Eastern Y Chromosomes in the Indian subcontinent

Looking at the Y chromosomes in the Indian subcontinent, it seems that haplogroups C (found in lots of Patels) and F are the only ones with “eastern” affinity that deeply rooted in the subcontinent. Thoughts? H is found in a lot of Adivasi, but seems more related to West Eurasian populations.

This is on my mind because the Uralic populations show the strong male-based spread of eastern Y chromosomes. Finns are 60% eastern on the Y and less than 1% on the mtDNA.

How much steppe is there in Pakistan?

In the annoying dick-swinging competition that are the comments-board, someone asserted Pakistanis have a lot of steppe even on the maternal side. Really?

We have Sintashta mtDNA and the discordance was shocking to me. But there are some groups in Pakistan with detectable Sintashta mtDNA. These samples from Hazara, Kho, Pashtun, Kashmiri,and Kalash. They identify 8.4% steppe mtDNA. Pakistan as a whole has a lot more “West Eurasian” mtDNA, but that’s obviously due to the legacy of the IVC. Anyway, Complete mitogenomes document substantial genetic contribution from the Eurasian Steppe into northern Pakistani Indo-Iranian speakers:

In summary, based on available archeological and high-resolution mitogenome data from northwestern Pakistan, especially from Iranian and Dardic populations, who are suggested to be the surviving traces of early Indo-Iranian groups, we identified the genetic contributions of different dispersals from west Eurasia into northern Pakistan during the Bronze Age onward. Importantly, we identified five haplogroups as the genetic legacy of IE speakers from the Eurasian Steppe, likely dispersed along with the migration of IE-speaking populations during the Bronze Age into northern Pakistan, thus implying that IE language expansion into South Asia was not simply mediated by cultural diffusion. This migration contributed 8.4% of the gene pool of northern Pakistani IE speakers, suggesting this demographic connection, which is a possible source of IE language diffusion, could be one part of the complex demographic history of the region. Our results also provide implications on the two main hypotheses of IE language origination, viz. Anatolia and Steppe hypotheses. Considering that Steppe components were observed in all Indo-Iranian groups in northern Pakistan in our study, as well as in other regions in South Asia [10], while lineages possibly representing the genetic legacy of Neolithic farmers, e.g., R2e, K1, were either absent or not found in all of the IE-speaking groups in northern Pakistan, our results lend more support to the Steppe hypothesis, at least from a matrilineal perspective. Furthermore, these IE speakers, as evidenced by the genetic legacy identified here, also moved southward and contributed genetically, though to a rather limited extent, to the Indian subcontinent, suggesting northern Pakistan as a corridor in the spread of IE languages during the Bronze Age dispersals into South Asia. Since our study is only based on mtDNA data, which only reflect maternal histories of populations, more investigations based on genome-wide data are also needed to intensively dissect the expansion of IE speakers into South Asia.

Steppe lineages in northern Pakisan

This is not the most important paper, but it is a contribution: Complete mitogenomes document substantial genetic contribution from the Eurasian Steppe into northern Pakistani Indo-Iranian speakers. Abstract:

To elucidate whether Bronze Age population dispersals from the Eurasian Steppe to South Asia contributed to the gene pool of Indo-Iranian-speaking groups, we analyzed 19,568 mitochondrial DNA (mtDNA) sequences from northern Pakistani and surrounding populations, including 213 newly generated mitochondrial genomes (mitogenomes) from Iranian and Dardic groups, both speakers from the ancient Indo-Iranian branch in northern Pakistan. Our results showed that 23% of mtDNA lineages with west Eurasian origin arose in situ in northern Pakistan since ~5000 years ago (kya), a time depth very close to the documented Indo-European dispersals into South Asia during the Bronze Age. Together with ancient mitogenomes from western Eurasia since the Neolithic, we identified five haplogroups (~8.4% of maternal gene pool) with roots in the Steppe region and subbranches arising (age ~5–2 kya old) in northern Pakistan as genetic legacies of Indo-Iranian speakers. Some of these haplogroups, such as W3a1b that have been found in the ancient samples from the late Bronze Age to the Iron Age period individuals of Swat Valley northern Pakistan, even have sub-lineages (age ~4 kya old) in the southern subcontinent, consistent with the southward spread of Indo-Iranian languages. By showing that substantial genetic components of Indo-Iranian speakers in northern Pakistan can be traced to Bronze Age in the Steppe region, our study suggests a demographic link with the spread of Indo-Iranian languages, and further highlights the corridor role of northern Pakistan in the southward dispersal of Indo-Iranian-speaking groups.

Don’t focus on the percentages too much. Rather, focus on the coalescence estimate. Basically, that indicates diversification and demographic expansion. The presence in the southern subcontinent is indicative of the fact that “steppe” ancestry and cultural influence extends far beyond the distribution of modern Indo-Aryan languages. R1a we know, as it is found in adivasis. And low fractions of steppe are found in most South Indian groups (but not all).

The Genetics of India Cloubhouse Event – Friday 9 PM CDT

I am hosting a Clubhouse room this Friday, 9 PM CDT (8:30 AM in India on Saturday). The topic will be the genetics of India, and I’ll be talking about my two posts on Substack:

The Stark Truth About Aryans

The Stark Truth About Humans

It’s basically going to be an interactive discussion. My friend David Mittelman will help me moderate (probably others too).

You have to have a Clubhouse account (iPhone only). If you want to follow me on Clubhouse, I’m @razibkhan just like on Twitter.

Why Scythians, Sakas, and Kushanas, are NOT the source of “steppe” ancestry

This is a common question/assertion in the comments pretty much every other week: why couldn’t the documented incursions of nomadic people in the first millennium A.D. be responsible for the steppe ancestry? There is actually a good explanation in The formation of human populations in South and Central Asia, so I’ll quote it:

By the Late Bronze Age, ESHG-related admixture became ubiquitous, as documented by our time transect from Kazakhstan
and ancient DNA data from the Iron Age and from later periods in Turan and the Central Steppe, including Scythians, Sarmatians, Kushans, and Huns (29, 52). Thus, these first millennium BCE to first millennium CE archaeological cultures with documented cultural and political impacts on South Asia cannot be important sources for the Steppe pastoralist–related ancestry widespread in South Asia today (because present-day South Asians have too little East Asian–related ancestry to be consistent with deriving from these groups), providing an example of how genetic data can rule out scenarios that are plausible on the basis of the archaeological and historical evidence alone (13) (fig. S52). Instead, our analysis shows that the only plausible source for the Steppe ancestry is Steppe Middle to Late Bronze Age groups, who not only fit as a source for South Asia but who we also document as having spread into Turan and mixed with BMAC-related individuals at sites in Kazakhstan in this period. Taken together, these results identify a narrow time window (first half of the second millennium BCE) when the Steppe ancestry that is widespread today in South Asia must have arrived.

There is now a large database of Scythian, etc., ancient DNA, thanks to the preservation conditions on the Eurasian steppe. Most of their ancestry derives from the same broad group as the Andronovo horizon of which the Sintashta were part. But, unlike the earlier steppe populations, these groups are highly variable in ancestry, as well as usually having substantial minority East Asian components. The Indian groups with a lot of steppes, such as Jatts and Northern Brahmins, lack this.

There are two objections. The weaker one is that they didn’t have statistical power to detect the admixture. I haven’t run simulations, but I’m sure they have. If you have Jatts who are perhaps more than 30% steppe they would have detected trace East Asian (as you can find in many Muslim individuals from Pakistan).

The stronger objection is that there is unsampled structure on the steppe, and groups without East Asian admixture that are direct descendants of the Sintashta without dilution. This is not entirely unreasonable or implausible, though at this point I’d say this is unlikely for two reasons:

  1. Central Eurasia is pretty well sampled due to interest and conditions
  2. The steppe ancestry in South Asia is pretty widespread. Hard to imagine it percolating so far in 1,500 years

Also, the statistical tests I’ve done show Bengalis got East Asian admixture 1,500 years ago. 10-20% of the ancestry. The steppe percentage in Bengalis is 10-15%. But I never get any hits using older less sensitive methods of admixture. That means that it has to be way older a mix than 500 AD.

Stark Truth About Aryans: a story of India (part 1)

My Substack piece is up, Stark Truth About Aryans: a story of India. I’m pretty proud of this, as it wasn’t a single-sitting blog post, but something I worked over several times. Since it’s for paid subscribers I’ll post the first few paragraphs below, with an infographic that I think illustrates a lot of what’s going on.

Continue reading “Stark Truth About Aryans: a story of India (part 1)”

Tibeto-Burmans, Munda, and Bengalis


I’m pretty sure I posted this Chaubey lab work as a preprint, but it’s now a published paper. For those who can’t understand the table, it illustrates a big difference between Tibeto-Burmans and Munda. The samples from Bangladesh look to be generic Bangladeshis, the 10% frequency for O2a seems to match the other data I’ve seen for East Bengalis.

This confirms that the East Asian admixture into Bengalis was not Munda. And, the Tibeto-Burmans of the nTibeortheast have no assimilated Munda ancestry. I think it does lend more credence to the idea that the Munda arrived in the Indian subcontinent across the Bay of Bengal, landing in Odisha, rather than from the northeast.

The rise of Indicus!

A few years ago an ancient DNA paper on cattle was published, Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. It’s a pretty good paper with interesting results. The paper confirmed pretty strikingly that there was a punctuated and massive expansion of indicus ancestry across the Near East between 3,500 and 4,000 years ago.

The interesting aspect of cattle is that there are really two species that intermix. Using mtDNA researchers estimate indicus and taurus diverged 300,000 to 2,000,000 years ago. But the main thing you have to remember is cattle generations are about 20% as long as human generations. So 300,000 cattle years are equivalent to 1.5 million human years. And, for technical reasons (smaller effective population size) one should probably assume mtDNA underestimates the divergence.

Ancient cattle from the Near East are all taurus. The PCA plot shows that most of the variance is on PC 1 which separates indicus and taurus (a secondary dimension is PC 2, between African and Near Eastern/European lineages). The figure at the top of this post shows that there is a massive jump in genome-wide indicus ancestry across the Near East between 2000 and 1500 BC. As the authors note this can’t be diffusion; the jump is too sudden and sweeping.

So what happened during this period? As noted in the paper: Bronze Age civilization almost collapsed around ~2000 BC. More concretely, after 2000 BC is when we see evidence of Indo-Europeans in the Near East. The Indo-Aryan Mittani show up in Mesopotamia in ~1600 BC. The Indo-European Hittites, the Nesa, are known from Anatolia a bit earlier.

This is also the period that small, but detectable, levels of “steppe” ancestry show up in some ancient samples.

Before this paper, I would have leaned to the position that the Mittani Indo-Aryans migrated directly from the Sintashta homeland without much contact with Indian Indo-Aryans. These data are too suggestive of a widespread zone of expanding agro-pastoralists that existed between western South Asia and the Near East between 2000 BC and 1500 BC.

One of the things we know from the barbarian period during the Fall of Rome is that barbarian groups had strong channels of information flow. For example, a group of Saxons arrived with the Lombards in Italy in the second half of the 6th century. But, through various channels, these Saxon warriors learned that their co-ethnics had established dominance in what was to become England, and there are texts which allude to the reality that they decamped and crossed the Alps, presumably on the way to what was going to be England. The point here is that there was a “Saxon international.”

Aside from the Mittani the evidence of Indo-Aryans in the Near East is tenuous, though some of the Kassites of Babylonia may have had Indo-European affinities. There is not nearly as strong a genetic imprint of steppe in the Fertile Crescent as in Northwest India. The Hittites were very different from Indo-Aryans, who seem to have the closest relationship to the Slavic language family.

The indicus breed is adapted to tropical dry climates. It seems plausible that the Indo-Aryan international facilitated the spread of this breed in the centuries before 1500 BC.

Population structure in West Bengal and Bangladesh

The Genomes Asia 100K has put their Indian paper out. It’s OK, and mostly focuses on the fact that Indians are enriched for inbreeding vis-a-vis other world populations. There are several layers to this. In some cases, as among South Indian Hindus and Muslims, there is cousin-marriage. But, in other cases, for example, Scheduled Castes and Scheduled Tribes, there seem to be extreme bottleneck effects due to delimited marriage networks. Finally, even among large population groups, such as Iyers, there seems to be some elevation of runs of homozygosity due to endogamy.

But that’s really not what I’m interested in. This preprint has a lot of Bengalis from Birbhum district in West Bengal of various castes. The UMAP (an advance over PCA in some ways) figures aren’t super informative, but you can see that their pooled sample recapitulates the Indian subcontinent. In fact, West Bengals on the whole are to the “west” of Bangladesh samples. Totally unsurprisingly.

The main reason I’m putting this post up is the UMAP plot below. It’s hard to read (they will clean it up for final publication), and I don’t know all the castes (I’m assuming “Nabasudra” is a typo). But some things that jump out

1) Bengali Brahmins are distinct.

2) Kayastha are generic West Bengalis.

3) Some of the West Bengal samples are in the Bangladesh (collected from Dhaka) distribution. These are probably descendants of Bangal migrants from the east.

4) Some groups are very distinct. That’s partly due to strong endogamy, and in the case of Santhals high East Asian ancestry (they’re Munda). Other groups are less distinct. The “Namasudra” seem to be two groups. One overlaps with the main Bengali cluster (slight bias toward Bangladeshis), while a second group is shifted toward Scheduled Castes.

I assume readers can make more heads or tails of this, as I don’t know much about caste in West Bengal (and yes, the figure is very badly labeled/colored; this is a preprint)

Addendum: Not comments about Jatts please. I will delete them.

Ancient Pakistanis were Hindu

Over at my other blog, Pakistani British Are Very Much Like Indians Genetically. The title doesn’t refer to genome-wide worldwide affinities. Rather, the preprint looks at British Pakistanis, and finds a pattern that is not going to surprise Indians: endogamy seems to have kicked in for these groups starting 1,500 to 2,000 years ago. This is exactly what you see in the Indian jati data. The similarity is pretty incredible, and to me is a strong rejection of the model that these groups were strongly anti-caste so on the margins of Indic civilization.

There is a second wave of endogamy though, dated from 150-500 years ago, roughly. I think this is likely Islamicization and adherence to cousin-marriage. These Pakistani groups seem to show the tendency of jati endogamy common among Hindus, and, cousin-marriage patterns of the Islamic world.

Finally, the reason I posted over on the other blog is that I think this might speak to the long-term trajectories of Bangladesh and Pakistan: Bangladesh is not in the same mold as Indo-Pak societies. The 1000 Genomes data indicate few runs of homozygosity and not much internal structure. That is, no jati endogamy, and, low levels of cousin-marriage.

If you believe Joe Henrich, this means good things for Bangladesh in the future… (vs. Pakistan)

(the Henrich podcast is already available for Patrons)