods is all that can be conceived in our natural philosophy.

 
• Category: Science • Tags: Genetics, Khoisan, Population genomics 
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The inimitable Joe Pickrell has dropped his Khoisan-are-part-Italian preprint onto arXiv, Ancient west Eurasian ancestry in southern and eastern Africa. I’m being glib in my characterization of the paper’s core conclusion, but there’s a reason for such a flip response: the inferences that he seems to draw from the genetic data strike me as verging on crazy. But that’s OK, what genetics is telling us is that history was a whole lot crazier than we had imagined.

Let’s back up for a moment here. For several decades now geneticists have assumed that the Bushmen of the Kalahari, the Khoisan-qua-Khoisan, Africa’s last hunter-gatherers who retain their ancestral language along with the Hadza, are the ur-humans. The basal lineage that first diverged from the rest of mankind at the cusp of the Out of Africa event. This is evident in Y chromosomal and mtDNA phylogenies, where the Bushmen and their kin harbor variants which coalesce deeply in time with those of others. And, a few years ago another group revealed the likelihood that Bushmen also are products of an admixture event in the last ~50,000 years with a distinct hominin lineage which diverged ~1 million years before the present from the main line which led up to anatomically modern humanity. Now Pickrell et al. present us with a twist which is perhaps even more astringent than a lime: in their genomes the Bushmen and their Khoisan kin, the Khoe herders, reflect an ancient admixture event with East Africans, who themselves were the outcomes of hybridizations between West Eurasians and indigenous African populations. More relevantly for my concise summation of the conclusion, the West Eurasian component does not necessarily reflect modern Middle Eastern populations, so much as Southern Europeans!

How did they infer such bizarre results? Magic? No. Basically the authors looked at patterns of linkage disequilibrium. Got it? Probably not. If you are curious, confused, and intent upon understanding the thrust of their methods in your bones, you probably need to read Loh et al. Barring that trust in the great hive-mind that is the Reich lab, or attempt to swallow my trite condensation.

If you consider a short to medium length sequence of the genome, there are genetic variants, alleles, segregating across that sequence. The frequency of these alleles vary across populations. And, there are on occasion correlations of allelic combinations, seen together across a single sequence than would be likely if the alleles across the loci assorted at random. A concrete example would be a population which is the product of a recent admixture event between Africans and Europeans. Recombination would take many generations to break apart all the associations between alleles which are diagnostic and distinctive of African and European ancestry, so long blocks of ancestry tracts could be inferred simply by phasing the genome on the individual level (i.e., you know the sequence of each homolog inherited from each parent, instead of just genotype values). There would be linkage disequilibrium within the population because particular variants would be associated with others across loci due to recent distinct ancestry at the genomic level. If you noticed that SNP 1 had an African allele, then SNP 2 located nearby in the locus is also more likely to have an African allele than expectation, until the point that linkage equilibrium is attained.

As I noted above, these associations are broken apart over time in a regular fashion by genetic recombination. Therefore, the decay in linkage disequilibrium across the genome can allow you to infer time since a putative admixture event. This works at various time depths. African Americans have long range LD because the admixture was relatively recent. To date older admixture events one must be more cunning, as the LD decays and becomes exceedingly faint as recombination hacks apart previous distinctive associations as two genetic backgrounds merge. But what about multiple admixture events and the consequent linkage disequilibrium patterns? What the authors did in the above paper was to test the fit of the data to a composite of LD curves in scenarios where it seems likely that there were two possible admixture events. And, they found multiple populations which did fit this model.

Dispensing with the technicalities, here are the results of admixture events as inferred from the LD decay curves:

The most parsimonious model that Pickrell et al. propose is simple as it is crazy.

1) An ancient initial admixture event in the environs of the Horn of Africa between a proto-West Eurasian population and a proto-Sudanic population

2) A second admixture event which occurs when a population derived downstream from event 1 encounters the ancestors of the Khoisan

Pickrell et al. infer a ~3,000 year old admixture event between West Eurasians and Africans for the Semitic populations of the Ethiopian plateau in keeping with Pagani et al.’s only marginally less crazy results. Then you have step 2, with an admixture between proto-Bushmen/proto-Khoe and the hybrid East Africans ~1,500 years ago. Let us accept these genetic results on the face of it. What they bring home to me is the power of culture. Though vastly diminished today, groups such as the Khoe Nama managed to preserve their integrity and independence down to the period of European colonialism (only being truly decimated in Namibia in the early 20th century by the Germans). A wave of Bantu farmers overwhelmed most of southern Africa, but select groups of Khoisan managed to maintain zones of habitation where they persisted with their unique cultural traditions and perpetuated their language. Some of this surely was ecology, as the vast Karoo region is not particularly amenable to the Bantu cultural toolkit. But, I also suspect that institutional and economic (e.g. cattle culture) influences that the East Africans had upon the Khoe, and perhaps even indirectly the Bushmen, also made these populations more robust to the Bantu expansion than otherwise would have been the case.

Being a preprint on arXiv, the paper of which I speak here is free to you, and copiously explained in loving detail in the supplements in terms of method and madness. I am not particularly enthusiastic about having long discussions about how these results are crazy and can not be right. They are crazy. But I know enough about the methodology here to understand the logic, and accept that the authors are grasping at something very strange and true, even if their particular interpretation and specific results may be disputable. Let me quote the paper at this point:

The hypothesis that west Eurasian ancestry entered eastern Africa through Arabia must be reconciled with the observation that the best modern proxies for this ancestry are often found in southern Europe rather than the Middle East (Supplementary Table 4). This observation can be interpreted in the context of ancient DNA work in Europe, which has shown that, approximately 5,000 years ago, people genetically closely related to modern southern Europeans were present as far north as Scandinavia [Keller et al., 2012; Skoglund et al., 2012]. We thus find it plausible that the people living in the Middle East today are not representative of the people who were living the Middle East 3,000 years ago. Indeed, even in historical times, there have been extensive population movements from and to the Middle East [Davies, 1997; Kennedy, 2008].

Think on that. If Pickrell et. al. are right do you think that the Middle East is particularly special in this regard? I will say that it comes to mind that the high consanguinity may result in strange outcomes if one is not careful with the sampling strategy (I’m thinking of the Samaritans I see in their data), though I doubt that this is an incautious group. But I do think it is plausible that some European populations are better proxies for the ancient Levantines than the modern Levantines because the latter have been washed over by multiple demographic waves (though I want to see more comparisons with Christian Arab* samples).

A second bombshell dropped by Pickrell et. al.:

We note that we have interpreted admixture signals in terms of large-scale movements of people. An alternative frame for interpreting these results might instead propose an isolation-by-distance model in which populations primarily remain in a single location but individuals choose mates from within some relatively small radius. In principle, this sort of model could introduce west Eurasian ancestry into southern Africa via a “diffusion-like” process. Two observations argue against this possibility. First, the gene ow we observe is asymmetric: while some eastern African populations have up to 50% west Eurasian ancestry, levels of sub-Saharan African ancestry in the Middle East and Europe are considerably lower than this (maximum of 15% [Moorjani et al., 2011]) and do not appear to consist of ancestry related to the Khoisan. Second, the signal of west Eurasian ancestry is present in southern Africa but absent from central Africa, despite the fact that central Africa is geographically closer to the putative source of the ancestry. These geographically-specific and asymmetric dispersal patterns are most parsimoniously explained by migration from west Eurasia into eastern Africa, and then from eastern to southern Africa.

Isolation-by-distance is alluded to implicitly when we speak of human genetic variation as clinal. And it’s not totally lacking in utility as a null model. But I think we need to add another layer of complexity upon this parsimonious elegance of human clans eternally exchanging mates in monotonous step-wise fashion. Multiple populations over the past 10,000 years (and likely earlier!) were rocked massive demographic turmoil, as foreigners from afar amalgamated themselves upon the local substrate, and abolished the old to bring forth something new. The author of this post is himself a product of such an event. The genetic story of mankind is not just one of continuous and diffuse gene flow gradually over a landscape of small-sale societies. No, this placid background condition was periodically perturbed by an explosion of translocating peoples, likely triggered by a technological or cultural revolution of some sort. The genetic impact in many cases is too great to be anything but a folk wandering.

Unlike isolation-by-distance these patterns do not flow linearly across space, but exhibit discordant lashing patterns through ecologically fertile terrain. Rather than a mist gliding across the plains, imaging a flash flood scouring a ravine. A more gentle analogy would be that these are demographic ripples, which expand outward, temporarily distorting the calm surface of isolation-by-distance dynamics, and eventually fading back into the background and becoming the new normal. But once the ripple has faded how do we know that it was once? That is a difficult thing indeed, and these results indicate the problems inherent. It may be that the echoes of the ripple that Pickrell et al. detect issue from a source which no longer exists. Are the scions of the first farmers of the ancient Levant hidden away in the valleys of Tuscany and the plains of Tanzania? A crazy proposition also, but not necessarily a false one.

Citation: arXiv:1307.8014v1 [q-bio.PE]

* I know some Christian Arabs do not want to be called Arabs.

(Republished from Discover/GNXP by permission of author or representative)
 
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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.

(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 http://www.razib.com"