Genetic variation in South Asia

I don’t have too much time right now. So a quick data post. The map above shows India’s scale in relation to Europe.

Below is an NJ tree that shows pairwise Fst values (genetic distance):

Please notice the small genetic difference between Britain/Spain/Poland. Compare to Gujrati vs. Sindhi, let alone Gujrati vs. Telegu.

Now, PCA:

Genetically Sindhis occupy a place between South Indians and Iranians. Some Gujaratis are nearly where Sindhis are, but many are far more shifted toward South Indians. The Fst display masks this since it aggregates populations.

Treemix shows the relationships and their scale. South Asians have a lot of drift between them.

Some of you are probably bored by this post and wonder about it’s practical implication. If so, keep on paging down (or up).

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Genetical observations on caste

One of the more interesting and definite aspects of David Reich’s Who We Are and How We Got Here is on caste. In short, it looks like most Indian jatis have been genetically endogamous for ~2,000 years, and, varna groups exhibit some consistent genetic differences.

This is relevant because it makes the social constructionist view rather untenable. The genetic distinctiveness of jati groups is very hard to deny, it jumps out of the data. The assertions about varna are fuzzier. But, on the whole Brahmins across South Asia have the most ancestry from ancient “steppe” groups, while Dalits across South Asia have the least. Kshatriya is closer to Brahmins. Vaisya has lower fractions of “steppe”. And so on. These varna generalizations aren’t as clear and distinct as jati endogamy. Sudras from Punjab may have as much or more “steppe” than South Indian Brahmins. But the coarse patterns are striking.

As a geneticist, and as an irreligious atheist, a lot of the conversations about “caste” are irrelevant to me. They’re semantical.

You can tell me that true Hinduism doesn’t have caste, that it was “invented” by Westerners. They may not have had caste, but the genetical data is clear that South Asians were endogamous for 2,000 years to an extreme degree. Additionally, the classical caste hierarchy seems to correlate with particular ancestry fractions.

Second, you can say Islam, Sikhism, Jainism, and Buddhism don’t have caste. That they picked it up from Hinduism. Or Indian culture. That’s true. But I think Islam, Sikhism, Jainism, and Buddhism are all made up, just like Hinduism. I don’t care if made up ideologies don’t have caste in their made up religious system. I am curious about the revealed patterns genetically.

I have a pretty big data set of South Asians. Some of them are from the 1000 Genomes. Here is where the 1000 Genomes South Asians were collected:

Gujarati Indians from Houston, Texas
Punjabi from Lahore, Pakistan
Bengali from Dhaka, Bangladesh
Sri Lankan Tamil from the UK
Indian Telugu from the UK

Some of the groups showed a lot of genetic variation, so I split them based on how much “Ancestral North Indian” (ANI) they had. So Gujurati_ANI_1 has more ANI than Gujurati_ANI_2 and so forth.

Continue reading “Genetical observations on caste”

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Intellectual Dark Web

I would define the “intellectual dark web” as the confluence and convergence of leaders from classical European enlightenment, hard sciences, technology (including neuroscience, bio-engineering, genetics, artificial intelligence), and east philosophy streams. Among the intellectual dark web’s many members are Dr. Richard Haier, Jordan Peterson, Jonathan Haidt, Ben Shapiro, Weinstein brothers, Sam Harris, Glenn Loury, John McWhorter, Yuval Noah Harari, Thomas Friedman, Maajid Nawaz, Neil deGrasse Tyson, Michio Kaku , Dr. VS Ramachandran, Steven Pinker, Armin Navabi, Ali Rizvi, Farhan Qureshi, Peter Beinart, Gad Saad, Nassim Nicholas Taleb, Dave Rubin, Joe Rogan, Russell Brand.  If Steve Jobs were still alive, I would include him among them. They defy easy labels and are high on openness. I hesitate to label others without their permission, but our very own Razib Khan strikes me as a potential leader of the “intellectual dark web”; although I will withdraw this nomination if he wishes. 😉

Some see the intellectual dark web as the primary global resistance to post modernism. I don’t agree. Rather I see them as ideation and intuition leaders thinking different:

Continue reading “Intellectual Dark Web”

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Closing the genetic chapter

Indus Valley People Did Not Have Genetic Contribution From The Steppes: Head Of Ancient DNA Lab Testing Rakhigarhi Samples:

In other words, the preprint observes that the migration from the steppes to South Asia was the source of the Indo-European languages in the subcontinent. Commenting on this, Rai said, “any model of migration of Indo-Europeans from South Asia simply cannot fit the data that is now available.”

Some more comments at my other weblog.

At this point, we need to move to other things. I think the broad genetic framework is pretty clear.

1) The Indus Valley Civilization (IVC) people were a mix of eastern West Asian (from modern Iran) people and native South Asian peoples (~80% of South Asian mtDNA are haplogroup M).

2) ~1500 BC a major incursion from the steppe occurred and overlaid upon #1 to various extents as a function of region, language, and caste.

3) ~0 to 500 AD the strong endogamy that characterizes modern South Asians seems to have established itself.

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The water rises and Canute drowns

The Genetic History of Indians: Are We What We Think We Are?. The answer is that people of all races have always been what they always were. What we think about what we were…well, that changes.

“I KNOW PEOPLE won’t be happy to hear this,” geneticist Niraj Rai says over the phone from Lucknow. “But I don’t think we can refute it anymore. A migration into [ancient] India did happen.” As head of the Ancient DNA Lab at Lucknow’s Birbal Sahni Institute of Palaeosciences (BSIP), he earlier worked at the CCMB in Hyderabad and has been part of several studies that employed genetics to examine lineages. “It is clear now more than ever before,” he says, “that people from Central Asia came here and mingled with [local residents]. Most of us, in varying degrees, are all descendants of those people.”

Some researchers, even those associated with the current study like Shinde, aren’t quite convinced that an ancient influx of people into the subcontinent from the northwest has finally been established by the latest findings. Shinde does not like the word ‘migration’. “It is better to say movement,” he says, implying a two-way pattern. “Everyone back then was moving to and fro. Some people were moving here and some were moving out. There was contact, yes. There was trade. But local people were involved in the development of several things. So I am not very sure of the interpretation.”

As Rai points out, the analysis of the DNA sample they will present will be of a period before the Steppe people supposedly arrived in India. If R1a is absent in the Indus Valley sample, it suggests that it was brought into South Asia, perhaps by a proto-Indo- European speaking group, from elsewhere. “How do I say it? See, I am a nationalist,” Rai says over the phone. “People will be upset. But that’s how it is. All the studies are showing that people came here from elsewhere.”

I’ve been hearing from Indian journalists that some of these researchers have only “evolved” over the last few months. First, it’s a credit to them if they changed their views on the new data. If the above is correct they got usable DNA from one Rakhigarhi sample. I predict it will be like “Indus Periphery”, but with more AASI. It seems rather clear they’re going to submit a preprint within a month or so (that’s the plan, but it’s been the plan for a year!), but the results are being written up now.

Meanwhile, the ancient DNA tsunami is going to come in further waves in the near future. Various groups have huge data sets from Central Eurasia that are going to surface. Unfortunately, samples are going to be thin on the ground from India, but we have enough now that in broad sketches most people are now falling in line with what happened demographically from the northwest. The “AASI” ancestry is deeply rooted in South Asia, and it doesn’t look like there’s much of an impact of this outside of the subcontinent aside from nearby regions.

The real action is now in understanding the cultural and archaeological processes involved in the perturbation in the years after 2000 BCE. I’ve talked to a few of the geneticists working in this area over the past month or so, and they agree.

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South Asian genetics, the penultimate chapter

A long post at my other blog, The Maturation Of The South Asian Genetic Landscape, a reflection on the important preprint The Genomic Formation of South and Central Asia. Shorter:

  1. The original inhabitants of the Indian subcontinent who descent from the “out of Africa” migration separated very quickly, ~50,000 years ago, from other eastern populations (East Asians, Andaman Islanders, Papuans, etc.). These are the “Ancient Ancestral South Indians” (AASI).
  2. Agriculturalists from what is today Iran seem to have entered and mixed with the AASI in the Indus Valley earlier than 5,000 years ago, and possibly as early as 9,000 years ago. The only samples they have are from extra-Indian sites, in Central Asia and eastern Iran, as outlier individuals. They call these “Indus_Periphery” (I call then InPe).
  3. The “Ancestral South Indians” (ASI) were created from a mixing of InPe with AASI still extant in much of South Asia ~4,000 years ago.
  4. Between ~4,000 and ~3,200 years ago populations from the steppe arrive, carrying admixture from Iranian farmers, as well as people from the steppe (Andronovo-Sintashta?). They mix with the ASI population, though a few groups, such as the Kalash, mix directly with InPe, and create unmixed “Ancestral North Indian” (ANI).
  5. Subsequent mixing between ASI and ANI populations in various fractions accounts for most of the variation in South Asia.
  6. Some groups are enriched for “steppe” as opposed to the Iranian agriculturalist that first came with InPe. In particular, Brahmins. The hypothesis then is differential ancestry of Indo-Aryan heritage persists to this day.
  7. The Munda of northeast India have a somewhat different origin, mixing Southeast Asian ancestry with ASI and further AASI. The fact that unmixed AASI were present in South Asia indicates that the Munda arrived before the full mixture was complete. Though Austro-Asiatic expansion into northern Vietnam dates to ~4,000 BC, so I think it can’t be that early.

Things I now think are unlikely:

  • Indo-Aryan interpenetration with non-Indo-Aryans in the IVC before 4,000 years ago (I was somewhat agnostic on this). The date for migration now seem very close to the “Classical Model” of arrival around 1500 BC.
  • The AASI is very diverged from the Onge, who form a clade with mainland Southeast Asian Negritos. I now think it is likely that the AASI were primal, and not migrants from Southeast Asia.

It would be nice if the results were published from the Rakhigarhi site, which dates to 4,600 years ago. But it seems less and less necessary. Perhaps at some point we’ll get enough samples from Pakistan to generate a reasonable model….

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The Indian chapter of Who We Are and How We Got Here

Since Who We Are and How We Got Here is out I thought I would spoil the “India chapter” (though you should buy the book!).

– The “Ancestral North Indians” are best modeled as a 50/50 ratio of Yamna-type people from the steppes & “Iranian farmers.” The implication is that the Indo-Aryans mixed with agriculturalists in the BMC on the way into South Asia.

– The “Ancestral South Indians” have about ~25% “Iranian farmer”, along with the indigenous component more like the Andaman Islanders.

Bow before me Dasa!

David Reich clearly believes in a model of the ethnogenesis of South Asian populations detailed in A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. Also, I think I can now say in public when I had lunch with him he indicated that he thinks this is the most likely model. Also, the West Eurasian admixture into South Asian populations is “male-mediated.” R1a1a-z93 for the win!

He also believes there were several admixtures. He notes that his group’s 2013 paper, Genetic Evidence for Recent Population Mixture in India, reported two admixture events in North India, but one in South India. And the North Indian populations had the most recent event. This makes more sense if you consider that much of the admixture probably happened in the Northwest, as a mixed population spread across the subcontinent.

Reich contends that long tracts of ANI ancestry in some North Indians indicate that later people arrived from the first ANI wave. Also, several populations have an atypical Yamna-Iranian ratio in their ANI ancestry, being enriched for Yamna, and not so enriched for Iranian. These are all Brahmin groups.

Finally, he unmasks some of the backstories of difficulties collaborating with researchers in India, who have to be sensitive to cultural and political pressures. 2009’s Reconstructing Indian Population History was hailed in India as refuting the “Aryan invasion theory,” but the evidence was on the contrary, and I said so at the time.

In Who We Are and How We Got Here David Reich makes an explicit analogy between the Indian subcontinent and Europe. Both protrusions from Eurasia are characterized by a synthesis of indigenous hunter-gatherers, intrusive pastoralists from the Eurasian steppe, and migrating West Asian farmers.

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Notes on South Asian genetics, 2018

A “pure” Tamil Brahmin, Chandrasekhar

In the post below Zach observes that the progressive author of a piece criticizing Ajit Pai has to note she too is a Gaud Saraswat Brahmin. Of course, she is progressive and opposes casteism no doubt. But to me “caste-dropping” that you are a Brahmin is like criticizing standardized testing, while observing that you also aced your standardized test. Not that that matters. Or that it proves anything.

But I’m posting this because there was a section on the genetic purity of Gaud Saraswat Brahmin’s of Karnataka. It caught my attention because I knew it was likely false. I’ve looked at South Indian Brahmins, and they generally look like they have gene flow from other South Indians. Also, if you use something called your eyes you can see that some South Indian Brahmins do not look like pure Indo-Aryan specimens at all.

Several years ago my friend Zack collected a bunch of data via his Harappa project. We’ve come further since then, but it’s still one of the best sources of information we have. Looking at the data there, and elsewhere, we can say a few things about South Asian genetics.

  • Jatts are different. I don’t know much about Jatts personally, aside from the fact that they are quite proud of being Jatt online. But in Zack’s data, and my own analysis in the SAGP, Jatts are highly inflated for “European-like” ancestry compared to populations around them. They have the highest proportions in their part of South Asia. Even higher than Pathans.

If you asked me to say why, at this I do think Jatts do have a more recent gene flow than other groups in South Asia. If you talk to Jatts online about their history, you will know what their hypothesis for this exotic element is.

  • Brahmins are different from other South Asians, and from each other. It will surprise no one that Brahmins are often somewhat different from non-Brahmins genetically. But, they also differ from each other.

Both South Indian and Bengali Brahmins mixed with the local population. Probably on the order of ~25% of the ancestry of these two Brahmin communities can be attributed to the local substrate. But, if you correct for East Asian admixture Bengali Brahmins are actually quite similar to the Brahmins of the Gangetic plains to the west. This comports with history.

A similar fraction seems reasonable for South Indian Brahmins, though perhaps more. The key issue that I have in this case is that the “European-like” proportion of South Indian Brahmins is about half of that of North Indian Brahmins. This would indicate half dilution. The admixture was probably from the higher end of the non-Brahmin caste hierarchy.

To get a sense of what I’m talking about, here are some percentages:

EthnicityDatasetNSIndianBalochCaucasianNEEuroNEEuro ratio
ap-brahminxing2549%36%3%6%6%
iyengar-brahminharappa847%37%4%6%6%
iyer-brahminharappa1147%37%5%5%5%
brahmin-tamil-nadumetspalu247%38%6%5%5%
tn-brahminxing1447%38%6%4%5%
karnataka-brahminharappa546%35%5%6%7%
oriya-brahminharappa245%35%2%8%9%
kerala-brahminharappa143%39%4%6%6%
brahmin-uttar-pradeshmetspalu842%36%5%12%12%
bengali-brahminharappa841%33%5%10%11%
up-brahminharappa439%37%7%11%12%
bihari-brahminharappa139%38%5%11%12%
rajasthani-brahminharappa234%36%8%12%13%
punjabi-brahminharappa334%39%10%11%11%
        
kashmiriharappa330%37%14%9%10%
pashtunharappa719%34%20%11%13%
maharashtrianharappa646%35%5%5%6%
tamil-nadarharappa557%31%2%0%0%
gujarati-patelharappa255%41%0%0%0%
bengaliharappa1147%27%2%4%5%
ap-reddyharappa654%36%3%0%0%

Don’t take the percentages as literal populations.

  • Some groups that think they are special are not so special. Kashmiri Pandits, for example, fancy themselves as somewhat better than other South Asians, often because of their West Asian or even European physical appearance. But the genetic data indicates ancestrally they’re not surprising in any way in the context of their geographic locale.
  • Geography is not that predictive. Well, it sort of is. But you see that groups like Chamars in Uttar Pradesh are similar to South Indian populations.
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