The Unz Review - Mobile
A Collection of Interesting, Important, and Controversial Perspectives Largely Excluded from the American Mainstream Media
 Gene Expression BlogTeasers
South Asians Are Not Descended from Four Populations

Rplot36
The above plot I generated using the 1000 Genomes data set. BEB = Bangladeshis from Dhaka, STU are Sri Lankan Tamils, ITU are Telegus, while PJL are Punjabis from Lahore, and GIH are Gujaratis (collected in Houston). These are big categories. The South Indian population sets exhibit some structure in terms of caste; there are a few Brahmins, as well as some Dalits. The Bengalis are strangely coherent for a South Asian population, shifted toward Cambodians. The Gujarati are differentiated between a large number of Patels, and other various groups. To my surprise the Punjabi samples are very diverse.

nihms137159f3 To a great extent it recapitulates the results of the 2009 paper Reconstructing Indian Population History. What you see to the left is the “ANI-ASI cline.” Basically South Asians, from Pashtuns all the way to Paniyas fall along a spectrum of genetic distance from West Asian and European populations. A secondary element is that some groups, such as Bengalis and many Austro-Asiatic tribes, are shifted toward East Asians. An old hypothesis of the ethnogenesis of South Asian peoples is that they are a variegated mix of “Caucasoid” populations intrusive to the subcontinent, which was originally inhabited by an “Australoid” element. Malala_and_Freida_Pinto_meet_the_Youth_For_Change_panel_cropped_frida Though these terms are somewhat archaic, the general point seems to get at something visually clear: some South Asians look nearly Mediterranean in appearance, while others are hard to distinguish from Australian Aboriginals (at least superficially). And of course, most of us are somewhere in the middle.

nihms137159f4 The insight of the Reich group was to use Andaman Islanders as a proxy for a primal indigenous population, and infer that the admixture alluded to above consisted of a very West Eurasian-like population, the Ancestral North Indians (ANI), and an indigenous group closer to East Eurasians, though very diverged, the Ancestral South Indians (ASI). Ergo, the ANI-ASI cline. Using the most closely related population to infer the “ghost population,” they were able to infer admixture proportions even though no “pure” ASI group was available as a reference against which they could judge. Clever strategies like this are important, because the reference populations you use to adduce admixture events (or lack thereof) strongly impact the nature of your results. Using simple PCA or model-based clustering, as with ADMIXTURE, one would fix South Indian Dalits and tribal populations as the “purest” aboriginal people. ~100% “Australoid.” And other groups could be modeled as a “Caucasoid/Australoid” mix. But this model was not satisfactory because even low caste South Indian groups were more shifted toward West Eurasians than you’d expect.

Using a statistic called the F4 ratio the they estimated that ANI ranges from 65-75% in the Northwest Indian populations, down to 15-30% in the lower caste South Indian ones. A 2013 paper, Genetic Evidence for Recent Population Mixture in India, attempted to infer an admixture period (two to four thousand years before the present), as well as a possible secondary pulse in some Indo-European groups. This stands to reason today when you note that most Indian groups share the most unique drift trajectory with the ancient Caucasian hunter-gatherer found in Kotias, but a minority, mostly upper caste, are closer to Sintashta steppe culture.

I’m putting this post up because people are asking me about a paper profiled in ArsTechnica, The caste system has left its mark on Indians’ genomes. Actually the 2009 Reich lab paper already concluded this. So what’s the major finding of this paper that makes it unique? We’ll start with the abstract, Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure:

India, harboring more than one-sixth of the world population, has been underrepresented in genome-wide studies of variation. Our analysis reveals that there are four dominant ancestries in mainland populations of India, contrary to two ancestries inferred earlier. We also show that (i) there is a distinctive ancestry of the Andaman and Nicobar Islands populations that is likely ancestral also to Oceanic populations, and (ii) the extant mainland populations admixed widely irrespective of ancestry, which was rapidly replaced by endogamy, particularly among Indo-European–speaking upper castes, about 70 generations ago. This coincides with the historical period of formulation and adoption of some relevant sociocultural norms.

So the two major results which warrant this paper being published are that instead of two ancestral populations, they posit four, and, the admixture between some of these is considerably more recent than in the 2013 paper. I think the first conclusion is wrong, and the second is too strong.

The authors make much of the fact that they have new samples. And their SNP-chip has a high density. But I’m confused why they didn’t integrate the 1000 Genomes data. The paper was received in early July 2015, and I know there was 1000 Genomes data from all the above groups by then. They didn’t even bother to use the HapMap GIH sample, which was definitely there!

Screenshot from 2016-01-26 23:29:21 The figure to the right shows the crux of their results. They used ADMIXTURE to break apart the ancestries of their Indian data set into four clusters. Through cross-validation they established that a K = 4 was optimal parameter fit for their data. Two of the populations are previously known: ANI and ASI. But they also find that there is an “Ancestral Austro-Asiatic,” and “Ancestral Tibeto-Burman,” cluster, AAA and ATB repectively. Because they did not use full labels, it can be hard to decipher, but they use this plot to assert that people of the Khatri caste are nearly 100% ANI, while Paniyas are nearly 100% ASI. Additionally, they found several groups which were nearly 100% AAA and 100% ATB.

Long-time readers will see the immediate problem: you can’t use ADMIXTURE like this! There is no guarantee that a group that is 100% x actually is in a situation where x corresponds to a genuine discrete ancestral population that existed in reality. That is, these sorts of models push a certain number of ancestral populations, and force individuals into being combinations of those. The model is constrained by the data you are putting into it to generate the results. For example, if I took Uygurs and Europeans, and did a K = 2, the Uygurs may form one cluster, and the Europeans another, at 100% levels. But we know from history and other methodologies that the Uygurs are a recently mixed group (within the last 2,000 years). Nevertheless if you tell the package to assume K = 2 with Uygurs and Northern Europeans, then it will place these into two distinct groups. And in fact, the result tells you something real and significant about the relatedness of the individuals in the data…but it doesn’t tell you necessarily anything about the real population history.

There’s a fair amount of evidence that Austro-Asiatic populations in India are not indigenous, nor are they pure. A major hole in this paper is the total lack of acknowledgement that Austro-Asiatic languages are much more common in Southeast Asia, and it seems likely that they were intrusive to India. If so, modern Austro-Asiatic peoples can be thought of us a compound of migrants with the local substrate.

The ATB element is found only in Austro-Asiatic tribes and Bengali Brahmins. That’s reasonable, because both populations exhibit a relationship to East Asian groups. While the Brahmins of South India absorbed a minor element of local Dravidian ancestry, those of Bengal absorbed Tibeto-Burman and Austro-Asiatic, which is found in higher concentrations among Bengalis proper.

To repeat, ADMIXTURE does not necessarily give you real population combinations!!! In fact, populations are to some extent a social construct, insofar as they’re just really collapsing the genetic variation which is the result of a particular demographic and pedigree history. The “ANI” group proffered here is an artifact. The Khatri are not a representative of a pure population which is similar to the ancestral ANI. The Paniya are not 100% ASI, they are just the most ASI. The Birhor are not 100% Ancestral Austro-Asiatic, they are just the most distinctively Austro-Asiatic. The Jamatia are not pure Ancestral Tibeto-Burman; most of these Northeastern tribes have some ANI/ASI admixture. They’re just the most Tibeto-Burman.

Instead of relying on ADMIXTURE so much, they should have also utilized D-stats and f-stats (not as sensitive to drift), as well as TreeMix. I think that would have quickly shown that some of these “pure” groups were mixed.

Second, there is the issue of time-since-admixture. They obtained lower values than the 2013 paper. Why? Because they use source populations (and probably the methodology) which are somewhat different from that earlier work. Honestly if some of these populations are compounds, then it doesn’t make sense to necessarily use them as idealized donors in an admixture event. The AAA tracts are most definitely artifacts in my opinion, since the tracts are the outcome of a previous admixture event.

Finally, the authors allude to a “Southern Route” out of Africa, and, imply that the Austro-Asiatic arrived with this. The best work today suggests that Austro-Asiatic peoples expanded with an agricultural wave ~4,000 years ago, with a locus of origin in the uplands of South China. Therefore, they are not primal. A simple inspection of the map of Austro-Asiatic languages forces one to ask the question of direction of migration.

I offer this critique in the spirit of post-publication review. Perhaps the authors will clarify, as I’m genuinely puzzled by the interpretations they offered.

 
• Category: Science • Tags: South Asian Genetics 
Email This Page to Someone

 Remember My Information



=>
Commenters to Ignore...to FollowEndorsed Only
[Filtered by Reply Thread]
  1. Here’s a news report on this study on the caste system endogamy and how long it has been around.

    http://www.thehindu.com/sci-tech/science/caste-system-has-left-imprints-on-genes-study/article8155444.ece?homepage=true

    Read More
    ReplyAgree/Disagree/Etc.
    AgreeDisagreeLOLTroll
    These buttons register your public Agreement, Disagreement, Troll, or LOL with the selected comment. They are only available to recent, frequent commenters who have saved their Name+Email using the 'Remember My Information' checkbox, and may also only be used once per hour.
    Sharing Comment via Twitter
    http://www.unz.com/gnxp/south-asians-are-not-descended-from-four-populations/#comment-1308777
    More... This Commenter Display All Comments
  2. Yes of course, almost everyone who is new to the game and indeed many who are not overinterpret structure/Admixture results, as described in my blogpost http://paintmychromosomes.blogspot.cz/2013/01/simple-admixture-and-more-complicated.html or in great deal in this paper: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005397

    Read More
    • Replies: @Razib Khan
    yeah, y they should have done f statistics and such. i know that some of these indian groups are very drifted. i suspect the AAA cluster is an artifact of this....
  3. @Daniel Falush
    Yes of course, almost everyone who is new to the game and indeed many who are not overinterpret structure/Admixture results, as described in my blogpost http://paintmychromosomes.blogspot.cz/2013/01/simple-admixture-and-more-complicated.html or in great deal in this paper: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005397

    yeah, y they should have done f statistics and such. i know that some of these indian groups are very drifted. i suspect the AAA cluster is an artifact of this….

    Read More
  4. Anonymous says:     Show CommentNext New Comment

    Razib, I’m also very suspicious of the “AAA” cluster. Comparing the lower-K results makes it clear that the “AAA” cluster absorbs a lot of “ASI”-ish and some East-Asian. What gives me pause (beyond that I was suspicious of the Caucasus/Gedrosia cluster back in the day and that turned out real) is that all the ANI populations show up with fairly even “AAA” and “ASI”. If “AAA” is just an artifact, why would Admixture do this instead of just use “ASI”? Possibilities off the top of my head:

    -Both the “ASI” and “AAA” groups are pretty drifted away from older, more-NW ASI that was absorbed into the ANI populations, so Admixture couldn’t really model the older, more-NW ASI as one or the other. But the CV error is minimized, and while I’m no expert, I haven’t noticed Admixture pulling new components out of drift (eg Kalash) until K is higher than the min CV error.

    -Maybe there was structure in the hunter-gatherer population, with NW being related but somewhat different than far E or S. Admixture doesn’t know what to do with the NW for lack of less-admixed samples so splits the difference.

    -Or maybe there is some structure between the hunter-gatherer in “ASI” and “AAA”, but ANI admixed with some of both prior to geographical dispersal to areas where one or the other hunter-gatherer dominated. This strikes me as a stretch.

    Read More
    • Replies: @Razib Khan
    i think it is drift and the fact that they are a mix of ANI/ASI + east asian that has no indo-aryan. i also think ASI structure is a plausible hypothesis. would like to see 4 and 3 pop tests + treemix. y not?
  5. @Anonymous
    Razib, I'm also very suspicious of the "AAA" cluster. Comparing the lower-K results makes it clear that the "AAA" cluster absorbs a lot of "ASI"-ish and some East-Asian. What gives me pause (beyond that I was suspicious of the Caucasus/Gedrosia cluster back in the day and that turned out real) is that all the ANI populations show up with fairly even "AAA" and "ASI". If "AAA" is just an artifact, why would Admixture do this instead of just use "ASI"? Possibilities off the top of my head:

    -Both the "ASI" and "AAA" groups are pretty drifted away from older, more-NW ASI that was absorbed into the ANI populations, so Admixture couldn't really model the older, more-NW ASI as one or the other. But the CV error is minimized, and while I'm no expert, I haven't noticed Admixture pulling new components out of drift (eg Kalash) until K is higher than the min CV error.

    -Maybe there was structure in the hunter-gatherer population, with NW being related but somewhat different than far E or S. Admixture doesn't know what to do with the NW for lack of less-admixed samples so splits the difference.

    -Or maybe there is some structure between the hunter-gatherer in "ASI" and "AAA", but ANI admixed with some of both prior to geographical dispersal to areas where one or the other hunter-gatherer dominated. This strikes me as a stretch.

    i think it is drift and the fact that they are a mix of ANI/ASI + east asian that has no indo-aryan. i also think ASI structure is a plausible hypothesis. would like to see 4 and 3 pop tests + treemix. y not?

    Read More
  6. As I read the OP it seems to contradict the title, “South Asians Are Not Descended from Four Populations”.

    Surely, mainland residents of India do have ANI, ASI, Austro-Asiatic and Tibeto-Burman ancestors. Those populations may not be precisely those identified in Admixture, and may actually be present in different proportions, but I don’t think anyone has ever really doubted that proposition even in the original Reich paper which simply didn’t fixate on the potential AA and TB contributions – the former being a minor part of most Indian people’s ancestry, and the latter being geographically confined to a quite localized part of the country in the NE for the most part.

    The case that the ASI-Onge distinction is largely a statistical artifact in this case, and that the admixture percentages produced by Admixture are misleading are still valid, of course. It would be particularly helpful to see f4 and D statistics and TreeMix analysis of this point.

    I’m also a bit surprised that there isn’t some small and fairly recent Austronesian component, although the sampling strategy of what is probably a geographically limited component would be missed. I wonder if 23andMe will release South Asian summary statistics to see if the more high coverage studies are confirmed by larger but shallower data sets. This would be really helpful information even if it isn’t a statistically random sampling and would thus be subject to bias (something not entirely absent from the existing samples as you note in several instances).

    One point I thought that you might make very explicitly, given the title, but didn’t, is that ANI (prior to historic era contributions) is itself probably the product of multiple layers. At a minimum: (1) a pre-Neolithic Indus Valley and Northern Indian hunter-gatherer component (this probably had a gradual N-S cline), (2) a Neolithic revolution sourced West Asian component that gave rise to a distinctive relatively isolated Harappan layer originally in the IVC which migrated to the Ganges when the Saravasti River dried up (perhaps the CHG affinities), and (3) an Indo-Aryan component which should resemble steppe populations (which you note). There might also be in ANI a widespread historic era Islamic expansion component and a widespread historical era colonial period component. In addition, there might be some isolated communities (e.g. the Parsi community) as a result of particular isolated historic era migrations to particular areas.

    Another odd methodological point about the paper is that it uses a very short 22.5 year generation to date the strengthening of caste endogamy. The standard assumption of a 29 year generation would imply a date of 15 BCE instead, which is an excellent fit for the composition of the Manusmriti (there is an accent in there that I don’t know how to type beneath the letter “r”), which dates to 200 BCE to 200 CE, and is very pertinent since is one of the earliest clear codifications of the four tier varna system and other details of caste in practice. Written codification of rules related to caste would coincide perfectly with a sudden ossification of caste endogamy at the same time. This would precede the earliest Gupta kings by about 300 years and there is really nothing in the Gupta empire that screams out for a major change in caste practices. If anything, the fact that a warrior caste rather than Brahmin caste dynasty could rule India was considered somewhat scandalous at the time. Ideas can be more powerful than unified political power in the cultural sphere.

    I agree that it is a pity that this study didn’t include 1000 Genomes. It has 13 tribal populations (including outliers is important in this work but they make up such a small percentage of the total) and 6 high caste populations, with only one population in between, a gap that could have been filled in part by including prior 1000 Genomes and/or Reich data.

    It seems that tribal status in India does not correspond very close to autochronous as various negrito populations of Asia seem to. It would be interesting to hear your insight on the population histories of these peoples in South Asia.

    Ideally, a more ambitious study would have also juxtaposed this results with the abundant available uniparental data for many of the same geographic areas and with more linguistic and archaeological and historical context.

    Read More
    • Replies: @thinking about it
    This is why armchair wikipedia research has the reputation it does. You throw around fancy terms like manusmriti to give the impression you know what you're talking about. Those who know even less than you about Indian history might be wowed. But I'm not.

    Brahmins were NEVER considered the natural ruling caste. They were the highest caste, but they were meant to be priests and scholars. The rulers, even in the manusmriti which you mention, were supposed to come from the second-ranked caste, the Kshatriya.

    If you lack the knowledge of even this basic element of Indian culture, which even an illiterate peasant in India would know, one has to wonder how seriously one should take your pontifications.
  7. “These are big categories. The South Indian population sets exhibit some structure in terms of caste; there are a few Brahmins, as well as some Dalits. The Bengalis are strangely coherent for a South Asian population, shifted toward Cambodians. The Gujarati are differentiated between a large number of Patels, and other various groups. To my surprise the Punjabi samples are very diverse.”

    I don’t think genomes1000 have any information on caste of people who gave samples.

    Read More
  8. Hey, nice article. Btw, Iyers are not a monolithic group. The Gurukkal Tamil Brahmin group that are usually employed as priests in Saivite temples in South India and Sri Lanka are definitely a different group. My father belongs to this section of TamBrahms

    Read More
  9. I don’t think genomes1000 have any information on caste of people who gave samples.

    pretty easy to map individuals’ whose castes you know onto the 1000 genomes and figure things out. e.g., i know which individuals are s indian brahmins. they are just like the ones i have in my personal data set.

    Hey, nice article. Btw, Iyers are not a monolithic group. The Gurukkal Tamil Brahmin group that are usually employed as priests in Saivite temples in South India and Sri Lanka are definitely a different group. My father belongs to this section of TamBrahms

    probably genetically the same. all s. indian brahmins are pretty similar, though subtle regional differences.

    Read More
    • Replies: @TamilGuy
    Hey, thanks for replying

    Tbh, I don't think so. You can't really tell the difference between a SL TB and your average SL Tamil , whereas in India it's quite easy to spot the difference. Or atleast, they came from a period much before the other Iyers came and are thus more admixed with local Tamils. I suspect the minor Dravidian ancestry in Iyers in India come from marriage with Gurukkals
  10. This is a rather pedestrian question – but can someone tell me which group it is that is labeled “BIR”? Man am I having a hard time deciphering their labels.

    Read More
  11. @CupOfCanada
    This is a rather pedestrian question - but can someone tell me which group it is that is labeled "BIR"? Man am I having a hard time deciphering their labels.
    Read More
  12. @Razib,

    KSH – Khatri Sikh ?

    GBR = Guj Brahmin ?

    WBR = West Bengal Brahmin >

    IYR = Iyer ?

    MRT = Maratha ?

    PLN = ?

    KDR = ?

    Thanks

    Read More
    • Replies: @Razib Khan
    the paper is open access. click the link for god's sake.
  13. Immigrant from former USSR [AKA "Florida Resident"] says:     Show CommentNext New Comment

    Dear Mr. Khan:
    Any comments on
    “Schizophrenia risk from complex variation of complement component 4″ ?

    http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16549.html

    Traditional … .

    Read More
    • Replies: @Razib Khan
    please ask this sort of thing on open thread. i will have to read the paper soon...it's a big deal though.
  14. @rec1man
    @Razib,

    KSH - Khatri Sikh ?

    GBR = Guj Brahmin ?

    WBR = West Bengal Brahmin >

    IYR = Iyer ?

    MRT = Maratha ?

    PLN = ?

    KDR = ?

    Thanks

    the paper is open access. click the link for god’s sake.

    Read More
    • Replies: @CupOfCanada
    Yah, I didn't notice that at first and was looking through the SIs only. My bad.

    Rec1man - table 1 in the paper has the labels.
  15. @Razib Khan
    the paper is open access. click the link for god's sake.

    Yah, I didn’t notice that at first and was looking through the SIs only. My bad.

    Rec1man – table 1 in the paper has the labels.

    Read More
  16. @Immigrant from former USSR
    Dear Mr. Khan:
    Any comments on
    "Schizophrenia risk from complex variation of complement component 4" ?
    http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16549.html
    Traditional ... .

    please ask this sort of thing on open thread. i will have to read the paper soon…it’s a big deal though.

    Read More
  17. @ohwilleke
    As I read the OP it seems to contradict the title, "South Asians Are Not Descended from Four Populations".

    Surely, mainland residents of India do have ANI, ASI, Austro-Asiatic and Tibeto-Burman ancestors. Those populations may not be precisely those identified in Admixture, and may actually be present in different proportions, but I don't think anyone has ever really doubted that proposition even in the original Reich paper which simply didn't fixate on the potential AA and TB contributions - the former being a minor part of most Indian people's ancestry, and the latter being geographically confined to a quite localized part of the country in the NE for the most part.

    The case that the ASI-Onge distinction is largely a statistical artifact in this case, and that the admixture percentages produced by Admixture are misleading are still valid, of course. It would be particularly helpful to see f4 and D statistics and TreeMix analysis of this point.

    I'm also a bit surprised that there isn't some small and fairly recent Austronesian component, although the sampling strategy of what is probably a geographically limited component would be missed. I wonder if 23andMe will release South Asian summary statistics to see if the more high coverage studies are confirmed by larger but shallower data sets. This would be really helpful information even if it isn't a statistically random sampling and would thus be subject to bias (something not entirely absent from the existing samples as you note in several instances).

    One point I thought that you might make very explicitly, given the title, but didn't, is that ANI (prior to historic era contributions) is itself probably the product of multiple layers. At a minimum: (1) a pre-Neolithic Indus Valley and Northern Indian hunter-gatherer component (this probably had a gradual N-S cline), (2) a Neolithic revolution sourced West Asian component that gave rise to a distinctive relatively isolated Harappan layer originally in the IVC which migrated to the Ganges when the Saravasti River dried up (perhaps the CHG affinities), and (3) an Indo-Aryan component which should resemble steppe populations (which you note). There might also be in ANI a widespread historic era Islamic expansion component and a widespread historical era colonial period component. In addition, there might be some isolated communities (e.g. the Parsi community) as a result of particular isolated historic era migrations to particular areas.

    Another odd methodological point about the paper is that it uses a very short 22.5 year generation to date the strengthening of caste endogamy. The standard assumption of a 29 year generation would imply a date of 15 BCE instead, which is an excellent fit for the composition of the Manusmriti (there is an accent in there that I don't know how to type beneath the letter "r"), which dates to 200 BCE to 200 CE, and is very pertinent since is one of the earliest clear codifications of the four tier varna system and other details of caste in practice. Written codification of rules related to caste would coincide perfectly with a sudden ossification of caste endogamy at the same time. This would precede the earliest Gupta kings by about 300 years and there is really nothing in the Gupta empire that screams out for a major change in caste practices. If anything, the fact that a warrior caste rather than Brahmin caste dynasty could rule India was considered somewhat scandalous at the time. Ideas can be more powerful than unified political power in the cultural sphere.

    I agree that it is a pity that this study didn't include 1000 Genomes. It has 13 tribal populations (including outliers is important in this work but they make up such a small percentage of the total) and 6 high caste populations, with only one population in between, a gap that could have been filled in part by including prior 1000 Genomes and/or Reich data.

    It seems that tribal status in India does not correspond very close to autochronous as various negrito populations of Asia seem to. It would be interesting to hear your insight on the population histories of these peoples in South Asia.

    Ideally, a more ambitious study would have also juxtaposed this results with the abundant available uniparental data for many of the same geographic areas and with more linguistic and archaeological and historical context.

    This is why armchair wikipedia research has the reputation it does. You throw around fancy terms like manusmriti to give the impression you know what you’re talking about. Those who know even less than you about Indian history might be wowed. But I’m not.

    Brahmins were NEVER considered the natural ruling caste. They were the highest caste, but they were meant to be priests and scholars. The rulers, even in the manusmriti which you mention, were supposed to come from the second-ranked caste, the Kshatriya.

    If you lack the knowledge of even this basic element of Indian culture, which even an illiterate peasant in India would know, one has to wonder how seriously one should take your pontifications.

    Read More
    • Replies: @CupOfCanada
    The point is more that the Manusmriti is where a hereditary caste system is first codified.
    , @greysquirrell
    " Brahmins were NEVER considered the natural ruling caste. They were the highest caste, but they were meant to be priests and scholars. The rulers, even in the manusmriti which you mention, were supposed to come from the second-ranked caste, the Kshatriya."

    Traditionally Brahmins were/are the highest caste but there was an article I read some years back referenching a pre-modern comment from Kshatriya stating that they were originally the highest caste but Brahmins with their scheming upended them. I do not have the link handy right now.

    It does make sense when you consider that Indo-European groups were warlike and the warrior was extolled. In the Rig Veda the Indo-Aryan society was raiding and fighting each other and others. Tribal Pashtuns are known for tribal infighting . Outside of the SubContinent, IE tribes were also militaristic and took over non IE cultures (Minoans, Hattians, elite of the Mitanni kingdom, Elamites being dominated). In these other IE cultures, there isn't a dominant priestly elite that towers over the Warrior nobility. Which is why I think the article I read about the Kshatriya originally being the highest caste is accurate.
  18. The analysis in this paper does leave something to be desired and I am surprised that the reviewers did not insist on the authors doing a more thorough job. Perhaps since this is from a third world country these was “the soft bigotry of low expectations”.

    Nevertheless, I agree, along with ohwilleke, that the authors are right about four or more ancestral sources for South Asians. In particular, the authors are probably correct that the Austro-Asiatic influence is quite pervasive and that almost all South Asians have some of this kind of ancestry. Even as far back as 2001 O2a-M95, which is characteristic of Austro-Asiatics was found in low frequency in low and middle caste populations in South India – see Table 1 in the following paper.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC56946/

    The Tibeto-Burman influence is however restricted to the North and Northeast.

    Read More
    • Replies: @Razib Khan
    the research i've seen suggest that AA groups are a compound between an ANI (pre-indo-aryan)/ASI group, and an east asian group (which may have picked up austro-melanesian in SE asia?). IOW, it is like saying ANI-ASI is an ancestral population. no, it's a compound. mind you, ANI itself is something of a compound between basal eurasian, WHG-like, and for indo-aryan part ANE-like. but in the context of india i take saying a group is a "founding population" to mean that >5 K it was found in unadmixed form. or at least when it entered india. this is so for tibeto-burman (who contribute clearly to bengalis), ANI and ASI. but the AAA group is a feature of the indian landscape, though yes, i agree it must have been admixed later into the indian population to some extent.
  19. PLN = Pallan

    In the paper it is described as lower-middle caste

    It is actually a dalit caste from Tamil Nadu, still has 49% ANI, in line with most dravidian populations

    KSH = Khatri = 97% ANI

    a large % of bollywood stars are Khatri, and thats why they look nearly Mediterranean white

    Khatri surnames include – Malhotra ( Sunny Leone aka Karina Malhotra ) ; Tandon ( Raveena Tandon ) ; Khanna ( Twinkle Khanna ) ; Lamba ( Minisha Lamba ) ; Kapoor ( Kareena Kapoor ) ;
    Chopra ( Priyanka Chopra , Meera Chopra ) ;

    Read More
    • Replies: @greysquirrell
    " KSH = Khatri = 97% ANI "

    That is a very high ANI % , what is the source? The articles I read on ANI % says Kashmiris have the highest ANI % , around 75 % .
  20. @Balaji
    The analysis in this paper does leave something to be desired and I am surprised that the reviewers did not insist on the authors doing a more thorough job. Perhaps since this is from a third world country these was “the soft bigotry of low expectations”.

    Nevertheless, I agree, along with ohwilleke, that the authors are right about four or more ancestral sources for South Asians. In particular, the authors are probably correct that the Austro-Asiatic influence is quite pervasive and that almost all South Asians have some of this kind of ancestry. Even as far back as 2001 O2a-M95, which is characteristic of Austro-Asiatics was found in low frequency in low and middle caste populations in South India – see Table 1 in the following paper.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC56946/

    The Tibeto-Burman influence is however restricted to the North and Northeast.

    the research i’ve seen suggest that AA groups are a compound between an ANI (pre-indo-aryan)/ASI group, and an east asian group (which may have picked up austro-melanesian in SE asia?). IOW, it is like saying ANI-ASI is an ancestral population. no, it’s a compound. mind you, ANI itself is something of a compound between basal eurasian, WHG-like, and for indo-aryan part ANE-like. but in the context of india i take saying a group is a “founding population” to mean that >5 K it was found in unadmixed form. or at least when it entered india. this is so for tibeto-burman (who contribute clearly to bengalis), ANI and ASI. but the AAA group is a feature of the indian landscape, though yes, i agree it must have been admixed later into the indian population to some extent.

    Read More
    • Replies: @CupOfCanada
    Do you think a deeper, more widespread layer of East Asian admixture is plausible, even if it's not specific to AA?
  21. @thinking about it
    This is why armchair wikipedia research has the reputation it does. You throw around fancy terms like manusmriti to give the impression you know what you're talking about. Those who know even less than you about Indian history might be wowed. But I'm not.

    Brahmins were NEVER considered the natural ruling caste. They were the highest caste, but they were meant to be priests and scholars. The rulers, even in the manusmriti which you mention, were supposed to come from the second-ranked caste, the Kshatriya.

    If you lack the knowledge of even this basic element of Indian culture, which even an illiterate peasant in India would know, one has to wonder how seriously one should take your pontifications.

    The point is more that the Manusmriti is where a hereditary caste system is first codified.

    Read More
    • Replies: @rec1man
    The manusmriti is a later document - it says a lot of earlier allowed practises like inter-caste marriage are no longer allowed

    Brahmins have existed in a loosely hereditary form even around 1000 bc

    but they were allowed to marry low caste women, and the mixed children accepted into the fathers caste

    The father of Vyasa ( author of Mahabharata ) was brahmin, his mother a low caste fisher woman, and Vyasa was accepted as a brahmin
  22. @CupOfCanada
    The point is more that the Manusmriti is where a hereditary caste system is first codified.

    The manusmriti is a later document – it says a lot of earlier allowed practises like inter-caste marriage are no longer allowed

    Brahmins have existed in a loosely hereditary form even around 1000 bc

    but they were allowed to marry low caste women, and the mixed children accepted into the fathers caste

    The father of Vyasa ( author of Mahabharata ) was brahmin, his mother a low caste fisher woman, and Vyasa was accepted as a brahmin

    Read More
  23. The khatri are one of the most fascinating castes in India, with all-round strengths

    *Many serve in the Indian Army, General Arora, who liberated Bangladesh in 1971 was a Khatri

    *All the Sikh guru were Khatri

    *They are skilled merchants and own much of urban New Delhi, and owned much of Lahore, pre-1947

    *Hargobind Khorana, who won a science Nobel in 1969, was a Khatri

    *Khatri atomic scientists were involved in the 1974 Indian nuke blast

    *In the California National Merit Semifinalist list, among Indian Americans, Khatri are well represented

    *And of course bollywood actresses are often Khatri, including Priyanka Chopra ( Quantico TV series )

    Read More
  24. @Razib Khan
    the research i've seen suggest that AA groups are a compound between an ANI (pre-indo-aryan)/ASI group, and an east asian group (which may have picked up austro-melanesian in SE asia?). IOW, it is like saying ANI-ASI is an ancestral population. no, it's a compound. mind you, ANI itself is something of a compound between basal eurasian, WHG-like, and for indo-aryan part ANE-like. but in the context of india i take saying a group is a "founding population" to mean that >5 K it was found in unadmixed form. or at least when it entered india. this is so for tibeto-burman (who contribute clearly to bengalis), ANI and ASI. but the AAA group is a feature of the indian landscape, though yes, i agree it must have been admixed later into the indian population to some extent.

    Do you think a deeper, more widespread layer of East Asian admixture is plausible, even if it’s not specific to AA?

    Read More
    • Replies: @Razib Khan
    if it is > 10,000 years ago, no. on the PCA the "ASI-cline" moves toward e. asians, until you put a group like andaman islanders there. it's obviously not east asian, just MORE east asian than west eurasian. the contrast here is with bengalis and assamese, two indo-aryan groups who have LOTS of east asian and it jumps out at you.
  25. @CupOfCanada
    Do you think a deeper, more widespread layer of East Asian admixture is plausible, even if it's not specific to AA?

    if it is > 10,000 years ago, no. on the PCA the “ASI-cline” moves toward e. asians, until you put a group like andaman islanders there. it’s obviously not east asian, just MORE east asian than west eurasian. the contrast here is with bengalis and assamese, two indo-aryan groups who have LOTS of east asian and it jumps out at you.

    Read More
  26. @Razib Khan
    I don’t think genomes1000 have any information on caste of people who gave samples.


    pretty easy to map individuals' whose castes you know onto the 1000 genomes and figure things out. e.g., i know which individuals are s indian brahmins. they are just like the ones i have in my personal data set.

    Hey, nice article. Btw, Iyers are not a monolithic group. The Gurukkal Tamil Brahmin group that are usually employed as priests in Saivite temples in South India and Sri Lanka are definitely a different group. My father belongs to this section of TamBrahms

    probably genetically the same. all s. indian brahmins are pretty similar, though subtle regional differences.

    Hey, thanks for replying

    Tbh, I don’t think so. You can’t really tell the difference between a SL TB and your average SL Tamil , whereas in India it’s quite easy to spot the difference. Or atleast, they came from a period much before the other Iyers came and are thus more admixed with local Tamils. I suspect the minor Dravidian ancestry in Iyers in India come from marriage with Gurukkals

    Read More
    • Replies: @rec1man
    I can usually spot the diff between Vadama Iyer vs Brahacharanam Iyer - Vadama means from the north and are recent migrants , within last 1500 years to Tamil Nadu ;

    and between Vadagalai Iyengar and Thenkalai Iyengar - Vadagalai means from the North

    Both Brahacharanam Iyer and Thenkalai Iyengar, have more dravidian admixture and are from an earlier Aryan migratory wave from North India to Tamil Nadu
  27. Actually Austroasiatics have very little ANI. The following is a quote from Lazaridis et al. “We also test relationships to the Kharia, an Austroasiatic-speaking population from India that does not appear to be part of the Indian Cline of varying West Eurasian-related Ancient North Indian ancestry—in particular, it seems to have little or no West Eurasian admixture unlike the Indo-European and Dravidian speaking populations in India—and instead appears to have some East Asian-related admixture.”

    We can see this also from the following plot generated by Davidski.

    https://drive.google.com/file/d/0B9o3EYTdM8lQYzlQWDRPZ0lELW8/view?usp=sharing

    This plot shows that Austroasiatics have less ANI than Paniya who according to Moorjani et al. have only 17%.

    What this suggests is that Austroasiatics arrived in what is now India before ANI did (ANI was in what is now Pakistan at least 9000 years ago and probably even earlier). This must have been more than 4000 years ago since the ANI admixture date for Vysya of Andhra Pradesh is 4200 years according to Moorjani et al.

    The Austroasiatics must have been able to spread into India from the East because they had some neolithic agricultural technology (rice). Just like EEF in Europe coexisted and gradually admixed with WHG in Europe, Austroasiatics must have done the same with ASI in India. After the arrival of ANI, Austroasiatics became marginalized.

    Perhaps there is indeed something to the “Para-Munda” hypothesis for influences on Sanskrit and Ma Ganga is truly cognate to Mekong.

    Read More
  28. @thinking about it
    This is why armchair wikipedia research has the reputation it does. You throw around fancy terms like manusmriti to give the impression you know what you're talking about. Those who know even less than you about Indian history might be wowed. But I'm not.

    Brahmins were NEVER considered the natural ruling caste. They were the highest caste, but they were meant to be priests and scholars. The rulers, even in the manusmriti which you mention, were supposed to come from the second-ranked caste, the Kshatriya.

    If you lack the knowledge of even this basic element of Indian culture, which even an illiterate peasant in India would know, one has to wonder how seriously one should take your pontifications.

    ” Brahmins were NEVER considered the natural ruling caste. They were the highest caste, but they were meant to be priests and scholars. The rulers, even in the manusmriti which you mention, were supposed to come from the second-ranked caste, the Kshatriya.”

    Traditionally Brahmins were/are the highest caste but there was an article I read some years back referenching a pre-modern comment from Kshatriya stating that they were originally the highest caste but Brahmins with their scheming upended them. I do not have the link handy right now.

    It does make sense when you consider that Indo-European groups were warlike and the warrior was extolled. In the Rig Veda the Indo-Aryan society was raiding and fighting each other and others. Tribal Pashtuns are known for tribal infighting . Outside of the SubContinent, IE tribes were also militaristic and took over non IE cultures (Minoans, Hattians, elite of the Mitanni kingdom, Elamites being dominated). In these other IE cultures, there isn’t a dominant priestly elite that towers over the Warrior nobility. Which is why I think the article I read about the Kshatriya originally being the highest caste is accurate.

    Read More
  29. Has the Reich labs made any comments on the Vedda people , on their relation to ASI? They are only found as a distinct group in Sri Lanka but their ancestry would be present in the India SubContinent.

    Accepted as the aboriginal people of Sri Lanka , their ancestry has to be one of the oldest in the SubContinent. Vedda speech is often described as a creole burrowing from Tamil and Sinhalese , mostly the later. Vedda language has distinct sounds , grammer and vocabularly that sets it apart from Sinhalese.

    Read More
  30. @rec1man
    PLN = Pallan

    In the paper it is described as lower-middle caste

    It is actually a dalit caste from Tamil Nadu, still has 49% ANI, in line with most dravidian populations

    --

    KSH = Khatri = 97% ANI

    a large % of bollywood stars are Khatri, and thats why they look nearly Mediterranean white

    Khatri surnames include - Malhotra ( Sunny Leone aka Karina Malhotra ) ; Tandon ( Raveena Tandon ) ; Khanna ( Twinkle Khanna ) ; Lamba ( Minisha Lamba ) ; Kapoor ( Kareena Kapoor ) ;
    Chopra ( Priyanka Chopra , Meera Chopra ) ;

    ” KSH = Khatri = 97% ANI ”

    That is a very high ANI % , what is the source? The articles I read on ANI % says Kashmiris have the highest ANI % , around 75 % .

    Read More
    • Replies: @Shaikorth
    It's from this new paper, and what they actually mean is "Khatri ADMIXTURE result is 97% component we label ANI". It's not comparable to Reich's ANI estimates - those were produced using formal mixture tests, which ADMIXTURE is not.
  31. @greysquirrell
    " KSH = Khatri = 97% ANI "

    That is a very high ANI % , what is the source? The articles I read on ANI % says Kashmiris have the highest ANI % , around 75 % .

    It’s from this new paper, and what they actually mean is “Khatri ADMIXTURE result is 97% component we label ANI”. It’s not comparable to Reich’s ANI estimates – those were produced using formal mixture tests, which ADMIXTURE is not.

    Read More
    • Replies: @greysquirrell
    This 2013 post from Dienekes refrences the 2013 Moorjani et al. paper on ANI % amongst various castes . The 2 Kshatriya groups -fromUttar Pradesh- come in at 54.6% and 60.9% . The Pathan group has the highest ANI at 70%.
    http://dienekes.blogspot.com/2013/08/major-admixture-in-india-took-place-42.html

    Looking at the 2016 Basu et al. paper, they have Iyer listed as Dravidian but they are a Brahmin group , which is Dravidian speaking but not Dravidian per se, though obviously they have admixture from the non Brahmin Dravidian speakers. They sampled lower caste and tribal Dravidian groups but not the traditionally dominant Dravidian castes that made up the royalty and merchants.

    http://www.pnas.org/content/early/2016/01/20/1513197113.full.pdf

  32. @Shaikorth
    It's from this new paper, and what they actually mean is "Khatri ADMIXTURE result is 97% component we label ANI". It's not comparable to Reich's ANI estimates - those were produced using formal mixture tests, which ADMIXTURE is not.

    This 2013 post from Dienekes refrences the 2013 Moorjani et al. paper on ANI % amongst various castes . The 2 Kshatriya groups -fromUttar Pradesh- come in at 54.6% and 60.9% . The Pathan group has the highest ANI at 70%.

    http://dienekes.blogspot.com/2013/08/major-admixture-in-india-took-place-42.html

    Looking at the 2016 Basu et al. paper, they have Iyer listed as Dravidian but they are a Brahmin group , which is Dravidian speaking but not Dravidian per se, though obviously they have admixture from the non Brahmin Dravidian speakers. They sampled lower caste and tribal Dravidian groups but not the traditionally dominant Dravidian castes that made up the royalty and merchants.

    http://www.pnas.org/content/early/2016/01/20/1513197113.full.pdf

    Read More
  33. @TamilGuy
    Hey, thanks for replying

    Tbh, I don't think so. You can't really tell the difference between a SL TB and your average SL Tamil , whereas in India it's quite easy to spot the difference. Or atleast, they came from a period much before the other Iyers came and are thus more admixed with local Tamils. I suspect the minor Dravidian ancestry in Iyers in India come from marriage with Gurukkals

    I can usually spot the diff between Vadama Iyer vs Brahacharanam Iyer – Vadama means from the north and are recent migrants , within last 1500 years to Tamil Nadu ;

    and between Vadagalai Iyengar and Thenkalai Iyengar – Vadagalai means from the North

    Both Brahacharanam Iyer and Thenkalai Iyengar, have more dravidian admixture and are from an earlier Aryan migratory wave from North India to Tamil Nadu

    Read More
  34. […] The sound is not completely optimal – there’s some echo now and then – but this should not keep you from watching the lecture. It’s quite good, and very accessible – I don’t really think you even need to know anything about genetics to follow most of what he’s talking about here; he introduces key concepts as needed and don’t go much into the details (of course also making the lecture somewhat superficial, but you can’t get everything). If you’re the sort of person who wants details not included in the lecture you’re probably already reading e.g. Razib Khan (who incidentally recently blogged/criticized a not too dissimilar paper, dealing with South Asia)… […]

    Read More

Comments are closed.