Razib Khan One-stop-shopping for all of my content

February 18, 2012

Kalash haplotype sharing

Filed under: Anthroplogy,Human Genetics,Kalash — Razib Khan @ 5:07 pm

Prompted by my posts, Dienekes, A teaser on the Kalash:

I am in the middle of a ChromoPainter/fineSTRUCTURE analysis of a broad dataset designed to explore certain mysteries that have often come up in my previous experiments. Barring the unexpected, the analysis should be completed sometime next week.

Below you can see the normalized number of “chunks” donated by various populations to the Kalash….

Here is the bar plot which Dienekes generated (left to right indicates extent of “donation” to the Kalash):

I highlighted the most significant non-South Asian donor. Dienekes states:

Of particular interest is the fact that all West Asian populations appear higher on the donor list than all Northern European ones, which confirms, using a haplotype-based approach, my previous inference that the Ancestral North Indian (ANI) component is related to West Asians.

The main issue I would point out is that “West Asians” are probably a major donor to both South Asians and Northern Europeans. In any case, the Lezgian are a North Caucasian non-Indo-Eurpean population. But this is what came to mind:

Geographical distribution of G:

In Turkey, the southern Caucasus region and Iran, haplogroup G reaches the highest percentage of a regional population worldwide. Among Turkish males 11% of the population is G.[4] In Iran, Haplogroup G reaches 13 to 15% of the population in various parts of the country. While it is found in percentages higher than 10% among the Bakhtiari, Gilaki and Mazandarani, it is closer to 5% among the Iranian Arabs and in some large cities.[25] Among the samples in the YHRD database from the southern Caucasus countries, 29% of the samples from Abazinia, 31% from Georgia, 18% from Azerbaijan and 11% from Armenia appear to be G samples.

In southern Asia, haplogroup G is found in concentrations of approximately 18%[26] to 20%[27] of Kalash, approximately 16% of Brahui,[27] and approximately 11.5% of sampled Pashtun,[26] but in only about 3% of the general Pakistani population.[26] The many groups in India and Bangla Desh have not been well studied. About 6% of the samples from Sri Lanka and Malaysia were reported as haplogroup G, but none were found in the other coastal lands of the Indian Ocean or Pacific Ocean in Asia.[28]

Otzi the Iceman was G, and G is found in mountains areas of Southern Europe, as well as among groups like Tamil Brahmins. My own hunch is that G came with men who first brought agriculture to Europe. This does not mean that they were among the first agriculturalists in South Asia, but there may be some deep connection to pulses out of the trans-Caucasian region.

As far as my initial assertion that the Kalash are a liminal South Asian population, that seems supported by the high matches to many South Asian groups. But my own contention was more specific: that the Kalash exhibit evidence of admixture with the indigenous people of Southern Eurasia, the “Ancestral South Indians” (ASI), attesting to their deep origins within the subcontinent. This is not necessarily true even if they share a lot of haplotypes with South Asians, because the Kalash and Indians proper may share common donors for “Ancestral North Indians” (ANI). Nevertheless, they seem to have some relationship to the ANI-ASI cline identified by Reich et al. (albeit, possibly more complex than that of the Pathans).

Kalash on the human tree

Filed under: Anthroplogy,Genetics,Human Genetics,Kalash — Razib Khan @ 11:07 am

A recent paper on Turkish genetics has a tree which illustrates a summary of how the Kalash shake out:

I say summary because this tree takes a lot of information and tries to generate the best fit representation. It does hide some information by the nature of its aggregation of patterns. For example, the position of the Burusho, or Turks, has to do with the fact that both of these have low, but noticeable, levels of East Asian admixture on top of a different base. If you removed this eastern element both groups would come much closer to similar groups. The extreme long branches leading to the Kalash and Mozabites are almost certainly a function of endogamy and inbreeding. Their allele frequencies diverged from nearby populations because of isolation.

But notice the nearby populations of the Kalash. They’re northwest South Asian. In many ways if you removed the drift and endogamy from the Kalash I suspect you’d been left with a group very similar to their Pathan neighbors.

Finally, as many of you know I put a substantial number of comments into ‘spam’ on this weblog. Here’s one related to the Kalash which you didn’t see:

“Because of their light skin and hair both the Kalash and Burusho have inspired claims that they are “lost white tribes.” This is almost certainly false for the Burusho. Aside from their moderate East Asian admixture, they’re not so different from other Pakistanis in their region genetically.”

LOL! You are in such denial! A lot of pseudo-scientific mumbo jumbo to spin a lie. OF COURSE they’re of European descent. Claiming European genes as indigenous makes Arabs, Iranians, Middle Easterners and Indians, like you, sound pathetic and desperate.

Geneticists like you could make BRAD PITT’S genes indigenous to South Asia if you wanted to. Where there’s a will there’s a way.

The interesting thing is that this sort of comment is routinely written by white nationalists, Afrocentrists, Indian nationalists, etc. etc. of Racial romanticism often has as great a difficulty accepting the nature of the human phylogeny as those who would like to elide any substantive differences. The only thing I would note though is that this person posted as “liz” at Amardeep Singh’s blog (email: beautifullydrawn@gmail.com, with an IP that traces to Alfred University) so it might beat false-flag troll.

September 12, 2010

Not all genes are equal in the eyes of man

Filed under: Anthroplogy,Genetics,Kafir,Kalash,Nuristan,race,Taxonomy — Razib Khan @ 11:19 pm

Kalashpeople_20100312A few days ago I was listening to an interview with a reporter who was kidnapped in the tribal areas of Pakistan (he eventually escaped). Because he was a Westerner he mentioned offhand that to “pass” as a native for his own safety he had his guides claim he was Nuristani when inquiries were made. The Nuristanis are an isolated group in Afghanistan notable for having relatively fair features. His giveaway to his eventual captors was that his accent was clearly not Nuristani, and master logicians that the Taliban are, the inference was made that he was likely a European pretending to be Nuristani.

I thought about this incident when looking over the supplements yesterday of Reconstructing Indian population history. On page 19 note S2 figure 1 includes the Kalash of Pakistan. These are the unconverted cousins of the Nuristanis who were not forcibly brought into the religion of peace in the late 1800s because their region of the Hindu Kush was under British rule, who naturally imposed their late 19th century European value that populations should not be converted by force to a particular religion (Nuristan means “land of light,” whereas before Afghans called it Kafiristan, “land of the unbelievers”). Despite the fair features of the Kalash, which has given rise to rumors that they are the descendants of Alexander the Great’s soldiers, they cluster with Central and South Asian populations, not Europeans. Like the Ainu of Japan it seems superficial similarities to Europeans, at least in relation to the majority population around them, has resulted in an inordinate expectation of total genome exoticism, when in reality a few particular loci are producing the distinctiveness.

Figure 1 from the 2007 paper, Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians, brings home the point:


The first panel shows a representation of the genetic distance across the genome. Or at least enough to give you a good sense of the phylogenetic relationships. South Asians and Europeans form a clade, as do Native Americans and East Asians. The subsequent panels show Fst values, between population variance, on five genes known at that time to be implicated in between population skin color differences. Note now much different the trees are from the one generated by a large number of loci. Since then more loci have come out of the woodwork, and the peculiar genetic architecture of pigmentation has been rather well characterized. Though most genetic variance may be found within continental races, pigmentation is quite often the exception to this rule. Most of the variance on these loci can be between the races. On SLC24A5 West Africans and Europeans have nearly 100% between population variance. The allele frequencies are disjoint. This shouldn’t be that surprising, skin color is highly heritable, and we already know that there’s a lot of between population difference. So from that one would infer that there would be a lot of genetic variation.

Our skin is our largest organ, and is extremely important as a visual marker of health, age, and identity. The fact that there is so much salient interpopulation difference matters a great deal in the “folk taxonomy” of our species. When considering the relevance of skin color in our taxonomies I thought back to Jared Diamond’s 1994 piece for Discover, Race Without Color:

Regarding hierarchy, traditional classifications that emphasize skin color face unresolvable ambiguities. Anthropology textbooks often recognize five major races: “whites,” “African blacks,” “Mongoloids,” “aboriginal Australians,” and “Khoisans,” each in turn divided into various numbers of sub-races. But there is no agreement on the number and delineation of the sub-races, or even of the major races. Are all five of the major races equally distinctive? Are Nigerians really less different from Xhosas than aboriginal Australians are from both? Should we recognize 3 or 15 sub-races of Mongoloids? These questions have remained unresolved because skin color and other traditional racial criteria are difficult to formulate mathematically.

16 years on I think we can reasonably answer many of Diamond’s questions with phylogenetic trees such as the one to the left. There are five races in the tree by coincidence, though the Khoisans are with Africans, and the Americas has its own branch. Yes, Nigerians are probably less different from the Xhosas than Aboriginal Australians. And I guess this tree implies closer to 15 “subraces” for “Mongoloids.” And with the rise of skin reflectance measures the trait isn’t that difficult to formulate mathematically actually.

But as for the salient phenotypic characteristics which humans use to classify each other, and which will remain important socially and culturally for the near future, it makes absolutely no sense to minimize the critical importance of skin pigmentation. Humans are a very visual species, and the complexion of our largest organ will always be of particular interest. This sort of phenetic classification is not scientifically rigorous, I don’t want cladists to hunt me down, but, it is not an arbitrary cultural construct. We can’t classify people by HLA profiles because we don’t have conscious access to such information (and the idea that we can “smell” HLA profiles is still unproven). Our innate pattern recognition competencies are such that naturally folk taxonomies will start with complexion, and use other characters to refine our categories. Just because something isn’t scientific doesn’t always mean it’s silly or arbitrary.

Image Credit: Outlook India

Addendum: I just realized that Jared Diamond’s article came out at the same time as The History and Geography of Human Genes. A quick consultation of this seminal work would have cleared up some of his questions.

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