Tag: Genetics

Someone in the comments posted the results from The Genomic Formation of South and Central Asia. I put the percentages with a few ratios in a Google doc. I don’t know what a lot of these groups are. Can readers illuminate? We need to be careful about the sample size, but I think there are a lot of interesting patterns in there.

Remember that “Steppe”, “Indus Periphery” and “Onge” are populations artifacts within a model. The way I explain it to people is that rather than focusing on the percentage, look at how the populations vary across the parameters. That is a pretty robust result. No matter what outgroups you’re going to use, Brahmins in most of South Asia seem to have more “West Eurasian” type ancestry than other populations (except in the NW). Because “Indus Periphery” has a minority of “Ancient Ancestral South Indians” (AASI) as part of its ancestry, the “Onge” fraction should be seen as a floor on AASI ancestry (the Onge ancestors diverged from the AASI ~40,000 years ago, so it’s a very large difference).

Continue reading “Genetic variation across many South Asian communities”

The above figure shows the frequencies of Y chromosomal haplogroups of men of South Asian who claim to be descended from the prophet or his tribe, as cross-referend with their surnames. The “Non-IHL” category indicates those who are not of these honored lineages.

The paper from which I drew the data, Y chromosomes of self-identified Syeds from the Indian subcontinent show evidence of elevated Arab ancestry but not of a recent common patrilineal origin, actually somewhat support the idea that these people descend from Muhammad or the Quraysh or the Ansar.

I think this is wrong.

But first, why do think these data results show Arab affinity? The “IHL” lineages have a higher proportion of haplogroup J, the most common haplogroup among Arabs. J is not exactly rare in South Asia (lots of <<<Brahmins>>> who are not sons of Indra have it because they are the scions of cunning Dasa priests), but there’s clearly a frequency discrepancy.

And yet this paper was published in 2010. We now know through various tests of confirmed descendants of Muhammad, and who descend in the male line from his cousin Ali, that they carry a branch of haplogroup J1.

Even among the Syeds, most do not descend from Muhammad assuredly. There are nearly as many scions of Lord Indra, R1a1, as those who bear haplogroup J. Of the J’s within the Syed community, I think the most likely scenario if they are not South Asia is that they are Iranian. J is found at frequencies of 35% in Iran, and Iranians, along with Turks, were the most common migrants into South Asia.

In other words, the Syeds of the Indian subcontinent are the sons of magians, not Muhammad.

Unless you have been sleeping under a rock, a mildly slanderous piece in The New York Times Magazine has taken aim at David Reich and his band of paleogeneticists, Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps? I address this piece at my other weblog.

One of the major themes of the piece are the legends and myths of the people of Vanuatu:

I asked him about how the concept of Lapita migration to empty islands had been received by people whose oral traditions said they came from a stone or a coconut tree.

The reason this is relevant is that paleogeneticists have probed the history of Vanuatu. And yet this is the past. The future is that the Reich lab is collaborating with other paleogeneticists to crack the nut of the history of the Indian subcontinent with ancient DNA. They’ve been working on this for years, and they are working on it now. There are 275,000 people who live in Vanuatu. There are 1.7 billion people who live in the Indian subcontinent.

Within the next year I believe that the Reich lab will publish results which will falsify the beliefs of a substantial number of Indians about the nature of the origins of the native peoples of the region. This will shatter world-views, undermine mythologies, and rock peoples’ worlds. There will be sophists who live in denial, but the truth will be plain to those who see.

I understand that some of you reading this disagree with this assessment. Ultimately I don’t care because the data are coming, and if I’m wrong, that’s OK too. I don’t have emotional baggage invested in alternative models. But, I do wonder why the mythological traditions of “non-indigenous” people seem to warrant less attention than smaller nations or premodern tribes.

Look at the R and H frequencies. Peach and violet respectively. Compare to South Asian haplogroup frequencies.

There was a comment below on the positions of Pathans genetically in relation to South Asians and Iranians. The “Pathan” samples are from Pakistan, while “Pashtun” are from Afghanistan. What you can see is that the “Pathan” samples are more like Punjabis, while Pashtuns are like Tajiks. The Iranian samples are from western Iran. You can see that the Pakistani Pathans are definitely a little closer to UP Brahmins than to Iranians. The Afghans are a bit closer to Iranians than UP Brahmins.

Here’s Treemix:

Continue reading “Pathans between Hind and Iran”

A new paper, The Genetic Ancestry of Modern Indus Valley Populations from Northwest India.

As some of you know I co-host a podcast on genetics and history with Spencer Wells. The very first podcast we recorded in late June of 2017 was about India, but we were still getting the hang of it to be honest, and we didn’t cover much territory.

A lot has happened between then and now, and so it’s time for an “update,” which is going to cover many more topics. That being said, we haven’t recorded yet and so I’m open to “questions from the audience” that we might integrate. So please use this post to leave comments about specific topics…. (please note we have only ~1 hour or so so might not get to everything)

Update: Podcast recorded.

At ASHG next Monday Niraj Rai will be presenting this poster, Reconstructing the peopling of old world south Asia: From modern to ancient genomes.

South Asia was one of the first geographic regions to be peopled by modern humans after their African exodus. Today, the diverse ethnic groups of South Asia comprise an array of tribes, castes, and religious groups, who are largely endogamous and have hence developed complex, multi-layered genetic differentiation. From such a complex structure, several questions have stood out from the research of our group and others that are only beginning to be resolved using modern sequencing techniques and targeted sampling of populations and archaeological specimens. Here, for the first time we have used ancient genomics approach to understand the deep population ancestry of Indian Sub- continent. Despite the rich sources available of modern Indian populations, success from ancient DNA specimens in the subcontinent have been limited. We have successfully analysed several museum samples and fresh excavation from the different part of India which provides us a wonderful opportunity to be able to relate these modern populations genetically with those in the past and build complex models of population mixture and migration in India. Using ancient genomics data from the human remains who have lived about 4-5 thousand years before present in North West and South of India, we are trying to understand the population history of Iron age people and their genetic relation with the North West of Indians and Iranian Farmers. Furthermore, we are providing a solid Genetic evidence that substantiates archaeological and linguistic evidence for the origins of Dravidian languages and the language of the Indus valley people.

I’ll probably be trying to make sure I catch Rai at the poster. I’m most interested in the South Indian samples. If they date to more than 4,000 years before the present, it will be quite interesting.

Below the fold is my response to a comment on The Roots of Indo-Iranian cultural genesis. My response is in bold. JR’s responses to my original comment are in italics.

Continue reading “Ancient Indian Genetics At ASHG”

There are lots of strange takes on the India Today piece, 4500-year-old DNA from Rakhigarhi reveals evidence that will unsettle Hindutva nationalists. I’m friendly with the author and saw an early draft. So I’m going to address a few things.

The genetic results are becoming more and more clear. A scaffold is building and becoming very firm. In the 2020s there will be a lot of medical genomics in India. But before that, there will be population genetics. Ancient DNA will be the cherry on the cake.

Here’s what genetics tells us. First, a component of South Asian ancestry, especially in North India, and especially in North Indian upper caste groups, seems to be the same as ancient agro-pastoralists who ranged between modern Ukraine and modern Tajikistan. Genetically, these people are very similar to certain peoples of Central and Eastern Europe of this time, though there is a varied dynamic of uptake of local Central Eurasian elements as they ranged eastward.

This ancestral component is often called “steppe.” This ancestral component is a synthesis of ancient European hunter-gatherer, Siberian, and West Asian. The steppe component seems to arrive in Central and South Asia after 2000 BC.

Second, another component of South Asian ancestry is very distinctive to the region. It is deeply but distantly related to branches of humanity which dominate Melanesia and eastern Eurasia, up into Siberia. The magnitude of the distance probably dates to ~50 thousand years ago, when the dominant element of modern humans expanded outward from West Asia, east, north, and west. These people are called “Ancient Ancestral South Indians,” or AASI. Their closest relatives today may be the natives of the Andaman Islands, but this is a very distant relationship.

AASI is the dominant component of what was once called “Ancestral South Indians,” or ASI. It turns out that “ASI” themselves were a compound synthetic population. This was long suspected by many (e.g., David W.). What was ASI a compound of? About ~75 percent of its ancestry was AASI, but the balance seems to have been a West Eurasian component related to farmers from western Iran. We can call this group “farmers.”

With a few samples from outside of the IVC region, and one (or two) samples from within the IVC region, geneticists are converging upon the likelihood that the profile in the greater IVC region before 2000 BC was a compound of these farmers with the AASI. But even within the IVC region, there seems to have been a range of variation in ancestry. The IVC was a huge zone. It may not have been dominated by a single ethnolinguistic group (even today there is the Burusho linguistic isolate in northern Pakistan). Note that the much smaller Mesopotamian civilization was multiethnic, with a  non-Semitic south and a Semitic north (Sumer and Akkad).

The key point is that it is very likely the IVC lacked the steppe ancestral component. That it did have AASI component. And, it did have a farmer component with likely ultimate provenance in western Iran. Additionally, there were smaller components derived from pre-steppe Central Eurasian people.

While the steppe people arrived in the last 4,000 years, and at least some of the ancestors of the AASI are likely to have been in South Asia for 40,000 years, the presence of the AASI-farmer synthesis genetically is conditional on when a massive presence of western farmers came to affect the northwestern quarter of South Asia. It seems unlikely to have been before Mehrgarh was settled 8,500 years ago. The genetic inferences to estimate the time of admixture between AASI and farmer are currently imprecise, but it seems likely to have begun at least a few thousand years before 2000 BC.  range of 8,500 and 6,000 years ago seems reasonable.

So 4,000 years ago the expanse of the IVC was dominated by a variable mix of farmer and AASI. One can call this “Indus Valley Indian” (IVI).

Just like ASI, there was an earlier abstract construct, “Ancestral North Indian” (ANI). Today it seems that that too was a compound. To be concise, ANI is a synthesis of steppe with IVI. The Kalash of northern Pakistan are very close genetically to ANI. This means that while ASI had West Eurasian ancestry, albeit to a minor extent. And ANI had AASI ancestry, albeit to a minor extent. The main qualitative difference is that ANI had a substantial minority of steppe ancestry.

To a great extent, the algebra of genetic composition across South Asia can be thought of as modulating these three components, farmer, steppe, and AASI.* Consider:

• Bhumihar people in Bihar tend to have more steppe than typical, but not more farmer than typical, and average amounts of AASI.
• Sindhi people in Pakistan tend to have lots of farmer, some steppe, and not much AASI.
• Reddy people in South India have lots of farmer, very little steppe, and average amounts of AASI.
• Kallar people in South India have some farmer, very little steppe, and lots of AASI.

For details of where I’m getting this, you can look at The Genomic Formation of South and Central Asia for quantities. But as a stylized fact farmer ancestry tends to peak around the Sindh. In Pakistan steppe ancestry increases as you go north. As you go east and south AASI increases pretty steadily, but there are groups further east, such as Jatts and Brahmins, who have a lot of steppe, almost as much as northern Pakistani groups. And curiously you get a pattern where some groups have more steppe and AASI, and less farmer, than is the case to the west (you see this in the Swat valley transect, as steppe & AASI increase in concert).

Going back to the history, by the time the steppe people arrived in South Asia, in the period between 2000 BC and 1000 BC, it may be that the IVI ancestry is what they mixed with predominantly. Though it is likely that the southern and eastern peripheries had “pure” AASI, by the time steppe people spread their culture to these fringes they were already thoroughly mixed with IVI populations, and so already had some AASI ancestry.

In contrast, the farmer populations likely mixed extensively with AASI in situations where the two populations were initially quite distinct.

Please note I have not used the words “Aryan” or “Dravidian.” The reason is that these are modern ethnolinguistic terms. Genetics is arriving at certain truths about population changes and connections, but we don’t have a time machine to go back to the past and determine what language people were speaking 4,000 years ago.

Our inferences rest on supposition, and a shaky synthesis of historical linguistics and archaeology and genetic demography, a synthesis which is unlikely to ever be brought together in one person due to vast chasm of disciplinary method and means.

It is highly likely that the steppe component is associated with Indo-European speaking peoples. Probably Indo-Aryan speaking peoples. The reason is that by historical time, the period after 1000 BC, Iran and Turan seem to already have been dominated by Indo-Iranian peoples. But, in the period around 2000 BC, western Iran was not Indo-Iranian. People like the Guti and the Elamites were not Indo-European, and they were not Semitic. We have some genetic transects which show that steppe ancestry did arrive in parts of Turan and Iran in the period after 2000 BC.

Where did the Dravidian languages come from? We don’t know. They could have been spoken by an AASI group. Or, they could be associated with farmers from the west. We don’t know. Ultimately, we may never know. Unlike Indo-European languages, there are no Dravidian languages outside of South Asia.

Various toponymic evidence indicates that Dravidian languages were spoken at least as far north and west as Gujurat. And Brahui exists today in Balochistan. Though I don’t have strong opinions, I think Dravidian languages probably are descended from a group of extinct languages that were present in Neolithic Iran.

Though unlike Indo-Aryan languages, Dravidian exploded onto the scene after a long period of incubation within South Asia, as part of at least one of the language groups dominant with the IVC and pre-IVC societies.

At least that’s my general assessment. I have strong opinions about the genetics. But am much more curious about what others have to say about linguistics and archaeology.

* Some groups, such as Munda and Indo-Aryan groups in Northeast India, have East Asian ancestry. Some groups in coastal Pakistan have African ancestry.