February 18, 2012

A teaser on the Kalash

UPDATE (Feb 22): The complete analysis can be found here.

Razib has a post on Kalash on the human tree. As it happens, 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. First, we normalize including intra-Kalash sharing:


Notice the extreme intra-Kalash haplotype sharing: Kalash individuals are recipient of "chunks" from other Kalash individuals ~5 standard deviations more often than the mean over this set of populations.

However, if we igonore intra-Kalash haplotype sharing, then the donor populations are:



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.

13 comments:

  1. D, can you be sure that the Kalash are recipitents of chunks from the other populations and not vice versa? Can we discount the possibility that the Kalash are a relic of the West Asian population that contributed substantially to the broad west Eurasian population during the Neolithic? Can your data be interpreted either way or is it unambiguous? Your analysis would seem to confirm that they have been a relatively isolated population and I am particularly intrigued by their blondism.

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  2. "my previous inference that the Ancestral North Indian (ANI) component is related to West Asians. "

    I think you mean that _MOST_ of the Ancestral North Indian component is related to West Asians. All the Autosomal results show also a north european component (but in low quantity).

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  3. IMO any genetic discussion of the Kalash has to include the Chuvash as well as their other Indian neighbours.

    In other studies it appeared that there was some kind of distinct population flow connecting the Chuvash and the Kalash. I think they stem from a common source population (most probably in West Asia).

    To me Western Europe looks like the Atlantic coastal folk, the inland river flow folk (most probably several waves), a minor component related to the Chuvash/Kalash, The Finnish east asians and a some other influences (Africans, Mongols, Gypsies etc) in approximately that order of magnitude.

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  4. I think you mean that _MOST_ of the Ancestral North Indian component is related to West Asians. All the Autosomal results show also a north european component (but in low quantity).

    Within the North European/West Asian cline, the relative levels of the "North European" component in South Asia are the same as (or lower than) in populations from the North Caucasus. So, if we are to place the ANI component within the variation of West Eurasians, it falls somewhere in the Transcaucasus.

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  5. D, can you be sure that the Kalash are recipitents of chunks from the other populations and not vice versa?

    The order of the populations is not particularly different in either case. In any case, when this analysis is completed (all 22 chromosomes for all population pairs), you can see how different populations act as donors/recipients.

    IMO any genetic discussion of the Kalash has to include the Chuvash as well as their other Indian neighbours.

    What do the Chuvash have to do with the Kalash? I don't see the connection.

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  6. Interesting analysis, Dienekes.

    Are you actually running all of your samples?

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  7. I'm running all the populations shown. These results are based on the last few chromosomes, as I am actually running the chromosomes from 22->1 (shortest first, to get immediate feedback).

    ETA for the whole thing is Tuesday/ Wednesday.

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  8. Within the North European/West Asian cline, the relative levels of the "North European" component in South Asia are the same as (or lower than) in populations from the North Caucasus. So, if we are to place the ANI component within the variation of West Eurasians, it falls somewhere in the Transcaucasus.

    Which modern population is closest to ANI? The Lezgin-Kalash connection and your previous findings about Lezgins make me think that it might be Lezgins.

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  9. "What do the Chuvash have to do with the Kalash? I don't see the connection."

    In several of the genetic map studies the Chuvash appear on a line of relatedness with the Kalash.

    For example:
    http://dienekes.blogspot.com.au/2011/01/genetic-map-of-west-eurasians.html

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  10. You cannot find not a single demonstration that North Indians derive from West Asians.

    The European, West Asian and Central Asian DNAs match with DNAs identifiable with ANI. This is because these populations emerged out from the population inhabiting North India before ANI and ASI admixture took place in India.

    These migrations took place between 55,000 years and 30,000 years back. With a more recent migration out of India into central asia, and europe, with the on set of agriculture.

    Sahoo et al had actually written the following words:“The perennial concept of people, language, and agriculture arriving to India together through thenorthwest corridor does not hold up to close scrutiny.Recent claims for a linkage of haplogroups J2, L, R1a,and R2 with a contemporaneous origin for the majority of the Indian castes’ paternal lineages from outside the subcontinent are rejected, although our findings do support a local origin of haplogroups F* and H.” .They also rule out arrivals from Southwest Asia because West Asian haplogroups (like Y-Hg G) are not found in India.

    Kivisild’s findings (2003) too had shown that humans could not have arrived from West Asia into Indiabecause of lack of West Asian Y-hgs E, G, I, J* and J2f. Kivisild
    et al wrote,“When compared with European and Middle Eastern populations (Semino et al. 2000), Indians (i) share with themclades J2 and M173 derived sister groups R1b and R1a, the latter of which is particularly frequent in India; and (ii) lack or show amarginal frequency of clades E, G, I, J*, and J2f.”

    Population structure in South Asia(Metspalu et al. 2011) West Eurasian diversity is derived from the more diverse South Asian gene pool

    ‘Researchers found that the Indian populations had more genetic diversity than Europeans and Central Asians and East Asians, which gives a good indicator of the age of a population” Genographic project IBM 2011.

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  11. In several of the genetic map studies the Chuvash appear on a line of relatedness with the Kalash.

    For example:
    http://dienekes.blogspot.com.au/2011/01/genetic-map-of-west-eurasians.html


    You probably need new eyeglasses if you think that figure shows that the Chuvash are related to the Kalash.

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  12. It looks obvious to me. I dont know why you cant see it.

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  13. Re: your second figure - does it indicate that the largest donor to the Kalash is from Kshatriya_M and lowest from Coenwall_1KG?
    Thanks.

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