Razib Khan One-stop-shopping for all of my content

June 27, 2018

South Asian Genotype Project, Summer 2018 Update

Filed under: India Genetics,India genomics,South Asian Genotype Project — Razib Khan @ 12:54 am


I’ve put another update on the South Asian Genotype Project. If you’ve contributed since March check it out.

Again, if you are interested: send me a 23andMe, Ancestry, MyHeritage, Family Tree DNA raw genotype file to contactgnxp -at- gmail.com.

In the subject please put:

  1. “South Asian Genotype Project”
  2. The state/province your family is from
  3. Ethnolinguistic group
  4. If applicable, caste

I decided to some poking around with some of the higher quality samples people have given me. 180,000 SNPs with almost no genotyping error. I also removed “relatives.” That means that a lot of Muslim groups from Pakistan had individuals dropping out. In the PCA above you can see 4 Burushos left! Not too many Pathans either.

Click to enlarge!

First, I decided to look at the Brahmin samples I had.

– Uttar Pradesh, Bihar, and the Gujarati Brahmin(s) I had are one cluster
– South Indian Brahmins (mostly Iyer) are another

To my surprise, the two Maharashtra Brahmins that I have are firmly in the South Indian cluster. The Bengali Brahmin is more like the North Indians. But there is a subtle skew toward the distant Bangladesh cluster. This individual seems less East Asian than even the typical Bengali Brahmin, but I think Bengali Brahmins can be modeled as North Indian Brahmin with non-Brahmin (and therefore East Asian) ancestry.

Click to enlarge!

Next, I wanted to look at Gujaratis. The 1000 Genomes has a large number of this population…but there’s not group identity. Years ago Zack Ajmal of Harappa DNA concluded that a large and relatively related cluster in these data were “Patels.” Someone who is a Bohra Muslim of presumably Patel background sent me their data. They did not fall in the Patel cluster. Rather, they were in the “Gujurati_ANI_1” group, which is more like Pakistanis than other Gujuratis. In fact, the Gujurati Brahmin is not in this cluster. An individual whos Solanki seems to be more ASI-shifted, like the Patels and Gujurati_ANI_4.

Overall, Gujarat has a lot of population structure in a rather small state (yes, I can’t spell Gujarat as you can see in my population labels).

Click to enlarge!

From Maharashtra, right to the south of Gujarat in western India, I have two Brahmins and one Kayastha. For non-South Asians, my understanding is that Kayasthas are literate non-Brahmin castes. In Bengal, they take the places of the Kshatriya in the caste hierarchy, and with Brahmins formed the traditional Hindu educated classes. I have seen Bengali Kayastha genotypes, and they look rather like other Bengalis (my mother’s father’s family is from a Kayastha family before their conversion to Islam judging from their customary surname).

There are Kayasthas in other parts of South Asia. I have a Kayastha sample from Maharashtra. Curiously on the PCA this individual is in the same position as the two Brahmins from the region, and South Indian Brahmins. I don’t know what this means.

Click to enlarge!

Next some odds and ends from the northwest of the subcontinent. I have a few Jatts who are not related. This group from Punjab is quite ANI-shifted. Someone who claims to be a Rajput from Rajasthan is where they should be on account of geography. The Punjabi 1000 Genome group is quite diverse. I have a Ramgarhia individual who seems to be somewhere between Punjabi_ANI_1 and Punjabi_ANI_2. The Jatt are on the edge (ANI-shifted) of Punjabi_ANI_1.

I have two individuals who claim to be Kashmiri. A Butt and a Syed. I have no idea what that means. But both are Punjabi_ANI_2…but they look somewhat East Asian shifted. This is not surprising. The curious thing about Kashmiris is that they are culturally and geographically quite distinct from Indians to their south. But genetically they are not so different. In fact, they are “more South Asian” (ASI) than Jatt, and considerably more than Iranian speaking groups like Pathans.

Finally, there is a Marwari individual. This community is from Rajasthan, though they occupy a mercantile role across the subcontinent. Strangely (or not?) they are very close to the Patels. Much more ASI-enriched than the Rajput.

Click to enlarge!

Shifting to South Indian samples, I plotted the Chamar samples, who I believe were collected from Uttar Pradesh in the north. These Dalits actually seem to cluster with a subset of the 1000 Genomes Tamil and Telugu samples I believe are Scheduled Caste (Dalit) as well. The Chamar are somewhat distinct. They are more ANI-shifted. But notice that the bulk of Tamils and Telugus are still more ANI-shifted than the Chamars are! This surprised me.

I have some Velama individuals, as well as a Reddy from Andhra Pradesh and a Padmashali. All these individuals are in the main distribution of South Indians. I do have a Mudaliar Tamil sample, and this individual is placed among the Chamars. Though not really in the Tamil Scheduled Caste group.

Click to enlarge!

Finally some odds & ends. The Nasrani samples from Kerala are between the South Indian Brahmins and middle caste South Indians. I suspect this is due to the origin of the Nasranis in the Nair community, who have mixed some with Brahmins. The Vania sample from Gujarat is clustered with South Indian Brahmins. The Dusadhs, an agricultural group from Uttar Pradesh and Bihar, that is depressed in some manner in relation to the dominant groups, are not quite Chamars, but they are quite ASI-shifted.

Some of you will be asking about admixture. I ran K = 4 unsupervised on the data set. You can find it here.

April 27, 2018

Rakhigarhi sample doesn’t have steppe ancestry (probably “Indus Periphery”)

Filed under: India Genetics,India genomics,Rakhigarhi — Razib Khan @ 12:02 am

We’ve been waiting for two years now, and it looks like they’re about to pull the trigger, Indus Valley People Did Not Have Genetic Contribution From The Steppes: Head Of Ancient DNA Lab Testing Rakhigarhi Samples:

Niraj Rai, the head of the Ancient DNA Laboratory at Lucknow’s Birbal Sahni Institute of Palaeosciences (BSIP), where the DNA samples from the Harappan site of Rakhigarhi in Haryana are being analysed, has revealed that a forthcoming paper on the work will show that there is no steppe contribution to the DNA of the Harappan people….

“It will show that there is no steppe contribution to the Indus Valley DNA,” Rai said. “The Indus Valley people were indigenous, but in the sense that their DNA had contributions from near eastern Iranian farmers mixed with the Indian hunter-gatherer DNA, that is still reflected in the DNA of the people of the Andaman islands.” He added that the paper based on the examination of the Rakhigarhi samples would soon be published on bioRxiv (pronounced “bio-archive”), a preprint repository of papers in the life sciences.

At this point none of this is surprising. I also wonder if this preprint was hastened by the release of The Genomic Formation of South and Central Asia. It seems that the results here are totally consonant with what came before. My expectation is that the lone sample that they got genetic material out of will be similar to the “Indus Periphery” (InPe) individuals in the earlier preprint: a mix of West Asian with ancestry strongly shifted toward eastern Iran, and indigenous South Asian “hunter-gatherer.”  That’s pretty much what Niraj Rai states in the piece. I think genetically the individual won’t be that different from the Chamars of modern day Punjab.

In fact, Rai, the lead researcher, ends by twisting the knife:

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.”

A major caveat here is that we’re talking about one sample from the eastern edge of the Indus Valley Civilization (IVC). I’m not sure that this should adjust our probabilities that much. From all the other things we know, as well as copious ancient DNA from Central Asia, our probability for the model which the Rakhigarhi result aligns with should already be quite high.

Again, since it’s one sample, we need to be cautious…but I bet once we have more samples from the IVC the Rakhigarhi individual will probably be enriched for AASI relative to other samples from the IVC. The InPe samples in The Genomic Formation of South and Central Asia exhibited some variation, and it’s likely that the IVC region was genetically heterogeneous.

But, this is going to be a DNA sample from an individual who lived 4,600 years ago within the orbit of the IVC when it was in its mature phase. That’s still a big deal. As most of you know the IVC is prehistory because we haven’t deciphered the seals which are associated with this civilization. But, the IVC clearly had relationships with West Asia and Central Asia, with parts of eastern Iran and the BMAC culture both being influenced and interaction with it. Traders who were likely from the IVC seem to be mentioned in Mesopotamian records.

Additionally, the genetics of one individual can be highly informative if it’s high-quality whole-genome data (I’m skeptical of that in this case). One could possibly even identify the time period that admixture between West Asian and AASI components occurred from a single genome, by looking at ancestry tract lengths.

A single sample isn’t going to falsify the idea held by some that steppe peoples were long present within the IVC. Perhaps they’ll show up in other samples? That’s possible, and it’s what I would argue if I held their position, but I think the constellation of evidence on the balance now does suggest that a relatively late incursion into South Asia is likely. The steppe ancestry with Northern European affinities shows up in BMAC only around 4,000 years ago. It is hard to imagine it was in South Asia before it was in Central Asia.

As I’ve been saying for a while it seems that though there will be more genetic work written on India in the near future, the real analysis is going to have to come out of archaeology and mythology.

It’s pretty clear that in Northern Europe the arrival of the Corded Ware peoples from the steppe zone resulted in great tumult. A linguistic analysis suggests that the languages of Northern Europe have words related to agriculture with a non-Indo-European origin, of common provenance.  But we don’t have much in the way of mythos about the arrival of the Corded Ware.

In contrast, India has a rich mythos which seems to date to the early period of the arrival of the Indo-Aryans. One interpretation has been that since these myths seem to take as a given that Indo-Aryans were autochtonous to India, they were. But the genetic data seem to be strongly suggesting that the arrival of pastoralists occurred in South Asia concomitant with their arrival in West Asia, and somewhat after their expansion westward into Europe. Indian tradition and mythos could actually be a window into the general process of how these pastoralists dealt with native peoples and an illustration of the sort of cultural synthesis that often occurred.

March 11, 2018

The population genomics of South Asia is complicated, and politics doesn’t make it easier

Filed under: India Genetics,India genomics — Razib Khan @ 11:27 am


Many people have been sending me links to this article, By rewriting history, Hindu nationalists aim to assert their dominance over India. Here’s a key section:

The RSS asserts that ancestors of all people of Indian origin – including 172 million Muslims – were Hindu and that they must accept their common ancestry as part of Bharat Mata, or Mother India. Modi has been a member of the RSS since childhood. An official biography of Culture Minister Sharma says he too has been a “dedicated follower” of the RSS for many years.

Sharma told Reuters he expects the conclusions of the committee to find their way into school textbooks and academic research. The panel is referred to in government documents as the committee for “holistic study of origin and evolution of Indian culture since 12,000 years before present and its interface with other cultures of the world.”

Sharma said this “Hindu first” version of Indian history will be added to a school curriculum which has long taught that people from central Asia arrived in India much more recently, some 3,000 to 4,000 years ago, and transformed the population

There are several threads here. First, it is a fact that the ancestors of South Asia’s non-Hindus were Hindu. There are minor exceptions, such as the Parsis, who are ~75% Iranian. One can quibble as to whether many tribal and peasant populations were truly Hindu in a formal and explicit sense. But I think this is a semantic dodge. Muslims would recognize these beliefs and practices as Hindu, no matter if one was a Brahmin monk or a member of a tribe which still sacrificed animals.

I’ve looked at the genotypes of a fair amount of South Asians of Muslim background. The overwhelming (usually exclusive) proportion of their ancestry is South Asian. It’s a fact that the ancestors of non-Hindu South Asians were Hindu.

But, the article and a dominant theme in Hindu nationalism today are that distinctive groups like Indo-Aryans are indigenous to South Asia. This is set against a narrative of invasions and migrations, which is presumed more friendly to a multicultural paradigm (I have a hard time keeping track of the political valence of all these things). To some extent, the reality of invasions and migrations cannot be denied, whether it be Alexander, the Kushans, or the various Muslim groups. But these historical invasions left little genetic imprint.

When 2009’s Reconstructing Indian Population History was published things changed for earlier migrations. By the time the ancient Greeks were noting India in Classical Antiquity, it was already noted as the most populous nation in the world. I was initially skeptical about the result inReconstructing Indian Population History, that there was massive admixture between a West Eurasian and indigenous South Asian group, because that would imply massive migration. Additionally, phenotypically the pigmentation genes didn’t seem to work out if the source population was European-like.

Nearly 10 years on we have a lot more clarity. Ancient DNA has clarified a lot. Massive migrations are common. And, the pigmentation and genetic profile of modern Europeans is recent. The source population(s) for “Ancestral North Indians” may not have been Europeans in the way we’d understand them. In fact, a follow-up paper, Genetic Evidence for Recent Population Mixture in India, hinted at two admixtures. There’s a fair amount of circumstantial evidence now that one component of “Ancestral North Indian” relates to West Asian populations and another component to the more classical steppe Indo-Aryans. The former is more widespread than the latter.

I do understand Indians who want to interpret their own history through the lens of their own cultural priors. The problem is that genetic science has proceeded so fast in the last few years that many propositions which were speculative in the 20th century are testable in the 21st. Some Hindu nationalist friends and acquaintances express embarrassment and worry about the track that Indians are going on this. I don’t know what to say, but Americans have their own delusions and propaganda, so I’m not going to be one pointing fingers. Other Indians have told me via Facebook that they “believe in the results from the 2000s” (when they were more congenial to their viewpoints?). I guess that’s one strategy; just keep up with the science until it starts refuting your model.

That being said, with the ubiquity of datasets one can explore questions oneself. Additionally, the Indian government may suppress analysis of ancient DNA through soft coercion and negative incentives, but I’m sure at some point Pakistan will let people dig things up.

I recently posted my South Asian Genotype Project results. Though the sample size is small, since I have provenance it allowed me to get more clarity on what’s going on in the 1000 Genomes samples for South Asians.

There are several things I can tell you. For example, I have samples for a Sindhi and Gujarati Lohanna. They cluster near each other, and with Sindhis. Similarly, a Gujarati Muslim sample is also in with the Sindhis. A Gujarati Muslim gives the same results.

In contrast, other Gujaratis are placed between Pakistani populations and South Indians. A Vania and Solanki sample helped me label “Gujarati Middle Caste.” The Gujarati Patel samples, in contrast, are even more shifted toward South Indians, and admixture analysis implies less Indo-Aryan in these samples than other Gujaratis.

Gujarat seems to be a state with a lot of connections to Sindh, so you see a wide range of variation in this state on the ANI-ASI cline.

I’ve collected enough Brahmin samples from the four states of Southern India to see that they are very similar genetically (one exception is a Niyogi Brahmin who seemed more ASI-shifted than usual). If they don’t come from the same migration event, they diverged at around the same time.

Brahmins from North India are different from South Indian Brahmins, in being more ANI-shifted. It seems that to a great extent Brahmins from outside the Gangetic heartland can be modeled as North Indian Brahmins with local admixture. Bengali and Maharashtra Brahmins have shifted away from North Indian Brahmins, but not as much as South Indian Brahmins. Bengali Brahmins are also East Asian shifted, confirming the reality of local admixture.

One result that surprises me is how genetically similar Dalits from North and South India are. The Chamar samples from Uttar Pradesh seem to have some levels of Indo-Aryan admixture, but overall they’re not that different from Dalits from Tamil Nadu.

Additionally, non-Brahmin and non-Dalit individuals from places like Bengal and Tamil Nadu/Sri Lanka, and Andhra Pradesh are very distinct from Dalits. In other words, the caste system is not simple the traditional upper castes vs. everyone else, but it’s deeply structured. The implication here is that caste may predate the Indo-Aryans (this is not a new inference). Or at least not be related them.

Finally, there is a curious pattern where gene flow into southern Pakistan (Sindh) is more shifted toward the Middle East than in northern Pakistan (Punjab, the Pathan areas). I suspect this is due to dynamics which date deep into prehistory, rather than more recent events.

 

January 18, 2018

The Dravidianization of India

Filed under: Dravidian,India Genetics,India genomics,Indo-Aryan — Razib Khan @ 9:36 pm

On this week’s The Insight Spencer Wells and I talk about the Indo-Aryan arrival to South Asia. This was recorded very early last summer, and I’m rather unguarded (it’s well before I had the piece published in India Today).

I think 2018 will finally be the year that a lot of South Asia will be “solved.” There has been some foot-dragging on papers and results, but that can only go so long.

All that being said I suppose I should make some suppositions I have arrived at on this topic more explicit, as in a discussion with an Indian friend he admitted had no idea about some of my views, though he reads this weblog when I expressed them. That’s because they are speculative and my confidence in them is weak, though you can infer my opinions if you look very closely.

The figure to the left is from Genomic insights into the origin of farming in the ancient Near East, a paper published about a year and a half ago. You see various South Asian populations being modeled as a mixture of four different source populations. The Onge are an Andaman Islander population (and the closest we can get to the aboriginal peoples of South Asia). Iran_N represents Neolithic Iranians, the canonical “eastern farmer” population. Steppe_EMBA represent Yamnaya pastoralists, who are themselves modeled as a mixture of Eastern European Hunter-Gatherers (EHG) and southern population which has affinities with the Iran_N cluster. EHG in their turn seems to exhibit ancestry from Western European Hunter-Gatherers (WHG), whose heritage dates to the late Pleistocene, and Ancient North Eurasians (ANE), who flourished in Siberia, and contributed ancestry to populations to the west and east (including the ancestors of Native Americans).

When I first saw this specific figure I was incredulous. I had long thought that “Ancient North Indians” (ANI) were a compound of two elements, one related to the farmers of West Asia (Iran_N), and the other steppe Indo-European (Steppe_EMBA/Yamnaya). But the fraction of Yamnaya/Indo-European/Indo-Aryan ancestry seemed far too high.

A few years later I am not less certain about my skepticism. The fractions here in the details are debatable. Within the text of the paper, the author admits that the true ancestral populations are probably not represented by the model. But they are close. In most cases, the “Han” ancestry is probably indicative of the fact that the non-ANI component of South Asian ancestry is most closely related to the Onge, but is significantly different nonetheless.

The ratio of Iran_N and Steppe_EMBA is the key. Here is a selection from the paper:

Group Iran_N Steppe_EMBA Ratio
Jew_Cochin 0.53 0.23 2.27
Brahui 0.60 0.30 1.98
Kharia 0.13 0.07 1.97
Balochi 0.57 0.32 1.75
Mala 0.23 0.18 1.25
Vishwabrahmin 0.25 0.20 1.21
GujaratiD 0.29 0.28 1.04
Sindhi 0.38 0.38 1.00
Bengali 0.22 0.25 0.91
Pathan 0.36 0.45 0.81
Punjabi 0.24 0.33 0.72
GujaratiB 0.27 0.38 0.72
Lodhi 0.21 0.29 0.72
Burusho 0.27 0.43 0.64
GujaratiC 0.23 0.37 0.61
Kalash 0.29 0.50 0.58
GujaratiA 0.26 0.46 0.57
Brahmin_Tiwari 0.23 0.44 0.51

Any way you slice it, a group like the Tiwari Brahmins of Northern India have more Onge-like ancestry than most of the groups in Pakistan. But also observe that the ratio toward Steppe_EMBA is more skewed in them than among even Pathans or Kalash.  The Lodhi, a non-upper caste population from Uttar Pradesh in north-central South Asia are more skewed toward Steppe_EMBA than Pathans.

It is important for me to reiterate that the key is to focus on ratios and not exact percentages. Though the Steppe_EMBA fraction did strike me as high, glimmers of these sorts of results were evident in model-based clustering approaches as early as 2010. The population in the list above most skewed toward Iran_N are Cochin Jews. This group has known Middle Eastern ancestry. But next on the list are Brahui, a Dravidian speaking group in Pakistan. There is a north-south cline within Pakistan, with northern populations (Burusho) being skewed toward Steppe_EMBA and southern ones (Sindhi) being skewed toward Iran_N. Additionally, Iranian groups such as Pathans and Baloch likely have had some continuous gene flow with Middle Eastern groups, probably inflating their Iran_N.

Trends I see in the data:

  1. There is a north-south cline within Pakistan with Steppe_EMBA vs. Iran_N
  2. There is a north-south cline within South Asia with Steppe_EMBA vs. Iran_N
  3. There is caste stratification within regions between Steppe_EMBA vs. Iran_N
  4. Though not clear in this table, there are strong suggestions that Indo-European speaking groups tend to be enriched in Steppe_EMBA, all things equal (e.g., the Bengalis in the 1000 Genomes look a lot like the middle-caste Telugus in the 1000 Genomes when you remove the East Asian ancestry…except for a noticeable small fraction of a component which I think points to Indo-European ancestry)

What does this mean in terms of a model of the settlement of South Asian over the past 4,000 years? One conclusion I have come to is that Dravidian speaking groups are not the aboriginal peoples of the subcontinent. Rather, their settlement across much of South Asia is very recent. Almost as recent as Indo-Aryan habitation. In First Farmers the archaeologist Peter Bellwood proposed this model, whereby Indo-Aryans and Dravidians both expanded across South Asia concurrently. Though I think elements of Bellwood’s model that are incorrect, it’s far more correct in my opinion than I believed when I first encountered it.

Why do I believe this?

  1. The Neolithic begins in South India in 3000 BC.
  2. Sri Lanka is Indo-European speaking
  3. The Dravidian languages of South India don’t seem particularly diverged from each other
  4. There is ancestry/caste stratification in South India even excluding Brahmins (e.g., Reddys and Naidus in Andhra Pradesh look somewhat different from Dalits and tribals)
  5. Some scholars claim that there isn’t a Dravidian substrate in the Gangetic plain
  6. R1a1a-Z93, almost certainly associated with Indo-Aryans, is found in South Indian tribal populations
  7. Using LD-based methods researchers are rather sure that the last admixture events between ANI and ASI (“Ancestral South Indians”) populations occurred around ~4,000 years ago

Here is my revised model as succinctly as I can outline it. The northwest fringes of South Asia, today Pakistan, and later to be the home of the Indus Valley Civilization (IVC), was populated by a mix of indigenous populations, a form of ASI, when West Asian agriculturalists arrived ~9,000 years ago from what is today Iran. These were the Iran_N or “eastern farmer” groups. The West Asian agricultural toolkit was serviceable in northwestern South Asia for reasons of climate and ecology, but could not expand further east and south for thousands of years.

There is where the first admixture occurred that led to a population was mixed between ANI and ASI. These people lacked Steppe_EMBA. They were pre-Indo-European. They were almost certainly not all Dravidian speaking. The Burusho people of northern Pakistan, for example, speak a language isolate (in India proper you have Nihali and Kusunda)

By ~3000 BC this proto-South Asian (in a modern sense) population began to expand, while the IVC matured and waxed. Eventually, the IVC waned, fragmented, and disappeared.

Around ~2000 BC, or perhaps somewhat later, Indo-Aryans arrive in South Asia. The situation at this stage in not one of a primordial and static Dravidian India, on which Indo-Aryans place themselves on top. Rather, it’s a dynamic one as the collapse of the IVC has opened up a disordered power vacuum, and a reconfiguration of cultural and sociopolitical alliances.

In the paper above the author alludes to the pervasiveness of both Iran_N and Steppe_EMBA ancestry in South Asia, including in South India. “Indo-European” Y chromosomal lineages are also found among many South Indian groups, albeit at attenuated proportions region-wide. In Peter Turchin’s formulation, I believe that “Indo-Aryan” and “Dravidian” identities became meta-ethnic coalitions in the post-IVC world. Genetically the two groups are different, on average. But some Dravidian populations assimilated and integrated Indo-Aryan tribes and bands, while Indo-Aryans as newcomers assimilated many Dravidian populations.

The reason that the ratio of Iran_N to Steppe_EMBA does not decline monotonically as one goes from west to east along North Indian plain is that Indo-Aryans were not expanding into a Dravidian India.  Dravidian India was expanding only somewhat ahead of Indo-Aryan India, and in some places not all at all. In the northwest fringe of South Asia there had long been a settled population of peasants with West Asian ancestry with Iran_N affinities. In contrast to the east the landscape was populated by nomadic tribal populations with ASI affinities. North Indian Brahmins may have more Steppe_EMBA than some populations in Pakistan and more ASI because they descend from Indo-Aryan groups who absorbed indigenous ASI populations as they expanded across the landscape.

Dravidian groups as they expanded also assimilated indigenous populations. This explains some groups with very high fractions of ASI. Their ASI ancestry is a compound, of an old admixture in Northwest India, and also later assimilation in South India. The presence of R1a1a-Z93 in these populations reflects the integration of some originally Indo-Aryan groups into the expanding Dravidian wavefront.

Where does this leave us?

  1. The Indo-Aryan vs. Dravidian dichotomy is not one of newcomers vs. aboriginals. It is of two different sociocultural configurations which came into their current shape in the waning days of the IVC. That is, it is less than 4,000 years old
  2. The two populations were clearly interacting closely around the time of the collapse and disintegration of the IVC and post-IVC societies. There has been gene flow between the two
  3. ~4000 years ago ANI and ASI populations existed in their “pure” form, but that is because ASI aboriginals still existed to the south and east of the IVC, while Indo-Aryans were a new intrusive presence in the Indian subcontinent

April 21, 2011

Visualization of genetic distances, part n

Zack Ajmal has been taking his Reference 3 data set for a stroll over at the Harappa Ancestry Project. Or, more accurately, he’s been driving his computer to crunch up ADMIXTURE results ascending up a later of K’s. Because it is the Harappa Ancestry Project Zack’s populations are overloaded a touch on South Asians. He managed to get a hold of the data set from Reconstructing Indian History. If you will recall this paper showed that the South Asian component which falls out of ancestry structure inference algorithms may actually be a stabilized hybrid of two ancient populations, “Ancestral North Indian” (ANI) and “Ancestral South Indian” (ASI). ANI are a population which can be compared pretty easily to other West Eurasians. There are no “pure” groups of ASI, but the indigenous peoples of the Andaman Islands are the closest, having diverged from the mainland ASI populations tens of thousands of years ago.

At K = 11, that is, 11 inferred ancestral populations, Zack seems to have now stumbled onto the patterns which one would expect from this hybrid model of South Asians. Let me quote him:

Now let’s take all the reference populations with an Onge component between 10% ...

March 28, 2011

Genetics as the myth buster: Indian edition

Filed under: Genetics,Genomics,India Genetics,India genomics,Vishwakarma — Razib Khan @ 12:17 pm

Whenever Zack Ajmal posts a new update to the Harappa Ancestry Project he appends some data to his ethnic database. This sends me to Wikipedia, because how many people are supposed to know what a “Muslim Rawther” means? Well, if you are a Muslim Rawther, and perhaps from Southern India, you would. But South Asian ethno-linguistic categories and hierarchies are notoriously Byzantine, and I have difficulty making sense of them. This isn’t too surprising in my case, as my family’s background is relatively mixed in the very recent past (e.g., Hindus and Muslims, and people of various caste backgrounds), so we’re not the sort who can go at length about our pure ancestry and all that stuff. Unfortunately, Wikipedia isn’t always useful, because the people editing the entries on particular South Asian ethnic groups are often people from those ethnic groups, so you get a lot of extraneous information, and a particular slant on how awesome and high achieving the group (also, sometimes there’s funny stuff about how notoriously good looking that particular caste!). On occasion there are other sources which are informative. For example, Zack has several individuals from the Tamil Nadar caste. I know ...

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