Indian genetics, the never-ending argument

I am at this point somewhat fatigued by Indian population genetics. The real results are going to be ancient DNA, and I’m waiting on that. But people keep asking me about an article in Swarajya, Genetics Might Be Settling The Aryan Migration Debate, But Not How Left-Liberals Believe.

First, the article attacks me as being racist. This is not true. The reality is that the people who attack me on the Left would probably attack magazines like Swarajya as highly “problematic” and “Islamophobic.” They would label Hindu nationalism as a Nazi derivative ideology. People should be careful the sort of allies they make, if you dance with snakes they will bite you in the end. Much of the media lies about me, and the Left constantly attacks me. I’m OK with that because I do believe that the day will come with all the ledgers will be balanced. The Far Left is an enemy of civilization of all stripes. I welcome being labeled an enemy of barbarians. My small readership, which is of diverse ideologies and professions, is aware of who I am and what I am, and that is sufficient. Either truth or power will be the ultimate arbiter of justice.

With that out of the way, there this one thing about the piece that I think is important to highlight:

To my surprise, it turned out that that Joseph had contacted Chaubey and sought his opinion for his article. Chaubey further told me he was shocked by the drift of the article that appeared eventually, and was extremely disappointed at the spin Joseph had placed on his work, and that his opinions seemed to have been selectively omitted by Joseph – a fact he let Joseph know immediately after the article was published, but to no avail.

Indeed, this itself would suggest there are very eminent geneticists who do not regard it as settled that the R1a may have entered the subcontinent from outside. Chaubey himself is one such, and is not very pleased that Joseph has not accurately presented the divergent views of scholars on the question, choosing, instead to present it as done and dusted.

I do wish Tony Joseph had quoted Gyaneshwer Chaubey’s response, and I’d like to know his opinions. Science benefits from skepticism. Unfortunately though the equivocation of science is not optimal for journalism, so oftentimes things are presented in a more stark and clear manner than perhaps is warranted. I’ve been in this position myself, when journalists are just looking for a quote that aligns with their own views. It’s frustrating.

There are many aspects of the Swarajya piece I could point out as somewhat weak. For example:

The genetic data at present resolution shows that the R1a branch present in India is a cousin clade of branches present in Europe, Central Asia, Middle East and the Caucasus; it had a common ancestry with these regions which is more than 6000 years old, but to argue that the Indian R1a branch has resulted from a migration from Central Asia, it should be derived from the Central Asian branch, which is not the case, as Chaubey pointed out.

The Srubna culture, the Scythians, and the people of the Altai today, all bear the “Indian” branch of R1a. First, these substantially post-date 6000 years ago. I think that that is likely due to the fact that South Asian R1a1a-Z93 and that of the Sbruna descend from a common ancestor. But in any case, the nature of the phylogeny of Z93 indicates rapid expansion and very little phylogenetic distance between the branches. Something happened 4-5,000 years ago. One could imagine simultaneous expansions in India and Central Asia/Eastern Europe. Or, one could imagine an expansion from a common ancestor around that time. The latter seems more parsimonious.

Additionally, while South Asians share ancestry with people in West Asia and Eastern Europe, these groups do not have distinctive South Asian (Ancestral South Indian) ancestry. This should weight out probabilities as to the direction of migration.

Second, I read some of the papers linked to in the article, such as Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia and Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. The first paper has good data, but I’ve always been confused by the interpretations. For example:

A few studies on mtDNA and Y-chromosome variation have interpreted their results in favor of the hypothesis,70–72 whereas others have found no genetic evidence to support it.3,6,73,74 However, any nonmarginal migration from Central Asia to South Asia should have also introduced readily apparent signals of East Asian ancestry into India (see Figure 2B). Because this ancestry component is absent from the region, we have to conclude that if such a dispersal event nevertheless took place, it occurred before the East Asian ancestry component reached Central Asia. The demographic history of Central Asia is, however, complex, and although it has been shown that demic diffusion coupled with influx of Turkic speakers during historical times has shaped the genetic makeup of Uzbeks75 (see also the double share of k7 yellow component in Uzbeks as compared to Turkmens and Tajiks in Figure 2B), it is not clear what was the extent of East Asian ancestry in Central Asian populations prior to these events.

Actually the historical and ancient DNA evidence both point to the fact that East Asian ancestry arrived in the last two thousand years. The spread of the first Gokturk Empire, and then the documented shift in the centuries around 1000 A.D. from Iranian to Turkic in what was Turan, signals the shift toward an East Asian genetic influx. Alexander the Great and other Greeks ventured into Central Asia. The people were described as Iranian looking (when Europeans encountered Turkic people like Khazars they did note their distinctive physical appearance).

We have ancient DNA from the Altai, and those individuals initially seemed overwhelmingly West Eurasian. Now that we have Scythian ancient DNA we see that they mixed with East Asians only on the far east of their range.

The second paper is very confused (or confusing):

The time divergence between Indian and European Y-chromosomes, based on the closest neighbour analysis, shows two different distinctive divergence times for J2 and R1a, suggesting that the European ancestry in India is much older (>10 kya) than what would be expected from a recent migration of Indo-European populations into India (~4 to 5 kya). Also the proportions suggest the effect might be less strong than generally assumed for the Indo-European migration. Interestingly, the ANI ancestry was recently suggested to be a mix of ancestries from early farmers of western Iran and people of the Bronze Age Eurasian steppe (Lazaridis et al. 2016). Our results agree with this suggestion. In addition, we also show that the divergence time of this ancestry is different, suggesting a different time to enter India.

Lazaridis et al. accept a mass migration from the steppe. In fact, the migration is to such a magnitude that I’m even skeptical. Also, there couldn’t have been a European migration to South Asia during the Pleistocene because Europeans as we understand them genetically did not exist then!!!

I assume that many of the dates of coalescence are sensitive to parameter conditions. Additionally, they admit limitations to their sampling.

Ultimately the final story will be more complex than we can imagine. R1a is too widespread to be explained by a simple Indo-Aryan migration in my opinion. But we can’t get to these genuine conundrums if we keep having to rebut ideologically motivated salvos.

Related: Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts. I wish David would be a touch more equivocal. But I have to admit, if the model fits, at some point you have to quit.

Indian media is finally reporting on the Aryan migration into South Asia

For various ideological reasons in India there has been a strong resistance to the idea that Aryans came from outside of South Asia. When David Reich’s Reconstructing Indian Population History was published 2009 the Indian media had a weird response. For example, Aryan-Dravidian divide a myth: Study.

Though Reich’s paper was equivocal, it was clear to me that it was likely going to be the launching point for a resurrection of the Aryan migration theory. Now Tony Joseph in The Hindu has published a pretty good survey of the literature, How genetics is settling the Aryan migration debate. Nothing new for readers of this weblog, but he some good quotes:

The avalanche of new data has been so overwhelming that many scientists who were either sceptical or neutral about significant Bronze Age migrations into India have changed their opinions. Dr. Underhill himself is one of them. In a 2010 paper, for example, he had written that there was evidence “against substantial patrilineal gene flow from East Europe to Asia, including to India” in the last five or six millennia. Today, Dr. Underhill says there is no comparison between the kind of data available in 2010 and now. “Then, it was like looking into a darkened room from the outside through a keyhole with a little torch in hand; you could see some corners but not all, and not the whole picture. With whole genome sequencing, we can now see nearly the entire room, in clearer light.”

In relation to online debates I have had Indian interlocutors tell me flat out that they believe in the papers published between 2005 and 2010. It is nice to get the scientists who actually published this work now admit that new results overturn the older theories.

Note: I am going to refer to this as a migration, because “invasion” seems to connote too much specificity as to how it happened. But I have a difficult time imagining that it was a peaceful process.

The last days of pre-ancient DNA Indian population genomics

If anyone wants to know about the population genetics of South Asia, I recommend three papers (all are open access):

Genetic Evidence for Recent Population Mixture in India

A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

The promise of disease gene discovery in South Asia

In the near future ancient DNA will do for South Asia what has been done for Europe, and to a lesser extent the Near East. It will pull back our veil of ignorance. But until then we have genomic inference from larger data sets with a greater number of markers. What can we say now?

– The 2009 work that modern South Asians are broadly a compound of two streams of the out of Africa populations is correct. One is much like other West Eurasians. Another is distantly related to other East Eurasians, with possible affinities to Paleolithic Southeast Asian hunter-gatherers.

– The West Eurasian ancestry of South Asians, the “Ancestral North Indians” (ANI), does likely seem to be a mixture at minimum between two groups. One element is related to the eastern farmers who first adopted agriculture on the slopes of the Zagros ~10,000 year ago. Another stream is closely related to the Yamna people who flourished on the Eurasian steppe north of the Black Sea ~5,000 years ago.

– The Munda peoples seem to have a distinct Southeast Asian component that ties them with other Austro-Asiatic peoples. Their migration was almost certainly tied to the Neolithic migration of rice farmers. They are likely not the primal aboriginals of South Asia.

– The R1a1a-Z93 Y chromosomal lineage found across much of South Asia, and especially the higher castes and the north, increased in frequency within the last 4,000 years. It is almost certainly exogenous to South Asia; ancient DNA from the steppe finds the Z93 in Iranic peoples, but no Indian ancestry in these groups.

As I said, ancient DNA will clarify lots of things. I expect that to happen in the next few years.

India = Nigeria + Italy in terms of fertility


The map above shows the most recent district level fertility rates in India. It is immediately clear why comparing India to Pakistan and Bangladesh (let alone Nepal, Sri Lanka, or Bhutan) is a major error.

In some of the northern regions of the Hindi-speaking “cow belt” as well as the lightly populated Northeast the total fertility rate is similar to what you find in Nigeria, between 5 and 6 children per woman. For comparison the TFR for Saudi Arabia is 2.75. For Bangladesh it is 2.20 and for Pakistan it is 3.6. In contrast, much of the South, Punjab, and West Bengal have below replacement fertility.

Here is 2017 data by state:

State/UT Fertility rate 2017
Sikkim 1.2
Andaman & Nicobar 1.5
Chandigarh 1.6
Kerala 1.6
Punjab 1.6
Puduchery 1.7
Goa 1.7
Daman & Diu 1.7
Tripura 1.7
Delhi 1.7
Tamil Nadu 1.7
Karnataka 1.8
Andhra Pradesh 1.8
Lakshadweep 1.8
West Bengal 1.8
Telangana 1.8
Maharashtra 1.9
Himachal Pradesh 1.9
Gujarat 2
Jammu and Kashmir 2
Arunachal Pradesh 2.1
Haryana 2.1
Uttarakhand 2.1
Odisha 2.1
Chhattisgarh 2.2
Assam 2.2
 India 2.2
Mizoram 2.3
Dadra Nagar Haveli 2.3
Madhya Pradesh 2.3
Rajasthan 2.4
Manipur 2.6
Jharkhand 2.6
Uttar Pradesh 2.7
Nagaland 2.7
Meghalaya 3
Bihar 3.4

The issue is how you experience Islam

Sadiq Khan: This sickening act has nothing to do with the Islam I know: To murder innocent people, especially during Ramadan, is a rejection of the true values of my religion. Since religion is made up I’ll take Khan’s assertion at face value and not dispute them.

The aspect that people like Khan are not emphasizing when they talk about violence having nothing to do with Islam is that most people are not Muslims, and most people (in the West) do not know Muslims in their personal life. So terrorist acts are quite salient as a representation of the religion when that’s the only time it comes to mind in a visceral sense.

This may not be fair to practitioners, but this is how human cognition works. As an analogy, there is a lot of diversity and range of experience for what it means to be an evangelical white Protestant. But for many young secular liberals the salient aspect of this religious movement is its attitude toward abortion and gays. All the charitable giving, or the incredible personal experience of redemption and reform of white evangelical Protestants, is not relevant in a broader social context to most people because these are two policy positions which are salient and distinctive.

Obviously for most Muslims their religion pervades their life, and most of their associations with the religion have to do with family and community. But non-Muslims are not generally part of this world, so it is not a major element of their perception of the religion in a concrete sense. So one strategy for disassociating Islam and violence would be further integration, so that more and more non-Muslims can experience the whole range of the religion. And yet even here it isn’t as if Muslim experiences are distinctive from other religions.

This does not address the elephant in room: Islam today as a religious civilization is in ferment and change, and a non-trivial element does engage in violent habitually, against other Muslims as well as non-Muslims.

Consider the lives of Hindus and Christians in Pakistan. The majority of Pakistanis would not condone attacks upon these communities, but a motivated minority of the Muslim majority are clearly targeting this two groups for persecution. From the perspective of non-Muslims in Pakistan it is the actions of the minority who are violent toward them that really matters, because their lives are on the line.

There are so simple answers here. Though in the public realm stylized simplicity dominates. That too is a human cognitive bias….

A reply to a stupid, ignorant, or malicious commenter

A commenter below who probably scores OK on an IQ test left a note which is worth responding to.

First, “If this was a Christian or Muslim emigrant to US who wanted to marry within religion.” In the original post I focused on marrying within subcaste for a reason. It’s generally socially acceptable to marry within religion for ideological reasons in American society. I’m not talking about within-religion marriage because that’s considerably more exogamous than what Ravi Patel was talking about. So the whole thrust of this element of the response either consciously misreads (malicious) what I’m saying, or, does not read in the first place (stupid).

Also, this is Brown Pundits. I think a tendency for Hasidic Jewish sects to in-marry is not optimal for individuals or society…but this is not a blog focused on Judaism.

Next, “Two, you link jati affiliation to hindu-muslim violence.” No I don’t. Please note that I don’t like it when readers engage in “close reading.” Because that’s usually an excuse to impute. I do think that a certain sort of jati-based endogamy is part of a cultural context where communal violence has also emerged. Left-wing Indian American commenters bring up these connections, often obnoxiously in my opinion. But this film was aimed at non-South Asians. So I just wanted to bring up what the obnoxious Indian Lefty would bring up just so that the contrast between Ravi’s liberal West LA lifestyle with a very regressive set of values even in the modern Indian middle class milieu would be more stark (it actually makes the documentary more powerful).

Finally:

Finally, on Nicholas Dirks, he like others notices the standard story of jatis classifying into 4 varnas is not correct. He mentions local accounts which are very different. But this was noticed by colonial anthropologists in the 19th century itself. See quote by CF Margath on Page 39 here, https://www.academia.edu/25376339/The_Impossibility_of_Refuting_or_Confirming_the_Arguments_about_the_Caste_System ,

But instead of noticing that the current theory is wrong, and doesnt correspond to the phenomena on the ground, they come with notions like ‘Hinduism’ and ‘caste-system’ where constructed in the colonial era. The fact that many Indians repeat these ideas can be used to support that they were constructed in the 19th century. But mostly, this talk is incoherent. Most people are not able to name 4 varnas and are dimly aware of groups beyond their local region, but would repeat textbook, newspaper accounts which in turn is based on 19th century scholarship.

I read the Dirks’ book about 15 years ago. It is a good and persuasive book, and certainly many aspects are true. But the last 15 years of genetics and genomics has confirmed in fact that broadly speaking varna maps onto real patterns which are at least 2,000 years ago. That is, genetic affinities and relatedness exist on a spectrum that maps very well onto varna spectrum, beyond Brahmins and Dalits.

Priya Moorjani’s paper Genetic Evidence for Recent Population Mixture in India is probably the best single recent summary. Though please see The promise of disease gene discovery in South Asia.

Dirks’ work, and others who emphasize constructionism, capture elements of the truth (e.g., Bengali Kayastha genetic profiles [my maternal grandfather’s family background for what it’s worth] seem a lot like other non-Brahmin Bengalis I’ve seen, so the recent “elevation” of this caste is plausible). But taking it to heart totally misleads people have the depth and nature of caste and jati in the South Asian context.

If you’re not a geneticist you’ll probably not understand the papers above, which is fine. But don’t expect your ignorant comments to be posted on my threads.

Stupidity and ignorance are obviously forgivable sins. The latter is even fixable. But misreadings with the aim of bolstering a rhetorical position are really unforgivable, because they’re a waste of everyone’s time.

Note: I should add that other contributors are more liberal than I am. So I will try not to ban people, though I may just delete comments a lot if I think they fall into one of the three above categories.

Romanticizing the regressive

A few months ago I happened to watch the film Meet the Patels. Though you do meet all the “Patels”, the film centers around the love life, or lack thereof, of the actor Ravi Patel.

Filmed by his sister, the documentary predates Patel’s current modest fame by many years (he has a small recurring role in Aziz Ansari’s Master of None). As his life has changed in many ways, perhaps his views and outlook have too. The comments I’m making in this post are not about Ravi Patel, but rather about the views he expressed many years ago in this documentary at a particular point in his life, and how it reflects a thread of South Asian American nostalgia and romanticism of our cultural roots.

Like many young Indian Americans Patel and his sister grew up between worlds. Their parents arrived in the United States among the very first wave of Indian immigrants, which today makes them somewhat unique, as there has been a huge migration since the 1990s from India due to the H-1B visa program. At one point the matriarch of the small American Patel clan bemoans how Americanized her children are compared to many other Indian Americans, who arrived later, when various South Asian American communities were more mature.

But Ravi and his sister are not entirely Americanized. Or they weren’t. Both avoided the conventional dating rituals of American life deep into their 20s, and as of filming Meet the Patels Ravi had had only one girlfriend, Audrey. Attractive, and depicted as level-headed and kind, on paper Audrey seems to have been the perfect girlfriend. But there was a major problem with her biodata: Audrey is a white American.

Eventually Ravi broke up with Audrey because of his confusions as to what he wanted in his life, and whether she belonged in it. Did he want what all his friends had? The American dream of love and marriage. Or, did he want what his parents had? An Indian arranged marriage with commonalities of culture.

But there is more to the Patels than just an Indian arranged marriage. Ravi Patel’s parents want him to marry someone from the same subcaste of Patels from the region of Gujarat that they come from. This is entirely typical of Indian culture. But it is rather peculiar in an American context. Though in some ways Ravi finds this all strange, some part of him also entertains the idea that his parents have a mutual comfort, a cultural identity, which he envies. At one point he goes back to Gujarat to a celebration of his people, his subcaste of Patels, and he looks around at wonderment at the safety and security of being among his his kith and kin. A sense of belong clearly has come over him.

As far back as Herodotus Indian society seems to have been characterized by caste. Genetically the castes, and more precisely jatis, are very distinct. And their persistence on the Indian scene suggest some level of functional utility.

Realistically Ravi could never recreate what he felt in Gujarat in the United States because such a community does not truly exist. Yes, there is kinship among Patels, as recounted by stories about Ravi and his family on the road, staying at Indian owned motels. But in the United States the Patels are a Diaspora, an archipelago of families scattered across the 50 states.

The romantic notions that Ravi airs in Meet the Patels about group solidarity, and cultural affinity of the sort his parents have, would seem creepy and disturbing if you posited it in the context of an upper middle class WASP from New England. But the strong group cohesion evident among the Patels of Gujarat, and many Indian communities, also generates as a byproduct the sort of exclusion illustrated in the 1970 film Love Story.

And the exclusionary tendencies of middle class Gujaratis is reflected in part on the social-political nature of the state of Gujarat. It is in this state that the current prime minister of India, a tribune of lower middle class Hindu nationalism, grew up, and originally came to power and prominence. It is in this state in the early 2000s that communal riots occurred, and accusations of organized genocide against Muslims have been leveled.

The connections between liberal Democratic Indian Americans and right-wing Hindu nationalism in India have been extensively discussed. That is not what I am getting at. Meet the Patels is not a political film, it is a personal one. There is no reason that Ravi should address political topics in the documentary, and much of what I am saying here would be implicit to any South Asian watching Meet the Patels. But to many Americans these darker realities would not be visible or implied in the cultural practices which Ravi admires.

The attitudes expressed in Meet the Patels is no different from pining for the “good old days.” The reality is that the old days were often not so good. Or they weren’t how you remembered them. And just as some people pine for the days of yore, others romanticize the “homeland”, where everyone was your uncle, and the aunties took care of you when your mother was a way. But this world is in many ways fundamentally regressive and constrained, and the benefits of communal responsibility are often correlated with inter-communal tension and conflict.

Again, there is no reason that Meet the Patels should have gone into this. But I wanted to put into the record what was unsaid so that those who see in it purely a charming inter-cultural story comprehend the other dilemmas latent within the narrative.

Related: Ravi’s AMA.