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51gumWkW0TL It is too much to assert to say that the Indian ocean is “our sea,” writ large as a species. But it does certainly seem to be the case that this body of water does punch above its weight. It is likely that anatomically modern humans emerged not too far from its shores, while the first, second, and third civilizations arose arose along its fringes (civilization being defined as having cities and some basic level of literacy). As humanity developed complex societies at the antipodes of Eurasia, in Europe and China, the focus on the Indian ocean basis became somewhat attenuated, but its centrality as a nexus between these two dynamic loci of economic and cultural activity persisted. In addition, both the world of Islam and Southeast Asia were deeply connected to the ocean, while for India it was the ocean.

Sanjeev Sanyal’s The Ocean of Churn: How the Indian Ocean Shaped Human History is a panoramic narrative which surveys the lands around this ocean, and how wrapped up they’ve been in human history. There are two broad themes which undergird The Ocean of Churn. First, Sanyal seems to (mostly) reject the Great Man theory of history, as well as deterministic Marxist models. Rather, he posits that historical processes are a complex adaptive system. This is probably true, but honestly I don’t see that it looms very large in The Ocean of Churn, which is mostly a descriptive narrative on the macroscale. If you deleted this nod to the theoretial framework it could be read perfectly fine. The second major theme, that the flow of ideas and peoples is bidirectional, rather than a sequential branching processes, permeates the book. In fact, it’s hard to ignore, because Sanyal begins by recounting how the Pallava dynasty of South India was refounded by a collateral branch from Cambodia!

Screenshot 2016-09-03 14.45.46The map to the left is a stylized representation of humanity’s expansion out of Africa. To a first approximation it gets a lot right. But because it only depicts unidirectional migration it misses a lot in the detail. The same could be said for culture. For example, the narrative of Islam is that it spread from Arabia, to the west and the east. But works such as Lost Enlightenment and Warriors of the Cloisters both argue that there was a massive reflux from the east after the transition between the Umayyads and the Abbasids. The Abbasid power base, and many of their courtiers, were from Khorasan in the northeast of modern Iran, and Transoxiana. While 7th century Islam crystallized in the matrix of a post-Roman Late Antique world, with the Umayyad center of power being in Syria, the Abbasids emerged from a milieu where Muslims, Christians, Zoroastrians, Buddhists, and even Hindus, mixed freely and exchanged ideas.

k8882 Like Empires of the Silk Road and Facing the Ocean: The Atlantic and Its Peoples 8000 BC-AD 1500, the The Ocean of Churn is a historical geography with a broad view and lacking a tight focus. It’s not a bug, it’s a feature. Additionally, Sanyal’s style is quite conversational and informal…dare I say, almost bloggish? He admits very early that he’s not writing an academic work. Rather, The Ocean of Churn is part travelogue, part historical commentary, and part review of the academic literature. Additionally, there is arguably somewhat of an Indo-centric bias, insofar as in a book which runs less than 300 pages India and its role at the center of events take up disproportionate space. This is somewhat ironic in light of the author’s conscious observation that previous histories of the Indian ocean were quite Eurocentric, but somewhat justified by the fact that India’s long history, relative influence around the basin of the Indian ocean, and demographic heft, probably warrant extra attention.

Sometimes this focus gets the better of Sanyal. The voyages of Zheng He somehow get drafted into the shift within maritime Southeast Asia from affiliation with the Dharmic set of cultures rooted in Hinduism and Buddhism toward that of Islam, where the machinations within the Chinese court were geared toward breaking the Indic affinities of this region to increase Chinese cultural hegemony.

There are two major problems I see with this. First, the swing from Hinduism and Buddhism to Islam in maritime Southeast Asia was a centuries long process, and occurred first in the Arabian sea, before shifting to the eastern regions of the Indian ocean. One can make the case that it was the rational thing to do for maritime facing Southeast Asian polities to realign their culture focus from Dharmic religions to Islam.

Second, there were longstanding dynamics at the court of the Ming dynasty which could explain much of the rationales for the voyages of Zheng He’s fleet, dynamics which can be traced as far back as the Song dynasty as to the proper role of the state in society and the world. This is a case where Sanyal’s narrative is too geographically and historically delimited to flesh out the more complex and messy dynamics at the heart of which was a civilizational pivot in Southeast Asia and sui generis maritime voyages out of the heart of the Chinese world.

But in general The Ocean of Churn does not suffer from narrowness. Rather, the footnotes and citations are a testament to Sanjeev Sanyal’s catholic tastes; they are wide-ranging, and warrant closer attention and follow-up. I did not, for example, know that the native Malagasy had retained a custom of boat burial even after they had to retreated to the highlands and become farmers with little experience of the sea. The Ocean of Churn is packed with many interesting details of this sort. It’s a gold-mine for those looking for more to read.

And yet in the course of inter-disciplinary work sometimes you’ll miss the trees from the forest. This occurs in Sanyal’s survey of the historical genetics literature. He gets most right, but gets some wrong. The first case is that Sanyal refers a few times to the 2013 paper, Genome-wide data substantiate Holocene gene flow from India to Australia. It came out in PNAS, a reputable journal, and includes an author, Mark Stoneking, which some prominence in the field. Additionally, the timing was such that it aligned well with a contemporaneous cultural change in humans, and the arrival of dingos. Unfortunately, the paper was certainly wrong. First, the data was not open, so I could not replicate, to see how robust the statistics were. I complained about this at the time. Second, several prominent statistical geneticists told me privately that they were very skeptical of the statistics. Third, recent research suggests that Aboriginal paternal lineages are very deeply rooted, Deep Roots for Aboriginal Australian Y Chromosomes. Indian Y chromosomes are very distinctive. There is evidence for them in Southeast Asia in regions without colonial era Indians, in particular Cambodia. Of course, it could be that only the female lineages persisted, but there is the reality that there’s been no evidence for recent Indian mtDNA in Australia to my knowledge (the divergences are very deep), and, no other paper which has access to Australian genome data has replicated this finding. Finally, from what I am hearing a new autosomal paper will come out soon and definitively render judgment against this paper’s result (this is why the Y chromosome paper came out).

r1a But the above is pretty small-ball. The major issue in the citation of historical genetic papers in The Ocean of Churn is that there are references to older works, as in five years old, that are totally out of date, and interpretations based on consensus understandings of the late 2000s that have been overturned.

Let’s start with R1a1a. This a male Y chromosomal lineage which is very common in South Asia, Central Asia, and West-Central Eurasia (Eastern Europe). When it comes to Y chromosomal lineages whole genome analyses have changed our understanding a lot of the phylogenetics of this topic. The earliest work uses highly mutable microsatellites, while later work focused on single nucleotide polymorphisms. Using these patterns of variation researchers created phylogenies, most of which have stood the test of time, and calibrated divergence times, many of which have not. Basically the Y chromosome doesn’t have enough SNP diversity to allow good calibration of divergence, while because of their high mutation rate microsatellites are not good for temporal inference.

Screenshot 2016-09-03 16.04.03 The plot above shows the R1a1a males in the 1000 Genomes data (it’s from Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences). The green are South Asians, the blue are Europeans. Because the 1000 Genomes data is biased toward West Europeans, there are far fewer R1a than R1b in the data from that continent. What they confirm is that South Asian and European R1a are two different clades. The South Asian clade is often termed Z93 because of a particular mutation. Z93 is overwhelming in South Asia, very rare in Europe, and relatively common among the R1a individuals in Central Asia (e.g., the Altai sample from the 1000 Genomes). The pattern of genetic diversity shows that there isn’t much, and, that the diversity is relatively shallow. That is indicative of two things. R1a went through a very recent massive population expansion. It’s a “star-shaped phylogeny.” Contrast that with J2, which has also undergone expansion since the rise of agriculture, but exhibits far more internal structure. J2 probably started expanding earlier, and, it’s expansion was never at any moment as explosive as that of R1a and R1b. Earlier work suggesting R1a diversification ~10,000 years ago does not hold up.

The second issue in relation to R1a is that now have ancient DNA . Both R1a and R1b are very rare before 4,000 years ago. Here’s a section from a paper published in 2015 out of David Reich’s lab:

Further evidence for a connection between the Srubnaya and populations of central/south Asia—which is absent in ancient central Europeans including people of the Corded Ware culture and is nearly absent in present-day Europeans…is provided by the occurrence in four Srubnaya and one Poltavka males of haplogroup R1a-Z93 which is common in present-day central/south Asians and Bronze Age people from the Altai…(Supplementary Data Table 1). This represents a direct link between the European steppe and central/south Asia, an intriguing observation that may be related to the spread of Indo-European languages in that direction.

The Srubna people seem to have flourished between the Dnieper and Volga, and south toward the Caucasus, about ~3,500 years ago. But the Srubna are not simple solution to the problem of Indo-Aryan origins. From the supplements of Genomic insights into the origin of farming in the ancient Near East:

The analysis in this section reconciles the evidence presented in the first paragraph regarding the origin of the ANI by showing that is may be related both to “southern” populations related to Iran and the Caucasus and to “northern” steppe populations. Our results do not resolve the relationship between ANI and the origin of Indo-European speakers in South Asia, in the sense that they reveal that South Asian populations have ancestry both from regions related to the Eurasian steppe and ancient Iran, which is compatible with alternative homeland solutions…

While the Early/Middle Bronze Age ‘Yamnaya’-related group (Steppe_EMBA) is a good genetic match (together with Neolithic Iran) for ANI, the later Middle/Late Bronze Age steppe population (Steppe_MLBA) is not. Steppe_MLBA includes Sintashta and Andronovo populations who have been proposed as identical to or related to ancestral Indo-Iranians…as well as the Srubnaya from eastern Europe which are related to South Asians by their possession of Y-chromosome haplogroup R1a1a1b2-Z935. A useful direction of future research is a more comprehensive sampling of ancient DNA from steppe populations, as well as populations of central Asia (east of Iran and south of the steppe), which may reveal more proximate sources of the ANI than the ones considered here, and of South Asia to determine the trajectory of population change in the area directly.

Basically, the Reich lab has used ancient DNA to confirm what genome bloggers started noticing around 2010: the “ANI” component of South Asian ancestry is itself a composition with different streams. In the initial analyses the division between ANI and ASI (“Ancestral South Indian”) dropped out so easily because the two groups were very genetically distinct. In contrast, the West Asian and Bronze Age Steppe streams of the ANI ancestry are rather genetically similar in comparison, making them harder to differentiate. Ancient DNA has been particularly useful because the differences were starker in the past.

All good so far. Much of this aligns with The Ocean of Churn and its thesis of bidirectionality. The problem I have is that Sanyal seems to be implicitly assuming that an “Out of India” theory for the emergence of Indo-Aryans is the correct position when there’s a lot of legitimate debate about this, and good reason to hold that this is not plausible. He refers to the Indo-Aryan Mitanni as “Indian,” when it fact this is likely to be an anachronism. Similarly, if it is found that a Dravidian language was spoken in southern Iran during the Bronze Age, I suspect that terming them “Indian” would also be an anachronism.

When I told Sanyal I was going to bring this up on Twitter he told me that I needed to cite peer-reviewed literature. This is reasonable, in light of the fact that when you’re navigating different disciplines you can’t familiarize yourself totally with the landscape…but, it highlights a problem with his citation pattern: he’s not a human population geneticist, and so hasn’t kept up with the field, nor does he know what papers are of high quality in retrospect and what papers are not. I suggested to him that I could actually run many of the analyses myself since the data is open, but he responded that this would be “he said/she said.” This is fair because most people do not have much familiarity with population genomics. But, it is unfair because I actually have familiarity with the field and can actually do the work myself, so perhaps my opinion should be weighted a bit higher?

Ultimately all this is going to be forgotten commentary when sites like Rakhigarhi start yielding ancient DNA. I have already made a bunch of predictions relating to that research. There have already been leaks in the Indian press, such as ‘Descendants of Harappans still living in Rakhigarhi’. I’m pretty sure that what they’ll find is that the people who inhabited the Northwest quadrant of South Asia at that point were already admixed. They simply lacked the Bronze Age Steppe component of ancestry, which probably arrived with the Indo-Aryans.

Of more interest to me is Sanyal’s assertion of Southeast Asian influences India. The 1000 Genomes data makes clear that there is substantial admixture from Southeast Asian populations in Bengal. But there is no historical record of this, but its impact has been significant. The Ocean of Churn makes much of matrlineal customs, and their diffusion from Southeast Asia to India through the vector of migration. I’m not so sure that migration (cultural diffusion) is the only explanation of this phenomenon, but it is certainly plausible. One quibble I would make here is the same as above in regards to India: a lot of the population dynamics of Southeast Asia date to the later Holocene. Not the Holocene-Pleistocene boundary, when Sundaland would have been inundated.

41yT8hhOZJL._SX339_BO1,204,203,200_ There is clearly recent gene flow from South Asia to Southeast Asia. The genetic data from Cambodia suggest it is even, which means it was a demographic movement which affected the whole people. The cultural connections between Indic Southeast Asia and India have long been known, but it has long been assumed that this was mostly a matter of ideas, not people. But clearly enough people went so that ~5% of Cambodian ancestry seems to be Indian! The question then proceeds about reverse migrations. The movement into Bengal was relatively recent, and my own analyses have shown that it can’t be explained as purely an Austro-Asiatic event. Rather, the Tai migrations which reshaped the cultural and to some extent demographic landscapes of mainland Southeast Asia seem to have had a spillover effect into Bengal, which was at that time rising to prominence under the Pala dynasty.

Ultimately The Ocean of Churn lives up to its name. The authors explores connections between Madagascar and the East African coast, the Indus Valley Civilization and Mesopotamia, and Southeast Asia and India. It is fertile ground, and despite my quibbles and concerns with portions of the book, it is an excellent place to start. If you want to continue in a more narrow and academic vein, I’d recommend The Shape of Ancient Thought: Comparative Studies in Greek and Indian Philosophies, a book which traces connections between the two civilizations, and also looks further as to deeper influences from Mesopotamia on both of them.

• Category: History, Science • Tags: India, Ocean of Churn 
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57348Like you, I am waiting on the Rakhigarhi DNA results. Whatever they come back with is going to definitely impact the textbooks. But until then, I thought this paper in Scientific Reports was interesting (sort of), Oxygen isotope in archaeological bioapatites from India: Implications to climate change and decline of Bronze Age Harappan civilization.

I say sort of because 1) a lot of archaeology is impenetrable to me 2) everything is about climate change. What is interesting to me is that these researchers seem to favor an old date for origins of the Harappan civilization within India. Here’s the relevant section:

At Bhirrana the earliest level has provided mean 14C age of 8.35 ± 0.14 ka BP (8597 to 8171 years BP8). The successive cultural levels at Bhirrana, as deciphered from archeological artefacts along with these 14C ages, are Pre-Harappan Hakra phase (~9.5–8 ka BP), Early Harappan (~8–6.5 ka BP), Early mature Harappan (~6.5–5 ka BP) and mature Harappan (~5–2.8 ka BP8,17,18,20,34).

Setting the Hakra culture to the side, Early Harappan at 6,000 BC suggests to me that the demographic parameters which led to the creation of the ANI-ASI genetic complex may already have been present then. If, the ASI are intrusive to the subcontinent it may even be that the Early Harappan were more West Asian than the final late stage Harappans.

• Category: History, Science • Tags: India 
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Mohenjo-daro_Priesterkönig At the Eurogenes blog there has been a lot of analysis of South Asian genetic history in light of ancient DNA recently. Part of this is probably due to the fact that “Euro” genes (that is, the genetic history of European peoples) are now understood to be inextricably tied to demographic pulses and shifts which are deeply rooted in Eur asian cultural revolutions over the past 4 to 10,000 years. Only a very small fraction of the ancestry of modern Europeans dates to the period before the Last Glacial Maximum ~20,000 years ago; at least according to ancient DNA. And most of the ancestry is conditional on events which occurred during the Holocene, the past 10,000 years.* To give a sense of how recent all this is, when the first cuneiform tablets were being written, the demographic-genetic revolution which was to begin the transformation of Northern Europeans into what we now know as Northern Europeans had not completed itself, and in many regions not even begun (e.g., the Swedish-Battle Axe culture begins in 2800 BCE, several hundred years after the earliest writing in Sumerian).

Screenshot 2016-05-28 16.24.36 They say you need two hands to clap. And India is the other hand that we have now when comes to understanding this process. There’s now a lot of circumstantial evidence to tie Indians to Europeans in moderately complex ways. To the left is a figure from the supplements of Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. You see that the phylogeny of R1a in South Asia really is a burst. There’s just not that much genetic difference between all of us South Asian R1a males, irrespective of region and caste. We’re pretty much all on a particular branch, Z93. Rare outside of South Asia today (it is found in the Altai and in Central Asia), it has been discovered in ancient males from the Srubna culture of eastern Ukraine ~4,000 years ago. In Europe R1a is found mostly in Northern Europe, and especially Eastern Europe. And yet if you look further up in the supplements you see that for haplogroup J2 most of the males are partitioned between South Asians and Southwest Europeans. Additionally, the two large branches of J2 have both South Asians and Southwest Europeans, suggesting that divergence in J2 predates the arrival of J2 bearing males to South Asia and Southwest Europe. Finally, unlike R1a you can see visually that the phylogeny of J2 is less explosive; there are more clean sequences of mutations to differentiate the various branches of this patrilineage. J2 is common, but it did not undergo nearly the same burst as R1a. It’s prevalence is due to more continuous and gradual demographic processes.

51IZQjMbVlL._SX346_BO1,204,203,200_ What does this mean? Various genome bloggers have been arguing since the late aughts that there seem to be two West Eurasian admixtures into South Asia, who are clearly a compound of West Eurasians and non-West Eurasians. This was supported to some extent by the 2013 publication of Genetic Evidence for Recent Population Mixture in India, which found evidence for more than one admixture event in a subset of populations. Then, ancient DNA from the Caucasus added more evidence, Upper Palaeolithic genomes reveal deep roots of modern Eurasians. If you dig deep into the paper you see that Indian populations which are likely to be due to one(ish) admixture event are best modeled as a synthesis between the Kotias Caucasus hunter-gatherer and a non-West Eurasian population (i.e., Ancient South Indians or ASI). But some groups, such as high caste North Indians, seem to be better modeled with ancient Eurasian steppe groups as the source population (these groups themselves have ancestry from a Kotias-related/descended group).

In 2016 the ultimate judge is going to be ancient DNA. In the next year or so I think it will tell the tale that we’ve been hearing in the winds of modern contemporary genetic variation. What I think is that it will confirm part of the narrative and model pushed forward in First Farmers, Peter Bellwood’s book from the middle aughts. The Dravidian languages were brought to India from West Asia in the early-to-middle Holocene by agriculturalists descended from or related to the hunter-gatherers of the Caucasus. They mixed with indigenous hunter-gatherer populations, and gave rise to the first people we would recognize as modern South Asians genetically. Eventually they built what we term the Indus Valley civilization. The relatively evenness of this mix between West Asian descended Ancestral North Indians (ANI) and ASI across South Asia is due to the fact that much of the subcontinent was sparsely populated, and the farmers demographically overwhelmed the indigenous groups. The fact the non-Brahmin upper and middle castes are genetically somewhat different from tribal populations and Dalits in South India is probably due to the fact that the indigenous populations were absorbed at the lower levels of the nascent civilization.

The arrival of Indo-Europeans may or may not have been an “invasion” in a classical sense, but it was highly disruptive. The phylogeny of R1a in South Asia is strongly indicative of an incredible reproductive advantage for males bearing this haplogroup. In fact, R1a is more expansive than Indo-Aryan languages, and is found across language and caste, including among tribal populations. Previously this was argued as a reason for why R1a in South Asia must be old and indigenous to South Asia. Next generation sequencing of the Y chromosome has looked closely, and that is unlikely. The expansion of R1a, and the South Asian branch, is very recent. It hints at cultural processes of male domination and elite diffusion of lineages which we do not have a good theoretical grasp of at this moment.

But this is not the end of the story. I have spoken only of West Eurasians. What of the other half of the ancestral glass, the ASI? I have not explored this literature in detail, but there is now suggestive evidence I believe that ASI themselves may have been intrusive to the subcontinent, perhaps as hunter-gatherers migration out of Pleistocene Southeast Asia. The closest modern population to the “pure” ASI ghost group are the Andaman Islanders, and they arrived where they are today not from the Indian subcontinent, but from Burma. There is now a modest amount of evidence through various angles that the ancestors of the Munda people of South Asia must have arrived as part of the Austro-Asiatic agricultural migrations from what is today interior South China. They are not primal. There is no reason to think that that this was the first eruption of humans from this region into South Asia. Those with more understanding of paleoclimatology need to weigh in, but it may be that in the drier conditions of the Pleistocene South Asia had a naturally smaller population than Southeast Asia, so that the latter was always going to be a source and the former a sink, in terms of demographics.

In any case, if the model fits, eventually a preprint you must submit. I think the age of speculations will give way to the age of understanding, though I have no inside information at this point….

* To unpack this, take a conventional idea of Europe today, bounded by Gibraltar on the southwest, the Bosporus on the southeast, and in the far east the Urals and far southeast the Caucasus. The majority of Southern European ancestry seems to derive from Early European Farmers (EEF), and these almost certainly are from Anatolia. In Northern Europe the ancestry is a compound of EEF, Indo-Europeans from the east, and probably residual hunter-gatherers (some researchers believe nearly all of the hunter-gatherer ancestry in Northern Europe is actually from the Indo-Europeans and EEF, with no true relic populations by 5,000 BC). Of the original Yamnaya Indo-European ancestry, the ~25% or so that is Ancestral North Eurasia (ANE) probably is extra-European in provenance. Specifically, a migration out of central Siberia or thereabouts. Nearly half of the remaining is similar to EEF, but we now know it is likely derived from a different Near Eastern farming populations which descend in part from hunter-gatherers from the Caucasus. The balance is from indigenous European hunter-gatherer ancestry which amalgamated with ANE. This last portion is indigenous to Europe broadly construed before the Holocene. I haven’t done the detailed math, but it seems difficult then to imagine a scenario where anything by a minority of the ancestors of modern white indigenous Europeans actually lived in Europe during the late Pleistocene.

• Category: Science • Tags: Genetics, India 
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ncomms9912-f451IZQjMbVlL._SX346_BO1,204,203,200_Update: Here is a post that you must read, A note on the early expansions of the Indo-Europeans. The post dates to the middle of December, and is similar in many ways to my own thoughts. But, the author rejects a two wave model where the first wave has a deep time history, and seems to give the balance of opinion that agriculture is predominantly indigenous in development to South Asia, and not primarily an exogenous event. Rather, they suggest that there were multiple waves of Indo-Aryans into South Asia, with the steppe cultures being parallel and pulses from the Indo-Iranian ur-heimat. The primary criticism of the genetic interpretation that I would make is that from what I am to understand LD decay methods seem to catch the last admixture event and/or underestimate time since initiation of mixture. Therefore, though I accept a substantial mixture event ~4,000 years before the present, my own model present below suggests that older ones occurred thousands of years earlier.

That being said, I have updated my own views to rather uncertain at this point. I would not be surprised if on the whole a model as the one proposed in the blog post is closer to the truth than the one below. My reasoning has less to do with the details of the argumentation, and more to do with authority.

1) the individual who wrote the above post has comparable mastery of the historical genetic descriptive results.

2) but, the individual has far superior understanding of the archaeology and philology in comparison to me.

Ignoring the details of any argument, on a priori grounds I find that the individual above could give a better appraisal of the probabilities in regards to South Asian archaeogenetics than I could. The main thing that is holding me back from suggesting that I now find their model more probable than mine is the issue in regards to LD and rolloff methods. But I’ve definitely increased my uncertainty, from ~25% to ~50%, with the balance split between the two models (or some combinations thereof).

End Update

Sometimes you see things in fragments, disparate threads, which only snap into focus in hindsight. In this post I will hazard a prediction of results which are going to come out of remains from Indus valley sites in South Asia, which will confirm that there were two major demographic pulses which entered the subcontinent from the Northwest over the past 10,000 year. The first wave was the dominant one in comparison to the second genetically, and began at Mehrgarh 9,000 years ago. Its locus of origin was in the highlands of Western Asia, between the Caucasus and the Fertile Crescent. The second wave though left its mark culturally, as it is associated with Indo-Aryans, and likely derives ultimately from the trans-Volga steppe societies. The genetic signatures of the former people are found in nearly every indigenous South Asian group, as they amalgamated with a deeply entrenched local group of peoples who were distantly related to those of Oceania and eastern Eurasia. In short, the latter are the “Ancestral South Indians” (ASI) and the former are the “Ancestral North Indians” (ANI, see Reconstructing Indian Population History).

Screenshot - 01022016 - 09:46:36 PM The figure above is from Upper Palaeolithic genomes reveal deep roots of modern Eurasians (open access), which found that ancient DNA from two samples in the northern Caucasus region are representatives of a population which contributed to the origins of the steppe people who swept into Northern Europe ~4,500 years ago. It shows how contemporary populations are best modeled as admixture events between reference populations. What you see is that most South Asian groups are well modeled as a mixture between “Caucasian hunter-gatherers” (CHG), and another element which is labeled “South Asian” because it is mostly restricted to the subcontinent. But wait there’s more! In the supporting materials the statistics show that though most South Asian groups have more potential mixture from the high quality CHG sequence, Kotias, a subset, unspecified Gujarati groups and Tiwaris, share more drift with the Afanasevo culture, which flourished in the Altai region of Central Asia between 5,500 and 4,500 years ago. We have enough ancient DNA to infer that the Afanasevo basically the same people as the Yamna culture, who were present between the Volga and Dnieper, far to the west. The Tiwari are an upper caste group which is present across Northern India. The second wave component is clearly strongest in the Northwest, as indicated by the Kalash sharing so much drift with Ma’lta. Before subsequent waves of gene flow into the steppe people, which brought dollops of European farmer and hunter-gatherer ancestry into the mix, they had a higher fraction of Ancestral North Eurasian (ANE) than any contemporary Northern European population. Their contribution to South Asian groups on the Northwest fringe of the subcontinent explains then the presence of high fractions of ANE there.

A final aspect which needs to be mentioned is that the Z93 subclade of R1a1a is found across much of South Asia. Though it is correlated with higher caste, and Indo-Aryan speaking, populations, it is not exclusive to them. In fact it is found in substantial fractions among notionally primal tribal people in South India who traditionally practice primitive slash and burn agriculture and engage in extensive hunting and gathering. Ancient DNA results from the Sbruna culture of Central Eurasia have yielded Z93 among buried males. This subclade is rather rare in this region today, and, it succeeded groups which were carrying R1b, today dominant across Western Europe. The details are to be worked out, but, I believe that are associated with, but more expansive than, the Indo-Aryans. Beyond the limits of the folk migrations were outrider groups of males who integrated themselves into indigenous societies, often taking elite positions as members of a dominant patrilineage. If there was a strong bias for male descendants of a small number of these individuals, but not female ones, to have higher reproductive fitness, than over time their Y chromosomes might be far more common than their total genome contribution (to illustrate what I’m talking about, a recent paper in Australian Aboriginals admits that 56% of their Y chromosomes introgressed over the past 200 years from Europeans!).

Bringing it together one implication of the above is that the Dravidian languages of the Indian subcontinent were probably brought by the West Asian farmers (perhaps confirming an ancient link to Elamite?). Therefore, the language(s) of the Indus valley civilization was probably a form of Dravidian. Another aspect to consider is that no South Asian population lacks the genetic imprint of these West Asian farmers. It seems likely that as in Europe the farmer populations which entered the subcontinent via the northwest totally marginalized most of the hunter-nihms137159f3 gatherer groups, which were numerically less substantial in any case. But, why do all South Asian groups also exhibit ASI ancestry, which is deeply rooted in the subcontinent? Just as in Europe the initial populations of farmers on the fringes of the subcontinent mixed with the local hunter-gatherers, producing a synthetic population which over time evolved its cultural toolkit to become more well adapted to South Asian geographies. Once the crucial cultural adaptations occurred then the synthetic population underwent a phase of massive demographic expansion beyond its delimited ghetto on the fringes, where West Asian climatic parameters allowed for the initial phase of near total cultural transplantation. As in Europe the expanding South Asian farmer groups absorbed hunter-gatherer substrate, accruing greater and greater ASI fractions on the wave of demographic advance, and so generating the ANI-ASI cline evident in genetic analyses. The presence of ASI in groups like the Pashtuns in Afghanistan is probably due to the fact that the synthetic populations, what we now term “South Asians” or “Indians” or “desis”, exhibited enough cultural hegemony and influence to reach deep into the plateau of modern Afghanistan and impacted both the pre-Iranic and East Iranic people of Afghanistan (also, note that Indians were very common as slaves in the cities of Afghanistan during the early Islamic period).

The reason I took time to put this post up now is that it looks like the publication of ancient South Asian genomes from the Indus valley period is imminent. From The Guardian on December 30th, Rakhigarhi: Indian town could unlock mystery of Indus civilisation:

One has stood out: who exactly were the people of the Indus civilisation? A response may come within weeks.

“Our research will most definitely provide an answer. This will be a major breakthrough. I am very excited,” said Vasant Shinde, an Indian archaeologist leading current excavations at Rakhigarhi, which was discovered in 1965.

Shinde’s conclusions will be published in the new year. They are based on DNA sequences derived from four skeletons – of two men, a woman and a child – excavated eight months ago and checked against DNA data from tens of thousands of people from all across the subcontinent, central Asia and Iran.

They looked somewhat like a recent Miss America!

They looked somewhat like a recent Miss America!

I predict that the Y chromosomal haplogroups will be H or J2. Both these are common in Dravidian speaking groups of Southern India, and, are found at some fractions in West Asia. I predict that these individuals who share gene flow with Kotias, and not with Central Eurasian groups. I predict that these individuals will not be enriched for ANE ancestry. I predict these individuals will have mtDNA lineages present in modern Indian populations, probably M. Though excavated in a region of South Asia where today lactase persistence (LP( is common, none of the individuals with carry the common derived Eurasian haplotype conferring LP. They will segregate for the derived variant of SLC24A5. On a PCA plot these individuals will cluster with non-Brahmin upper/middle caste South Indian populations, such as the Reddys of Andhra Pradesh.

Note: I’ve been told by friends for two years and more that there are efforts to sequence and type Indus valley individuals. But I have no inside information. If you are an individual in the media who has early access feel free to send me a PDF with the understanding that I will honor the embargo! (if you don’t send me the PDF I’m mildly confident I’ve already hit the major themes you are safeguarding)

• Category: Science • Tags: India, Indian Genetics 
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TaylorSwiftApr09 William Dalrymple in The New Yorker has a reflection up on the 1947 partition of the subcontinent, The Great Divide. It is fine so far as it goes. He reminds us of the scale of the tragedy, millions of deaths, as well as the depravity of the barbarity, as “infants were found literally roasted on spits.” Some day I will have to educate myself about this period, as I only have vague recollections of reading fragments of Freedom at Midnight as a child. I recall stopping at the point where the authors reported how a group of men broke into an obstetrics unit at a hospital and took a newborn who had just breathed their first and smashed its brains out on the walls, while the mother and hospital staff watched in horror. That was enough to get a flavor of the “action.” Fortunately my family did not suffer during this period, Bengal was relatively quiet in comparison to the atrocities washing over Punjab (as many of you are aware, my family experienced more hardship in the 1971 war, though as they were relatively privileged Muslims who were also not very involved in the arts or politics they were not actively targeted).

But there is one section whose assumptions and implications rub me the wrong way. Let me quote:

In the nineteenth century, India was still a place where traditions, languages, and cultures cut across religious groupings, and where people did not define themselves primarily through their religious faith. A Sunni Muslim weaver from Bengal would have had far more in common in his language, his outlook, and his fondness for fish with one of his Hindu colleagues than he would with a Karachi Shia or a Pashtun Sufi from the North-West Frontier.

Many writers persuasively blame the British for the gradual erosion of these shared traditions. As Alex von Tunzelmann observes in her history “Indian Summer,” when “the British started to define ‘communities’ based on religious identity and attach political representation to them, many Indians stopped accepting the diversity of their own thoughts and began to ask themselves in which of the boxes they belonged.” Indeed, the British scholar Yasmin Khan, in her acclaimed history “The Great Partition,” judges that Partition “stands testament to the follies of empire, which ruptures community evolution, distorts historical trajectories and forces violent state formation from societies that would otherwise have taken different—and unknowable—paths.”

Ten years ago I read Nicholas Dirks’ Castes of Mind. It is a work of history which shows how many caste identities were fashioned de novo under the impetus of British bureaucratic taxonomic impulse (see Census of 1891). Though Dirks is too subtle to assert that the caste system was created by the British, the general thrust of the work is clearly one which emphasizes the role of recent historical contingency in establishing the social order of South Asia as we understand it. The subhead is after all: “Colonialism and the Making of Modern India.” The British are then the agents who operate upon the formless void of the Indian subcontinent’s amorphous peasant culture. They came, they saw, and they created.

Even when I read Castes of Mind I was moderately skeptical of the narrative, as there had been enough genetics done to suggest that South Asian populations were stratified by caste. By this, I mean that caste status as much, or more, than geography predict the genetic structure of Indian society. It was already evident, for example, that South Indian Brahmins were closer to North Indian Brahmins than they were to South Indian Dalits when it came to genetic relatedness. Brahmins and Dalits are two caste groups which are clear and present throughout South Asia (the “middle castes” tend to vary from region to region, and the classical warrior and trader castes do not exist in South India, though there are notionally Sudra groups which occupy their roles). Even those who prioritize the role of the British would accept that the Brahmin and untouchable categories predate the reification of the colonial period. But what the latest genetics is telling us is that caste endogamy has been a feature of Indian life for at least 2,000 years, and perhaps longer. Not only are Brahmins distinct from Dalits, but castes with a less clear position in the classical varna typology, such as the Reddy community of South India, clearly have had long histories as a coherent groups. The British could not have been the dominant causal force in shaping caste as a ubiquitous feature of Indian life if they were already genetically endogamous even before the Muslims arrived.

And so with religion. The contemporary revisionism, which now is approaching mainstream orthodoxy, is that South Asian religious life before the arrival of the British, and the Western outlook more generally, was characterized by a quietist syncretism where communal boundaries were fluid to the point of confessional identity being a flimsy veil which could be shed or shifted dependent upon context. An alternative history then might be proposed of a united subcontinent, where Hindus and Muslims were coexistent, or, perhaps where a Hindu and Muslim identity did not even exist. The cognitive psychologist Pascal Boyer likes to characterize a theory as giving you “information for free.” You don’t really have to know anything, you can simply deduce from your axioms. Though the model of South Asian ethno-religious history I allude to above obviously integrates ethnographic and historical realities, it constructs a post-colonial fantasy-land, where South Asian religiosity was without form or edge before the arrival of Europeans and their gaze collapsed the wave function. Before the instigation of Europeans people of color were tolerant of religious diversity, varied sexual orientations, and practiced gender egalitarianism. In other words, India was like the campus of Oberlin college, except without the microaggressions, and more authentic spirituality!

51J39W7ZRFL._SX306_BO1,204,203,200_ The first problem with this model is empirical and specific to South Asia. Before white Europeans arrived in the Indian subcontinent to roil and upend its social order, to transform its culture, there was already a ruling race of self-consciously white people doing just that. They were the Turks, Persians, and a lesser extent Arabs, who introduced Islam to the subcontinent. As alluded to in Dalyrmple’s piece in some ways Islam was conceived of as a sect of the foreigners by the natives, as well as the Muslims themselves. This is not an entirely strange state of affairs, in the first century or so of Islam the religion was the tribal cult of the Arab ruling caste of the Caliphate. Only with the rise of the Abassids and maturation of Islamic civilization as a pan-ethnic and post-ethnic dispensation did the “converted peoples,” in particular the Persians and Turks, become full members of the Ummah, and turn it into the universal religion that we understand it today (though even today there is an ethnic dimension in Islam, for example, the Islamic State accepts that the Caliph must be an Arab of the Quraysh tribe).

For many centuries Islam in South Asia recapitulated this pattern ancient pattern, whereby those who descended from converts were received as second class citizens (and still called “Hindus,” which simply meant a native of Hindustan). And to this reality must be added the dimension of race, for the Muslims from the west viewed the native peoples as black, and many elite families with origins in Persia and Central Asia maintained their endogamy for generations partly as a matter of racial hygiene. When Muslim elites did intermarry with the descendants of converts, it was invariably with those descended from high caste groups. The Mughal Emperors did wed women from Hindu backgrounds, but these were the daughters of powerful Rajputs, whose values and armies fused with the Muslim invaders to create what we understand as Islamicate civilization.

Yet there are many other stories besides the standard one of the rise and fall of Mughal India. In Crossing the Threshold: Understanding Religious Identities in South Asia, the author shows how the arrival of Islam in the subcontinent often involved a complex process of cultural interaction mediated by esoteric strains of the Ismaili sect. It is not relevant for the purpose of this post to review the nature of Ismaili Islam, but it is important to note that Sunnis view this group as deviant and marginally Muslim. With the arrival of the Mughals there began a long period of persecution of Ismailis in the Indian subcontinent as the new arrivals attempted to enforce conformity on the Muslim population. Both Crossing the Threshold and Mullahs on the Mainframe, an ethnography of a particular Ismaili sect in Gujarat, report that many of the Sunni Muslim communities of the subcontinent may be descended from people who entered Islam via Ismailism. Under the Mughals heterodox Muslim sects like the Ismailis were subject to more persecution than non-Muslims (this echos a similar dynamic in Late Antiquity, where more of the Christian animus was directed toward heretical sects than pagans). In Gujarat this resulted in mass conversions to Sunni Islam. In other regions it might have resulted in a “compromise” state of shifting to a Twelver Shia identity, which though not Sunni, was generally accorded more respectability than Ismailism. These people would be anticipating the life of Muhammad Ali Jinnah, whose recent ancestors (most accounts state his grandfather) converted from Hinduism to Ismailism, but who himself was an entirely irreligious man who avowed a Twelver Shia faith for purposes of formality.

The author of Crossing the Threshold suggests that for many centuries there existed in the subcontinent under the more tenuous and patchwork pre-Mughal Islamic rulers many liminal communities, which straddled the line between Muslim and Hindu. So long as the Muslims of the Indian subcontinent viewed themselves as strangers in a land which offered them opportunities for profit, there was a certain freedom in being viewed as an amorphous black-skinned mass of “Hindus” whose only importance was in the tax that they provided their overlords. The Mughals changed that. Though they were in origin Timurid princes from Central Asia, their long ascendancy in the subcontinent produced a genuine synthesis with the indigenous substrate. By the later years of the dynasty their symbolic and ceremonial roles as Emperors of India became so entrenched that even resurgent Hindu groups such as the Marathas retained the Mughals as figureheads, much as the Zhou dynasty persisted for centuries after its genuine preeminence had faded.

516ZEEEK2XL._SX332_BO1,204,203,200_ Over the 150 years that the Mughals dominated South Asia with their armies they also changed the nature of Islam in the subcontinent thanks to their broader connections. The Naqshbandi Sufi ordered was associated with the dynasty, and objected when rulers such as Akbar bent or rejected what they perceived to be Sunni Islamic orthodoxy. And the Naqshbandi were in a place to judge what was orthodox, as they were an international order with branches across Sunni the Muslim world. The historian S. A. M. Adshead discusses the role of what he calls the “Naqshbandi International” in binding the Islamic world back together after the shattering of the Mongol invasions in Central Asia in World History. It was no coincidence that attempted to root out deviancy and enforce what they saw to be uprightness.

China was another zone of Naqshbandi influence. Unlike India China proper had (and has) never been ruled by Muslims. After period of prominence under the Yuan (Mongols) the Muslim groups became another minority, tolerated by the Han Chinese, but viewed with curiosity and confusion. While the Muslims of what is today called Xinjiang were part of the Turkic world, and even when conquered by the Manchus administered as a separate domain from China, those resident in the east were relatively isolated from the Ummah, and swam in a Han sea. The Dao of Muhammad: A Cultural History of Muslims in Late Imperial China tells the story of the intellectuals among the Muslims of eastern China, who were confronted with accommodating the reality that they existed at the sufferance of non-Muslims, and could only advance to prominence and prosperity playing the game according to the rules of the Han majority. At the popular level in places like Ningxia there emerged Muslim apocalyptic movements which bore a striking resemblance to heterodox variants of Pure Land Buddhism, but among the intellectuals there arose the conundrum of how to render compatible orthodox Islam and Neo-Confucianism. So long as China was reasonably isolated from the rest of the world, this process dynamic proceeded without interference and followed its own logic. What emerged can reasonably be described as a synthesis between Islam and Neo-Confucianism, which resembles in its broad outlines the sort of fusion which occurred in early Christianity after the ruling elites took up the religion and imparted upon it their own philosophical presumptions. Just as some Christians perceived in their religion the completion of the project of the ancient Greek philosophers, so Hui Muslim intellectuals in the cities of eastern China in the 18th century saw in Islam not the overturning of Chinese culture, but its extension and perfection.

Suffice it say this movement among educated Chinese Muslims did not give fruit to a vital modern tradition. Several waves of Islamic reform have blasted into China from the outside world, first from Central Asia, and later from the Middle East proper in the age of modern transport and pilgrimage. The Islamic-Confucian synthesis in its full elaboration was a stillborn sect, pushed aside by the popularity of world normative Islam and the decline in prestige in the 19th and 20th century of Neo-Confucianism. Similarly, the Islamic-Hindu synthesis championed by the Mughal prince Dara Shikoh and prefigured by his great-grandfather Akbar, was forestalled by the emergence of Aurangzeb. Remembered as pious and steadfast by many modern day Muslims, he is reviled by Hindus, and most Western historians, who perceive that the sun set on religious pluralism due to his actions, seem to take a dim view of him. But Aurangzeb was closely associated with the Naqshbandi over much of his life, and he may be less important to the broad social movement of South Asian Muslims being drawn into an international system, with a standard set of beliefs and practices, than we think. Rather, Aurangzeb’s life arc may be consonant with both the indigenization of Islam in the subcontinent, and its need to align itself with external norms.

513yXnWcqDL._SX322_BO1,204,203,200_ Though I use the Indian subcontinent as my primary illustration, the dynamic is likely more general. In The Next Christendom: The Coming of Global Christianity Phillip Jenkins notes that though many claims are made for indigenous African churches, that is, those which have no connection to global denominations and movements and tend to more freely integrate African practices, as African societies become more Christianized they tend to become more mainstream and orthodox in their affiliation. What Jenkins is observing is that with development and modernity indigenous and local practices tend to fade into the background, as African Christians become influenced by the ideas and traditions of Christians from other regions of the world. Individuals who consider themselves part of a religious community start to adhere to the practices and norms of that community’s history.

Despite the homogenization and delineation of identity categories in India there are still liminal communities in the mode envisaged by Crossing the Threshold. The Meo people of Northwest India are Muslims who maintain many Hindu traditions. But the trend among the Meo is to become progressively “more Muslim,” and those Meo who leave their homeland assimilate into the conventional Sunni Muslim milieu and lose their distinctiveness. The Ismaili Khoja community of India is another example of a Muslim group with many Hindu customs and beliefs which has become more “orthodox” within historical memory. In this case the arrival of their spiritual leader, the Aga Khan, from Iran in the 19th century seems to have triggered an Islamic reformation of views and mores. And just as there may have been many groups which moved toward a more standard Muslim identity, there were likely those who became more self-conscious in their Hinduism, as that tradition coalesced as a negation of the exclusive confessionalism of Islam. The Hussaini Brahmins customarily participated in Shia Ashura, and have an origin story which places them at Karbala on the side of the sons of Ali. As noted above it was not unknown for high caste Hindus to enter Islam and intermarry with the Muslim nobility. Over time their Hindu origins may have been obscured, as they constructed wholly Muslim origin narratives. The Hussaini Brahmin community might illustrate a case where the process was halted, and reversed, albeit with a retention of some of their Islamic practices and beliefs. In Crossing the Threshold the argument is made that it the critical aspect for the Sunni Muslim eminences enforcing the new orthodoxy was that Muslim and non-Muslim be clear and distinct categories. Therefore, better a Hindu than a heretic.

51k6n6ma-NL._SY344_BO1,204,203,200_ What have I left out of the story? Note that white Europeans are notably absent from the narrative. To some extent this is an artificiality. European “factories” were present on the margins of Mughal India. Jesuits supplanted Muslims as astronomers in the court of Ming China, and were disputants on religious topics in the court of Akbar the Great. Christianity, Islam, and Buddhism, were all closely associated with each other in Central Asia, to the point where it is difficult to tease apart the arrows of causality. In China it seems likely that some varieties of Christianity with ultimate roots in Persia and Central Asia were subsumed into strands of Pure Land Buddhism. But, the point is that history and peoples are subject to general patterns and dynamics, and European colonialism may be thought of as just one important contingent factor. A critical one, but one factor nonetheless.

41JdP75Eu8L._SX321_BO1,204,203,200_ It is hard to deny the influence of European culture and Christianity on Indian national and religious worldviews. Consider Hindutva. Conceived of as a form of Hindu racial nationalism by Vinayak Savarkar, himself an atheist who advocated the dismantling the caste system, it is difficult to understand it without considering the dominant winds of culture in the early 20th century. Those winds invariably blew out of Europe. The colonial imprint, the mirrored reflection of British racial nationalism, is real. Today the intellectual descendants of Savarkar promote bizarre beliefs like the idea that ancient Hindus had flying machines and nuclear weapons, and that astrology is a true science and Ayuvedic medicine is superior to that of the West. It is hard not to see in these beliefs a funhouse distortion of Western movements, such as Christian Science and Creationism. Similarly, the Islamic Creationism of Harun Yahya is explicitly indebted to American evangelical Protestants!

And yet within South Asia the broad trend of confessionalization predates the arrival and dominance of Europeans. It seems entirely likely that a division between Islam and what became Hinduism in the subcontinent was inevitable, as modernity and globalization seem to produce crisper identity groups, which are not diffuse, inchoate, and locally rooted. Yes, illiterate peasant naturally practice syncretistic traditions, but when the illiterate peasant becomes a town dweller a different sort of religious practice takes hold. There is a reason that the city-dwelling Christians of the Late Antique world were contemptuous of the marginally Christianized peasantry, the pagani. The last European people to convert to Christianity were the Lithuanians, in the late 14th century. But the peasantry retained enough of their customary religion that veneration and recollection of sacred groves seem to have persisted down to early modernity.

51W2mxRBC9L._SX326_BO1,204,203,200_ The Reformed Dutch scholar Atonie Wessels wrote a book titled Europe: Was it Ever Really Christian? His thesis is that from an orthodox Protestant perspective which privileges the beliefs and practices of the individual, it can be argued that much of the European peasantry was operationally pagan down to the Catholic and Protestant Reformations of the 16th and 17th century, followed by the secularization of the continent that began after the Peace of Westphalia. In short, during the period after the fall of Rome and Renaissance the elites were steadfastly Christian, but peasants were only nominally so, with their spiritual life dominated by superstitions rooted in local traditions. In contrast, the emergence of Protestant and Catholic identities during the Reformation resulted in a broad based Christian feeling and identity among the populace. So much so that when the Hohenzollerns converted to Calvinism in the early 17th century their subjects remained steadfast in their Lutheranism. But as the populace became more conventionally Christian, the elites began their long slide toward secularism, finally resulting the rise to power of Frederick the Great, who in matters of religion was apathetic at best.

The European example is important, because it shows that even without exogenous European colonialism confessionalism occurs as a society modernizes. The seeds of this confessionalization are clear in South Asia even before the rise to power of the British raj, as Hindu rulers such as Shivaji privileged their own native traditions as against that of the Muslims, while earlier the rulers of Vijayanagar had served as patrons of native religion while the north of the subcontinent was dominated by Muslim polities. It does seem fair to state that Sanatani is not comprehensible without it dialectic with Islam. But, it is important to remember that Buddhism as an organized religion with a missionary impulse predates Christianity by centuries. Obviously institutional religious identity in the subcontinent is not dependent upon the ideas of Europeans and Muslims. What differed with the arrival of Islam is that it was a Weltanschauung which was not digestible to the native cultural traditions.

Though the various Muslim ruling warrior castes held themselves aloof from the people of India, being within the subcontinent, but not of it, it seems inevitable they presumed that their domains were now a permanent part of the Dar-ul-Islam, just as Iran or Central Asia was. Certainly Ibn Battuta could travel in an entirely Muslim India, which operated in parallel with the practices of the vast majority. Over time no doubt the Muslims assumed that the subcontinent would be won over as Iran had. It is hard to remember now, but in the first few centuries of Islamic rule there were periodic anti-Muslim nativist religious eruptions which attempted to overthrow the Muslims, who were perceived as aliens. Prophets arose which told of a time when Islam would fall, and the old religion of the Iranians would come back to the pride of place that it had had. A detailed exploration of this lost world can be found in Patricia Crone’s The Nativist Prophets of Early Islamic Iran, but these movements always make cameos in even traditional works of early Islamic history, such as Hugh Kennedy’s When Baghdad Ruled the Muslim World. But by 1000 A.D. the majority of Persian peasants were Muslim, and Zoroastrianism and its affiliated movements slowly went into their long decline (though still retaining influence through various heterodox Islamic and post-Islamic religious movements).

61H+zZL41QL._SY344_BO1,204,203,200_ In India you have a world where the vision of the Iranian prophets came to be, where Islam which seemed eternal and ever waxing in numbers and influence, lost its hold on power and native dynasties which championed local religious traditions arose. There are many differences between the situation of Iran and India. In no particular order, India is far more populous than Iran, local non-Muslim rulers always managed to retain independence at the far corners even at the height of Islamic power and dominion, and the cultural distance between the Muslims and the natives of India was arguably greater than that between the Arabs and the Persians. Even though the Iranians and northern Indians share Aryan cultural roots and influence, reflected in language and religious ideas, those are distant affinities. In contrast, the Arabs had long been present on the margins of the western Iranian world, and the ecology of much of Iran and Mesopotamia was familiar to them.

One peculiarity of the historiography of India under the Muslims is that many scholars claim that local intellectuals, mostly Brahmins, behaved as if their conquerors did not even exist. This sort of involution though may be less strange than seems on first inspection. Ashkenazi Jews in Central and Eastern Europe are to a great extent a people without a history, as their intellectual class devoted its energies to Talmudic commentary, not recording the history of their people. India was massive, and transformations were pregnant within its cultural matrix in response to the Islamic challenge. The Sikh religion seems an obvious case of synthesis, which while that of Hindu reformist movements such as Arya Samaj seem to sublimate the external variables.

61LXo6U7a4L._SX331_BO1,204,203,200_Though the British may have been a proximate cause for the communal conflicts that tore apart the subcontinent in 1947, they were not the deep cause. As Victor Lieberman observes in Strange Parallels: Europe, Japan, China, South Asia, and the Islands, after 1000 AD there arose several polities dominated by cultural aliens along the edge of Eurasia, such as that of the Muslims in India, the Tai in Southeast Asia and the Manchu in China. But unlike the latter two cases the Islamic elites never sufficiently rooted themselves in the local culture to establish a coherent and unified national identity. While the Manchu racial sense of distinctiveness persisted down to their overthrow, their cultural assimilation to most Han mores was so total that rulers such as Kangxi Emperor arguably became exemplars of Confucian rulers. Though the Tai imposed their language of the Mon and Khmer people whom they conquered, they fostered a genuine cultural synthesis by patronizing the Theravada Buddhism of their subjects and espousing it as their national religion. While the kings of Thailand patronized Brahmins to give their rule a tincture of Hindu legitimacy, the Mughals were styling themselves as Padishahs.

If Dara Shikoh had defeated Aurangzeb and the British had never brought India into their Empire, would history have been different? I would like to hope so, but I doubt so. Akbar had attempted to create a new religion, but it did not last beyond his life. By the 17th century what was becoming Hinduism, and Indian Islam, were already sufficiently developed that they were becoming cultural attractors. Not through cognitive bias, but the weight of inertia of their cultural history and precedent. The transition from Akbar, to Jahangir, to Shah Jahan, and finally Aurangzeb, is one from an individual who brooked the displeasure of Naqsbhandi shiekhs, to one who worked hand in hand with them. An alternative vision is one where the heirs of Akbar turn their back on their dreams of Fergana, and rely upon Rajputs to dominate their lands instead of a mix of Central Asians and native Indians, Hindu and Muslim. Perhaps the Mughals would have become indigenized enough that they would transform into that they would have become fully Indian in their religious identity. Ultimately the answers of history are more complex than can be dreamt of in your post-colonial philosophy, and the white man is neither angel nor the devil, but a subaltern of historical forces.

• Category: History • Tags: History, India, Religion 
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parsi2 In the comments below I made the comment that the Parsi people of India, who reputedly arrived in India ~1000 years ago from Iran, are about 25 percent South Asian. By this, I mean that their ancestry is about 75 percent Iranian (presumably Persian), with 25 percent admixture from South Asian populations amongst whom they lived. But my feeling about this was vague, and I decided to check the scientific literature. Unfortunately there hasn’t been a lot of work done in this area with cutting edge genomics. But a cursory examination shows that there’s been substantial migration of Indian women into the Parsi lineage via the mtDNA. In the figure to the right you see that “PA”, the Parsis, have a lot of “South Asian” mtDNA lineages compared to the Iranian groups. This mostly consists of South Asian branches of haplogroup M. It jumps out to you immediately when looking at the haplotypes that the Parsis carry on their mtDNA. I found less on the Y chromosomes, which are less informative in differentiated South Asians from Iranians in any case (the mtDNA difference is much greater between these two regions), but what I did find is that Parsis can be modeled as 100% Iranian on their paternal lineages. This is probably an exaggeration, but as a stylized fact I think it gets to the heart of the matter.

But what would really be useful are autosomal results. Those were hard to find. Noah Rosenberg’s 2006 paper on Indian genetic differentiation using microsatellites did have a Parsi sample. If you look at the results the Parsi do seem South Asian, roughly equivalent to Pathans, an Iranian speaking group in Pakistan which has strong South Asian affinities. But the sample set does not include any Iranian groups from Iran proper, but rather Middle Eastern groups from the Arab world or the Caucasus. Without such a reference population it is hard to gauge Parsi relatedness.

There was one last hope. Harappa DNA has been collecting results for many years now, and I was hoping that there was a Parsi in the sample. There was, just one. I took the Parsi and compared this individual to various Iranian and a few select Indian groups. Here are the admixture results (edited to show only the relevant ancestral clusters):

Ethnicity S.Indian Baloch Caucasian NE.Euro Mediterranean SW.Asian
Kurd (Iraqi) 0 29 40 4 6 16
Iraqi Arab 1 11 30 0 5 44
Kurd (Iraqi) 1 26 43 5 5 16
Kurd (Iraqi) 1 28 43 5 5 13
Kurd (Iranian) 1 29 41 7 6 12
Kurd Zaza Turkey 2 23 43 6 6 13
Iranian 2 24 43 5 7 13
Kurd (Turkish) 2 26 46 6 6 10
Iranian 2 28 47 7 3 10
Iranian 2 29 43 3 8 8
Iranian 2 30 44 4 2 13
Iraqi Arab 3 20 39 0 10 19
Kurd Kurmanji Iraq 4 21 41 4 7 15
Kurd from Turkey 4 24 41 4 8 12
Iranian 4 26 39 7 7 12
Kurd Yezidi Iraq 4 26 39 4 7 13
Iranian 4 27 41 5 6 11
Iranian 4 29 37 4 4 12
Iraqi Arab 5 19 38 5 7 19
Kurd Kurmanji Iraq 5 24 39 4 8 13
Iranian 5 25 38 5 7 12
Kurd (Iraqi) 5 27 41 5 5 14
Iranian 6 25 37 6 6 12
Kurd (Feyli) 6 25 38 3 7 14
Iranian Khorasani 8 29 35 9 2 11
Afghan Pashtun 14 32 25 12 3 4
Pashtun (Kandahar) 15 34 25 10 0 5
Mumbai Parsi 16 28 28 5 4 12
Afghan Pashtun 20 36 17 11 0 5
Afghan Pashtun 21 33 17 9 2 2
Pashtun 21 35 18 10 0 5
Gujarati Khoja 28 47 13 7 0 1
Gujarati Patel Muslim 34 32 13 3 3 6
Gujarati Sunni Vohra Surti 35 34 13 5 2 4
Gujarati Ganchi 38 42 5 9 3 0
Gujarati Vaishnav Vania 45 36 4 4 1 3
Gujarati Jain 46 36 6 4 0 0
Gujarati Vaniya 52 37 2 6 0 1
Gujarati 53 43 0 0 2 0
Gujarati 56 39 0 0 2 0

The key is to focus on the “South Indian” ancestry. Though this is found in some Iranian groups, it drops off very rapidly once you move past groups like the Pathans. The Parsi individual has 16 percent South Indian ancestral component. Looking at the Iranian individuals, you can probably say that you might expect 5 percent from this population. The question is what is the Indian source population? There’s a lot of variation among these. But, if you take 50 percent South Indian for the South Asian source population, then you get:

(50 percent)*(0.25) + (5 percent)*(0.75) = 16.25%

So at least going by this one individual something like ~25 percent is probably correct for the Parsis in terms of how much “native” South Asian ancestry they’ve picked up. Since they are genetically quite homogeneous at this point an N = 1 might be sufficient to reach a conclusion. I’d be curious if anyone finds anything different.

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Citation: Genetic Evidence for Recent Population Mixture in India
Moorjani et al.

The Pith:In India 5,000 years ago there were the hunter-gathers. Then came the Dravidian farmers. Finally came the Indo-Aryan cattle herders.

There is a new paper out of the Reich lab, Genetic Evidence for Recent Population Mixture in India, which follows up on their seminal 2009 work, Reconstructing Indian Population History. I don’t have time right now to do justice to it, but as noted this morning in the press, it is “carefully and cautiously crafted.” Since I am not associated with the study, I do not have to be cautious and careful, so I will be frank in terms of what I think these results imply (note that confidence on many assertions below are modest). Though less crazy in a bald-faced sense than another recent result which came out of the Reich lab, this paper is arguably more explosive because of its historical and social valence in the Indian subcontinent. There has been a trend over the past few years of scholars in the humanities engaging in deconstruction and intellectual archaeology which overturns old historical orthodoxies, understandings, and leaves the historiography of a particular topic of study in a chaotic mess. From where I stand the Reich lab and its confederates are doing the same, but instead of attacking the past with cunning verbal sophistry (I’m looking at you postcolonial“theorists”), they are taking a sledge-hammer of statistical genetics and ripping apart paradigms woven together by innumerable threads. I am not sure that they even understand the depths of the havoc they’re going to unleash, but all the argumentation in the world will not stand up to science in the end, we know that.

Since the paper is not open access, let me give you the abstract first:

Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent. The date of mixture is unknown but has implications for understanding Indian history. We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that India experienced a demographic transformation several thousand years ago, from a region in which major population mixture was common to one in which mixture even between closely related groups became rare because of a shift to endogamy.

Young Stalin

I want to highlight one aspect which is not in the abstract: the closest population to the “Ancestral North Indians”, those who contributed the West Eurasian component to modern Indian ancestry, seem to be Georgians and other Caucasians. Since Reconstructing Indian Population History many have suspected this. I want to highlight in particular two genome bloggers, Dienekes and Zack Ajmal, who’ve prefigured that particular result. But wait, there’s more! The figure which I posted at the top illustrates that it looks like Indo-European speakers were subject to two waves of admixture, while Dravidian speakers were subject to one!

The authors were cautious indeed in not engaging in excessive speculation. The term “Indo-Aryan” only shows up in the notes, not in the body of the main paper. But the historical and philological literature is references:

The dates we report have significant implications for Indian history in the sense that they document a period of demographic and cultural change in which mixture between highly differentiated populations became pervasive before it eventually became uncommon. The period of around 1,900–4,200 years BP was a time of profound change in India, characterized by the deurbanization of the Indus civilization, increasing population density in the central and downstream portions of the Gangetic system, shifts in burial practices, and the likely first appearance of Indo-European languages and Vedic religion in the subcontinent. The shift from widespread mixture to strict endogamy that we document is mirrored in ancient Indian texts. [notes removed -Razib]

How does this “deconstruct” the contemporary scholarship? Here’s an Amazon summary of a book which I read years ago, Castes of Mind: Colonialism and the Making of Modern India:

When thinking of India, it is hard not to think of caste. In academic and common parlance alike, caste has become a central symbol for India, marking it as fundamentally different from other places while expressing its essence. Nicholas Dirks argues that caste is, in fact, neither an unchanged survival of ancient India nor a single system that reflects a core cultural value. Rather than a basic expression of Indian tradition, caste is a modern phenomenon–the product of a concrete historical encounter between India and British colonial rule. Dirks does not contend that caste was invented by the British. But under British domination caste did become a single term capable of naming and above all subsuming India’s diverse forms of social identity and organization.

The argument is not totally fallacious, as some castes are almost certainly recent constructions and interpretations, with fictive origin narratives. But the deep genetic structure of Indian castes, which go back ~4,000 years in some cases, falsifies a strong form of the constructivist narrative. The case of the Vysya is highlighted in the paper as a population with deep origins in Indian history. Interestingly they seem to be a caste which has changed its own status within the hierarchy over the past few hundred years. Where the postcolonial theorists were right is that caste identity as a group in relation to other castes was somewhat flexible (e.g., Jats and Marathas in the past, Nadars today). Where they seem to have been wrong is the implicit idea that many castes were an ad hoc crystallization of individuals only bound together by common interests relatively recently in time, and in reaction to colonial pressures. Rather, it seems that the colonial experience simply rearranged pieces of the puzzle which had deep indigenous roots.

Indra, slayer of Dasas? Credit: Gnanapiti

Stepping back in time from the early modern to the ancient, the implications of this research seem straightforward, if explosive. One common theme in contemporary Western treatments of the Vedic period is to interpret narratives of ethnic conflict coded in racialized terms as metaphor. So references to markers of ethnic differences may be tropes in Vedic culture, rather than concrete pointers to ancient socio-political dynamics. The description of the enemies of the Aryans as dark skinned and snub-nosed is not a racial observation in this reading, but analogous to the stylized conflicts between the Norse gods and their less aesthetically pleasing enemies, the Frost Giants. The mien of the Frost Giants was reflective of their symbolic role in the Norse cosmogony.


What these results imply is that there was admixture between very distinct populations in the period between 0 and 2000 B.C. By distinct, I mean to imply that the last common ancestors of the “Ancestral North Indians” and “Ancestral South Indians” probably date to ~50,000 years ago. The population in the Reich data set with the lowest fraction of ANI are the Paniya (~20%). One of those with higher fractions of ANI (70%) are Kashmiri Pandits. It does not take an Orientalist with colonial motives to infer that the ancient Vedic passages which are straightforwardly interpreted in physical anthropological terms may actually refer to ethnic conflicts in concrete terms, and not symbolic ones.

Finally, the authors note that uniparental lineages (mtDNA and Y) seem to imply that the last common ancestors of the ANI with other sampled West Eurasian groups dates to ~10,000 years before the present. This leads them to suggest that the ANI may not have come from afar necessarily. That is, the “Georgian” element is a signal of a population which perhaps diverged ~10,000 years ago, during the early period of agriculture in West Asia, and occupied the marginal fringes of South Asia, as in sites such as Mehrgarh in Balochistan. A plausible framework then is that expansion of institutional complexity resulted in an expansion of the agriculture complex ~3,000 B.C., and subsequent admixture with the indigenous hunter-gatherer substrate to the east and south during this period. One of the components that Zack Ajmal finds through ADMIXTURE analysis in South Asia, with higher fractions in higher castes even in non-Brahmins in South India, he terms “Baloch,” because it is modal in that population. This fraction is also high in the Dravidian speaking Brahui people, who coexist with the Baloch. It seems plausible to me that this widespread Baloch fraction is reflective of the initial ANI-ASI admixture event. In contrast, the Baloch and Brahui have very little of the “NE Euro” fraction, which is found at low frequencies in Indo-European speakers, and especially higher castes east and south of Punjab, as well as South Indian Brahmins. I believe that this component is correlated with the second, smaller wave of admixture, which brought the Indo-European speaking Indo-Aryans to much of the subcontinent. The Dasas described in the Vedas are not ASI, but hybrid populations. The collapse of the Indus Valley civilization was an explosive event for the rest of the subcontinent, as Moorjani et al. report that all indigenous Indian populations have ANI-ASI admixture (with the exceptions of Tibeto-Burman groups).

Overall I’d say that the authors of this paper covered their bases. Though I wish them well in avoiding getting caught up in ideologically tinged debates. Their papers routinely result in at least one email to me per week, ranging from confusion to frothing-at-the-mouth.

Related: The Gift of the Gopi.

Citation: et al., Genetic Evidence for Recent Population Mixture in India, The American Journal of Human
Genetics (2013),

(Republished from Discover/GNXP by permission of author or representative)
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Over at Econlog Bryan Caplan bets that India’s fertility will be sup-replacement within 20 years. My first inclination was to think that this was a totally easy call for Caplan to make. After all, much of southern India, and the northwest, is already sup-replacement. And then I realized that heterogeneity is a major issue. This is a big problem I see with political and social analysis. Large nations are social aggregations that are not always comparable to smaller nations (e.g., “Sweden has such incredible social metrics compared to the United States”; the appropriate analogy is the European Union as a whole).

So, for example, India obviously went ahead with its demographic transition earlier than Pakistan. But what this masks is that the two largest states in terms of population in India, in the far north, actually resemble Pakistan in demographics, not the rest of India. Uttar Pradesh, with a population 20 million larger than Pakistan, has similar fertility rate as India’s western neighbor. Bihar currently has a slightly higher fertility rate than Pakistan when you look at online sources (though the proportion under 25 is a little lower, indicating that its fertility 10-15 years ago was lower than Pakistan’s, it is simply that Pakistan is now transitioning toward replacement faster than Bihar).

The key for Caplan’s bet is that over time Uttar Pradesh and Bihar will become a larger and larger proportion of India’s population. Though they’ll probably drop in fertility, for the purposes of Caplan’s bet perhaps the better question is whether Uttar Pradesh and Bihar will attain sub-replacement fertility in 2032, not India. That’s a much different question than India as a whole. I think Caplan has an even chance of winning, but it’s not guaranteed.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Data Analysis, Demographics, India, Pakistan, Population 
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Update: Please do not take the labels below (e.g., “Baloch”) as literal ancestral elements. The most informative way to read them is that they indicate populations where this element is common, and, the relationship of proportions can tell us something. The literal proportion does not usually tell us much.

End Update

I was browsing the Harappa results, and two new things jumped out at me. Zack now has enough St. Thomas Christian samples from Kerala that I think we need to accept as the likely model that this community does not derive from the Brahmins of Kerala, as some of them claim. Their genetic profile is rather like many non-Brahmin South Indians, except the Nair, who have a peculiar attested history with the Brahmins of their region.

But that’s not the really interesting finding. Below is a table I constructed from Zack’s data.

Ethnicity Language S.Indian Baloch Caucasian NE.Euro
Karnataka Brahmin Dravidian 47% 38% 4% 6%
Karnataka Hebbar Iyengar Brahmin Dravidian 49% 36% 5% 5%
Karnataka Iyengar Dravidian 48% 39% 3% 5%
Karnataka Iyengar Brahmin Dravidian 48% 37% 3% 7%
Karnataka Kannada Brahmin Dravidian 51% 35% 3% 5%
Karnataka Konkani Brahmin Dravidian 47% 37% 2% 6%
Kerala Brahmin Dravidian 43% 39% 4% 6%
Tamil Brahmin Dravidian 46% 40% 3% 6%
Tamil Brahmin Dravidian 47% 40% 3% 5%
Tamil Brahmin Dravidian 48% 39% 9% 4%
Tamil Brahmin Dravidian 47% 38% 6% 4%
Tamil Brahmin Dravidian 48% 37% 6% 5%
Tamil Brahmin Dravidian 48% 37% 3% 5%
Tamil Brahmin Dravidian 48% 35% 5% 6%
Tamil Brahmin Iyengar Dravidian 47% 38% 6% 4%
Tamil Brahmin Iyengar Dravidian 47% 35% 6% 6%
Tamil Brahmin Iyengar Dravidian 50% 35% 2% 8%
Tamil Brahmin iyer/iyengar Dravidian 48% 38% 2% 5%
Tamil Brahmin iyer/iyengar Dravidian 48% 38% 4% 5%
Tamil Brahmin iyer/iyengar Dravidian 47% 37% 2% 5%
Tamil Brahmin iyer/iyengar Dravidian 47% 37% 6% 8%
Bengali Brahmin IE 43% 35% 4% 10%
Bengali Brahmin IE 45% 35% 2% 11%
Bengali Brahmin IE 44% 35% 5% 11%
Bihari Brahmin IE 39% 38% 5% 11%
Maharashtra/Madhya Pradesh Saraswat Brahmin IE 47% 39% 1% 6%
Mahrashtrian Desastha Brahmin IE 46% 38% 8% 5%
Oriya Brahmin IE 47% 36% 0% 9%
Punjabi Brahmin IE 33% 41% 13% 10%
Punjabi Brahmin IE 35% 40% 8% 11%
Rajasthani Brahmin IE 32% 38% 9% 15%
Sindhi Pushtikar/Pushkarna Brahmin IE 31% 36% 12% 10%
UP Brahmin IE 37% 38% 2% 14%
UP Brahmin IE 41% 37% 7% 11%

I was curious about the distribution of the “Northeast European” component in South Asia. This element is almost entirely lacking in non-Brahmin South Indians (except for the Nair), but, it is present in non-Brahmin Indo-European speaking Indians, including Biharis and Bengalis. And interestingly, it is present in the same rough fraction in North Indian and South Indian Brahmins regardless of locale, ~5 percent in the former case, and ~10-15 percent in the latter. I initially divided them into two language classes, but noticed that the Maharashtra samples were more like the South Indians.

Then I remembered something random: there is a tradition dividing Indian’s Brahmin communities in two, on a north-south split. The above partition does not perfectly reflect the oral history and custom, but it is very close. The Brahmins of South India are a particularly homogeneous lot. I’d bet that their diversity is a function of cultural evolution and adaptation to local circumstances, not disparate origins. Rather, they derive from some initial migration from a specific North Indian Brahmin community, and then admixed somewhat with another South Indian population (explaining their profiles being closer to the Southern average than that of Northern Brahmins).

Finally, most readers will be aware that I broadly accept the outline in Reconstructing Indian History. But, I do think there were multiple waves of northwest population intrusions into South Asia. In particular, I think the demographically preponderant wave was probably West Asian, while a later group brought some Eastern European ancestry into the mix as well. I think this explains nicely the fact that North Indian Brahmins have a “South Indian” cline but not a Northeast European cline (compare Bengali Brahmins to Punjabi Brahmins, and you’ll see what I mean). One possible model is that a very rapid sweep of an Indo-European speaking population may have occurred across the North Indian plain, overlain upon a local set of populations which had an ANI-ASI cline. The Genographic Project reportedly is going to present results which suggest that the Indian caste system pre-dates the arrival of the Aryans. That would comport well with this model, where earlier groups of northwesterners established a caste-like system, which the Aryans, who later formed the core of the twice-born castes, simply suited to their own needs upon arrival. If you look at Zack’s results using public data sets a very low proportion of “Northeastern European,” equivalent to what you see in South India, is found in a few groups:

- The Dravidian Brahui and Baloch

- Tribes and Dalits

- Austro-Asiatic populations

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Anthropology, India, Indian 
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After posting on Basque mtDNA I wanted to make something more explicit that I alluded to below, that uniparental lineages are highly informative, but they may not be representative of total genome content. This is plainly true in the case of mestizos from Latin America, but we don’t need genetics to point us in the right direction on this score, we have plenty of textual evidence for asymmetry in sexes when it came to admixture events in the post-Columbian era. Rather, I want to note again the issue of South Asia. When it comes to mtDNA the good majority of South Asian lineages are closer to those of East Asia than Western Eurasia. By this, I do not mean to say that that they’re particular close to East Asian lineages, only that if you go back in the phylogeny the South Asian lineages (I’m thinking here of haplogroup M) they tend to coalesce first with East Asian lineages before they do so with West Eurasian lineages.

Here is a quote from one of the definitive papers on this topic:

Broadly, the average proportion of mtDNAs from West Eurasia among Indian caste populations is 17% (Table 2). In the western States of India and in Pakistan their share is greater, reaching over 30% in Kashmir and Gujarat, nearly 40% in Indian Punjab, and peaking, expectedly, at approximately 50% in Pakistan (Table 11, see Additional file 6, Figure 11, panel A). These frequencies demonstrate a general decline (SAA p < 0.05 Figure 4) towards the south (23%, 11% and 15% in Maharashtra, Kerala and Sri Lanka, respectively) and even more so towards the east of India (13% in Uttar Pradesh and around 7% in West Bengal and Bangladesh).

In Iran, over 90 percent of the mtDNA lineages seem West Eurasian. Though I accepted these findings, I was always a bit concerned that the 40 unit chasm between Iran and Pakistan was so large. Additionally, the autosomal studies seem to show that Pakistani populations exhibited affinities to West Eurasians greater than than would be predicted by being ~50 percent West Eurasian. And, as many of you no doubt know the mtDNA does not align well with the Y chromosomal lineages, which seem to indicate a stronger affinity to West Eurasia.

The 2009 paper Reconstructing Indian History resolved some of these confusions. In it the authors inferred that South Asians were a compound population, about ~50 percent West Eurasian, and ~50 percent South Eurasian, with this latter component having distant, but still closer, affinities to East Asians. In other words, the latter component could be easily aligned with the mtDNA, while the former made sense of the Y chromosomal lineages. According to the above paper the West Eurasian component was present at 70-80 percent fractions in Pakistan at the total genome level. This is considerably above the 50 percent for mtDNA, and made more sense of the visible affinities of Pakistanis to West Eurasians on the phenotypic dimension. But look at the rapid drop off mtDNA fraction.

Here’s a table I generated combining the drop off in ANI and mtDNA across the two papers:

If you don’t know the geography of India, the West Eurasian mtDNA fraction falls off a cliff very quickly in Northwest India. In contrast, the autosomal ANI fraction drops, but not nearly as precipitously. The ratio between the two is 2:3 in Pakistan. In Bengal is 1:5, but it is already 1:4 in Uttar Pradesh, which is closer geographically to Pakistan than Bengal (though arguably more ecologically distinct from Pakistan, the linguistic dialects of Uttar Pradesh are far closer to those of Pakistan than of Bengal). I will let you develop your own the story in this case, as there’s obviously a lot there could be said speculatively. Rather, I simply wanted to illustrate the reality that the differences between patterns in uniparental lineages and autosomal DNA can tell you a great deal, despite their disagreements on occasion.

Finally, I want to end on a somewhat different note:

Elevated frequencies of haplogroups common in eastern Eurasia are observed in Bangladesh (17%) and Indian Kashmir (21%) and may be explained by admixture with the adjacent populations of Tibet and Myanmar (and possibly further east: from China and perhaps Thailand).

These proportions are both higher than anything in the autosomal DNA. My parents are both 10-15 percent Southeast Asian in ancestry. But I am willing to bet that they’re slightly on the high side even for Bangladeshis (going by geography). And as for Kashmiris, these populations do often show some East Asian admixture, but generally not so high as 20%. What explains this? I have posited that rather than being intrusive to Bengal, the East Asian populations (Munda?) may have been already present when Indo-Aryan speaking agriculturalists arrived. This could explain a sex bias in assimilation of these populations toward females. In general my rule of thumb is that later population arrivals are correlated with a male bias in ancestry.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Anthropology, Human Genetics, Human Genomics, India 
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With the current economic malaise in the developed economies and the rise of the “B.R.I.C.s” you hear a lot about “China” and “India.” There is often a tacit acknowledge that China and India are large diverse nations, but nevertheless in a few paragraphs they often get reduced to some very coarse generalizations. What’s worse is when you compare China and India to nations which simply aren’t on their scale. For example, over at Brown Pundits there is sometimes talk about India vs. Bangaldesh/Pakistan/Nepal/Sri Lanka. The problem is that the appropriate comparison are specific Indian states, not the whole nation. Uttar Pradesh, the largest Indian state in population, is actually in the same range as Bangladesh and Pakistan. Similarly, when comparing social metrics in Bangaldesh vs. India, one should focus on culturally similar regions, such as the state of West Bengal, not the sum average of India as a nation.

Similarly, we look at frenetic Chinese growth and worry about how they are “leaving us behind” (from an American perspective). But do take a step back to wonder how much the Chinese are leaving the Chinese behind?

Below are two charts which show the yawning chasm within these mega-nations on the scale of states (at a finer grain the variation is even greater). First a rank order of Chinese provinces by GDP PPP, with comparable nations interspersed within. PPP values shouldn’t be taken too literally, and the Chinese data seem to overestimate the values on a province level basis by 10-15%. But you get the general picture.

If these data are correct Shanghai is equivalent to a middle income European nation. With a population of ~25 million that’s not a bad analogy. In contrast isolated Guizhou is in the range of India. Guizhou also has the highest fertility in China, at 2.2.

Now let’s look at India.

Large South Indian states like Tamil Nadu, population ~70 million, have fertility rates around those of Northern European nation-states! In contrast, the huge population states like Uttar Pradesh and Bihar have fertility profiles similar to Sub-Saharan Africa.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: China, Data Analysis, India 
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Krishna with milk-maids

Unlike in some Asian societies dairy products are relatively well known in South Asia. Apparently at some point my paternal grandmother’s family operated a milk production business. This is notable because Bengal is not quite the land of pastoralists. In much of North India milk and milk-products loom larger, in particular ghee. People don’t tend to consume what makes them ill, and even accounting for some processing in the form of butter, most researchers have assumed a substantial number of South Asians must be lactase persistent. That is, they can extract nutritive value out of the lactose sugar present in milk (in addition to fat and protein). Additionally, many South Asians have the well known -13910 C>T common in Western Eurasia. How do I know this? Because I share my genetic information with lots of South Asians, and some of them, especially Punjabis, come up as “lactose tolerant” on that allele.

A new paper in Molecular Biology and Evolution confirms this with a larger data set, over 2000 samples from South Asia. The geographical pattern is exactly what you’d expect:

-13910 C>T is modal in Northwest India, where cattle culture is most widespread across society. It drops off as one moves south, east, and north, into zones where milk production and products are less integral, or lacking, in the cultural toolkit. The ability to digest lactose as an adult is interesting and nice because it’s a perfect illustration of the power of natural selection to reshape traits. Relatively genetically close populations can be very different depending on whether the trait is favored, or not.

What’s the case here? There are many statistical genetic tricks that they used, but I’ll spare you that. First, remember that lactase persistence has emerged multiple times. There’s a mutation which is very common in Northern Europe, which extends into Central Eurasia. This is the same one discussed in this paper. Other mutations are localized to the Arabian peninsula and East Africa. The convergent evolution suggests some combination of:

1) Strong selection pressure for this trait in dairying cultures

2) A large mutational target, in that a wide range of changes seem to effect the appropriate shift

3) Low levels of gene flow which allow for different variants to flourish. If gene flow was too ubiquitous than the earliest variant would sweep all the others before it

It turns out that the overwhelming majority of detected variants known to allow for lactase persistence in India is the West Eurasian one. This is interesting, because there are various genetic and cultural reasons to connect South Asia to West Eurasia (even Europe). There is some genetic evidence to imply that the West Eurasian mutation derives from the Volga region. Though the word does not appear in the text of the paper it does not take a rocket-scientist to infer that this allele may have been introduced by Indo-Aryans. The main counter-argument against this is that it seems that their statistical corrections imply that geography predicts the variation of the trait more than linguistic affinity (i.e., if there was a sharp difference between Indo-Europeans and Dravidians who were neighbors it would be of great interest) by and large (the Austro-Asiatics and Tibeto-Burmans are exceptions, language is a good predictor of the lack of lactase persistence). These results make me less skeptical of the possibility that most of the recent admixture from West Eurasia in South Asia was due to the Indo-Europeans. Perhaps they did push south in a continuous manner gradually, and culturally were discontinuous? This is theoretically not implausible. On the other hand, I do wonder if perhaps the West Eurasian mutations pre-dates the Indo-Europeans. The authors of the paper observe that pastoralism has a 7,000 year history in South Asia. Not as long as Europe, but a long time indeed.

But these results don’t tell us just about ancestry. The region around LCT in Europeans shows a lot of evidence of natural selection. What about in South Asians? It seem that some of the signatures do persist in India. Additionally, there is a strong correlation between pastoralism and lactase persistence. This stands to reason, but it is nice to have that confirmed. This suggests that we need to be careful about inferring too much in regards to ancestry from this locus: it is not a neutral proxy, as it is subject to positive or negative natural selection. The aggregate frequency in their pooled sample is ~0.20, with high bounds in the range of ~0.75. Based on earlier Y and mtDNA work the authors suggest that it is more likely that these frequency variations and the overall level is a function of natural selection more than ancestry. In other words, a small group of pastoralists brought the favored allele, which spread rapidly to ecologically favored niches.

(Republished from Discover/GNXP by permission of author or representative)
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One of the things that happens if you read ethnographically thick books like Nicholas Dirks’ Castes of Mind: Colonialism and the Making of Modern India is that you start to wonder if most castes were simply created by the British and for the British. Granted, even Dirks would not deny the existence of Brahmins prior to the British period, but those who work within his general paradigm might argue that a group like Kayasthas were the product of very recent developments (e.g., the uplift of a non-Brahmin literate group willing to serve Muslim and British rulers). The emergence of genomics complicates this sort narrative, because you can examine relationships and see how plausible they would be given a particular social model.

Zack Ajmal is now at 90 participants in the Harappa Ancestry Project. He’s still undersampling people from the Indo-Gangetic plain between Punjab and Bengal, but that’s not his fault. Hopefully that will change. He posted K = 4 recently for the last 10 participants, but I notice K = 12 in his spreadsheets. So this is what I did:

1) I aligned the ethnic identification information with the K = 12 results.

2) I removed relatives and those who were not 100% South Asian.

3) I added some reference populations in. These are all upper case below. All other rows are individuals (HRP numbers provided).

4) I removed five ancestral groups. The three Africans, Papuans, and Siberians.

Then I arranged the rows alphabetically by ethnic identification. Helpfully many people provided their caste information as well. I’ve uploaded a csv with the information. But skim the plots & table below. Those of you who are brown can probably make more sense of them than I can. But I think some of the patterns are pretty interesting already. For me the big thing that jumps out is how uniform some of these caste groups are. Remember that HRP22 and HRP23 are my parents. If the British made these groups up, they were very punctilious about their ancestral make up in constituting them!

First, this is the visualization of the genetic distance between the groups below:

Most South Asians in the Harappa Ancestry Project are S Asian + Baloch/Caucasian + European. In that order. But there are some weird patterns which other genome bloggers have already noted, but I thought would be nice to reiterate with Zack’s larger data set.

There’s a pretty interesting disjunction between the Baloch/Caucasian and European components. Mind you, these are very close genetically. But it’s very instructive that their lowest frequency in the northern parent of the continent is focused around the Brahui, a Dravidian group amongst the Baloch in Pakistan. To a great extent aside from the language, the Brahui, Baloch, and Makrani are interchangeable. And the Dravidian groups in Southern India seem to lack it, excluding those who are likely relatively newcomers, the Brahmins and the Jews.

ID Ethnicity S Asian Baloch/Cauc Kalash SE Asian SW Asian European NE Asian
HRP0060 Andhra Pradesh 78% 14% 1% 4% 0% 0% 1%
HRP0061 Andhra Pradesh 77% 14% 3% 3% 0% 0% 0%
HRP0024 Andhra Pradesh (Hyderabadi) 65% 21% 3% 4% 1% 5% 0%
HRP0009 Andhra Pradesh Reddy 76% 18% 2% 1% 0% 0% 2%
HRP0076 Andhra Pradesh Reddy 74% 21% 1% 1% 0% 0% 1%
BALOCHI 29% 57% 3% 0% 6% 1% 0%
BENE ISRAEL JEWS 47% 26% 2% 1% 17% 5% 0%
HRP0049 Bengali 69% 11% 4% 6% 0% 5% 3%
HRP0023 Bengali 64% 10% 2% 11% 1% 4% 2%
HRP0022 Bengali 63% 14% 1% 11% 0% 3% 5%
HRP0054 Bengali Brahmin 61% 20% 4% 3% 0% 10% 0%
HRP0077 Bengali Brahmin 58% 21% 5% 1% 0% 10% 2%
HRP0050 Bengali/Oriya 68% 14% 1% 5% 1% 4% 2%
HRP0003 Bihari Brahmin 55% 25% 4% 0% 0% 12% 2%
HRP0032 Bihari Kayastha 71% 14% 4% 3% 0% 5% 1%
BRAHUI 26% 60% 3% 0% 6% 1% 0%
BURUSHO 36% 36% 8% 2% 0% 7% 5%
HRP0028 Caribbean Indian 69% 15% 3% 3% 1% 5% 1%
HRP0027 Caribbean Indian 66% 13% 3% 5% 0% 5% 0%
COCHIN JEWS 60% 22% 1% 3% 8% 3% 0%
HRP0026 Goan Catholic Brahmin 64% 24% 4% 0% 0% 4% 3%
HRP0058 Gujarati 82% 13% 2% 0% 0% 3% 0%
HRP0068 Gujarati 82% 12% 3% 0% 0% 2% 0%
HRP0071 Gujarati 79% 13% 2% 1% 1% 3% 0%
GUJARATIS 75% 17% 2% 0% 0% 4% 0%
HRP0078 Karnataka 72% 17% 3% 3% 2% 1% 0%
HRP0017 Karnataka Iyengar 65% 24% 3% 2% 0% 5% 0%
HRP0079 Karnataka Iyengar Brahmin 66% 20% 4% 1% 1% 6% 0%
HRP0088 Karnataka Kannada Brahmin 67% 21% 3% 1% 0% 4% 0%
HRP0025 Karnataka Konkani Brahmin 66% 22% 1% 3% 1% 6% 0%
HRP0044 Kashmiri 49% 31% 6% 0% 1% 9% 3%
HRP0021 Kashmiri 43% 37% 6% 0% 1% 11% 0%
HRP0067 Kerala Brahmin 61% 27% 3% 2% 1% 3% 1%
HRP0038 Kerala Christian 67% 24% 3% 3% 1% 1% 0%
HRP0053 Kerala Muslim Rawther 72% 17% 3% 2% 1% 0% 3%
HRP0090 Maharashtra/Madhya Pradesh 65% 22% 4% 0% 0% 4% 2%
HRP0047 Mahrashtrian Desastha Brahmin 64% 24% 5% 1% 0% 4% 0%
MAKRANI 24% 58% 3% 0% 7% 1% 0%
MALAYAN – KERALA TRIBE 84% 0% 0% 8% 0% 0% 2%
NORTH KANNADI 87% 4% 0% 4% 1% 0% 1%
PATHAN 37% 41% 6% 1% 2% 11% 0%
HRP0064 Punjabi 59% 25% 4% 2% 0% 7% 0%
HRP0012 Punjabi 50% 35% 4% 0% 1% 7% 2%
HRP0073 Punjabi 49% 33% 6% 0% 1% 7% 1%
HRP0086 Punjabi (1/2), Sindhi (1/2) 45% 38% 7% 0% 2% 7% 0%
HRP0019 Punjabi Brahmin 50% 30% 5% 0% 0% 11% 1%
HRP0004 Punjabi Brahmin 46% 36% 6% 0% 0% 9% 0%
HRP0006 Punjabi Jatt 45% 36% 4% 1% 1% 12% 0%
HRP0005 Punjabi Jatt 44% 36% 5% 1% 0% 12% 0%
HRP0008 Punjabi Jatt 42% 37% 5% 0% 0% 15% 0%
HRP0033 Rajasthani Brahmin 47% 31% 5% 2% 0% 14% 0%
SAKILLI – TAMIL DALIT 86% 6% 0% 4% 1% 0% 1%
SINDHI 44% 40% 5% 0% 1% 5% 0%
HRP0062 Sindhi 40% 37% 9% 0% 2% 10% 0%
HRP0039 Sindhi (1/2), Balochi (1/2) 39% 45% 5% 1% 3% 3% 0%
SINGAPORE INDIANS 70% 18% 3% 3% 0% 3% 1%
HRP0055 Sourastrian 70% 16% 1% 4% 0% 5% 0%
HRP0031 Sri Lankan (1/2), Telegu (1/2) 82% 8% 2% 5% 0% 0% 0%
HRP0014 Tamil Brahmin 67% 24% 1% 1% 0% 5% 0%
HRP0084 Tamil Brahmin 66% 22% 4% 2% 0% 4% 1%
HRP0016 Tamil Brahmin 66% 26% 4% 1% 0% 3% 0%
HRP0057 Tamil Brahmin 64% 24% 3% 2% 0% 5% 0%
HRP0048 Tamil Brahmin 63% 25% 4% 2% 0% 4% 0%
HRP0072 Tam. Brah. Iyeng. (1/2) Hebbar/Karn. Iyeng. (1/2) 64% 22% 5% 1% 0% 4% 1%
HRP0041 Tamil Brahmin Iyer 67% 22% 2% 1% 0% 5% 1%
HRP0075 Tamil Brahmin Iyer 65% 21% 3% 2% 0% 7% 0%
HRP0013 Tamil Muslim 75% 11% 4% 6% 2% 0% 0%
HRP0066 Tamil Nadar 81% 11% 1% 2% 1% 0% 3%
HRP0007 Tamil Nadar 80% 9% 1% 5% 2% 0% 0%
HRP0065 Tamil Nadar 78% 14% 0% 3% 1% 0% 1%
HRP0070 Tamil Vishwakarma 87% 3% 0% 2% 2% 0% 4%
HRP0069 Tamil Vishwakarma 83% 8% 0% 3% 1% 0% 0%
HRP0085 Thathai Bhatia 40% 41% 8% 0% 0% 9% 0%
HRP0051 UP 54% 22% 2% 4% 6% 8% 0%
HRP0029 UP Brahmin 56% 23% 8% 1% 0% 10% 0%
HRP0063 UP Brahmin 55% 25% 5% 1% 0% 11% 0%
HRP0052 UP Kayasth 65% 23% 3% 3% 0% 4% 0%
HRP0056 UP/MP/Marathi 54% 29% 5% 0% 0% 7% 2%
(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Anthropology, Genetics, Genomics, India 
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School girls in Hunza, Pakistan

A few days ago I observed that pseudonymous blogger Dienekes Pontikos seemed intent on throwing as much data and interpretation into the public domain via his Dodecad Ancestry Project as possible. What are the long term implications of this? I know that Dienekes has been cited in the academic literature, but it seems more plausible that this sort of project will simply distort the nature of academic investigation. Distort has negative connotations, but it need not be deleterious at all. Academic institutions have legal constraints on what data they can use and how they can use it (see why Genomes Unzipped started). Not so with Dienekes’ project. He began soliciting for data ~2 months ago, and Dodecad has already yielded a rich set of results (granted, it would not be possible without academically funded public domain software, such as ADMIXTURE). Even if researchers don’t cite his results (and no doubt some will), he’s reshaping the broader framework. In other words, he’s implicitly updating everyone’s priors. Sometimes it isn’t even a matter of new information, as much as putting a spotlight on information which was already there. Below is a slice of a bar plot from Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. It uses STRUCTURE with K = 7. To the right of the STRUCTURE slice are two plots of individual data on French and French Basque from the same HGDP data set using ADMIXTURE at K = 10 from Dodecad.


Repeated runs and higher K’s make it clear that the French Basque lack a “West Asian” aspect which other French, and Iberians as well, have. Some of this is clear in the paper I referenced above as well…the key is you have to look at the supplements at K = 6. Because the Basque are the only native non-Indo-European speakers in Western Europe, their origin and relationship to nearby populations has always been of interest (they also have the highest Rh- frequency of world populations). Granted, the French Basque are very similar genetically to the French as a whole. But, it is obviously highly informative that they lack an ancestral component in totality which seems to exist at low but consistent levels across Western European populations. The only other European population at K = 15 who lack the West Asian component in totality are Finns (the Lithuanians come very close).

This is all preamble to a discussion of a post Dienekes put up today, A solution to the problem of Indo-Aryan origins. Remember that Dienekes has been “playing” with ADMIXTURE for only a few months. To claim to have found a ‘solution’ to a problem as intellectually and politically intractable and explosive as this is rather bold. The crux of the matter is that at a certain confluences of K’s and population sets Dienekes has discovered a distinctive signature of ancestry which seems to be modal on the north slope of the Caucasus, and spans India and Europe. He terms this “Dagestani,” due to the fact that among a population sample from this province in Russia this ancestral component is overwhelmingly dominant. The patterns of Dagestani admixture in Europe and India are curious and suggestive.

1 – In Europe the frequencies are low, but irregularly distributed (excepting around the North Caucasus). Scandinavians and British have appreciable fractions, Finns and Southern Europeans do not. Here’s Dienekes:

Interpreting this pattern is not easy, but it does seem that this component seems to have a V-like distribution, achieving its maximum in Caucasus and its environs, then undergoing a diminution, and achieving a secondary (lower) frequency mode in NW Europe.

The surprising appearance of the homonymous Dagestan component in India suggests a widespread presence of a common ancestry element. The West Asian element, by comparison seems to have a more normal /-like distribution around its center in Anatolia-Caucasus-Iran region. It does reach the Atlantic coast, but is lacking in Scandinavia and Finland, and also in India itself.

2 – South Indian Brahmins have appreciable fractions, but non-Brahmins in the same region do not. In contrast, those who come from Indo-Aryan speaking backgrounds do seem to have Dagestani ancestral components, irrespective of other aspects of ancestry. For example Pakistanis don’t have that much more Dagestani than South Indian Brahmins or Gujaratis. Also compare the relatively narrow window of Dagestani ancestry variance among Dodecad South Asians (I’m DOD075). DOD088 is from what I recall a Reddy from Andhara Pradesh, a non-Brahmin but non-low caste. It is interesting that they have a high proportion of “Pakistan,” but no Dagestani. I have ~10% Dagestani, but no Pakistani.

Below is K = 10 for a selection of populations. Dienekes has now included in two non-Indo-European speaking Pakistani populations: the Brahui (Dravidian) and Burusho (linguistic isolate in the mountains of Pakistan):

Some general patterns are evident. The light blue is indicative of generic “Indian” ancestry. It is not found in appreciable proportions outside of subcontinental populations (or those of recent subcontinental origin). The same with the red, and light orange. For your reference the dark orange is a “Northern European” component, modal in Lithuania. The light and dark Green are both East Asian components. The dark blue is a “West Asian” component modal in Georgia, and prominent across Europe with declining as a function of distance from the eastern shore of the Black Sea (this is surely the West Asian which distinguishes the French from the French Basque). I believe that the light purple dominant in the Brahui and the light red dominant in the Burusho probably form as a compound the aforementioned Pakistani component. The dark purple is the Dagestani.

587px-Dravidische_SprachenFirst, a word on the Brahui. These are a group of tribes who reside in northern Balochistan in Pakistan. A small number are even to be found in Afghanistan. Historically they have had close relations with the Baloch, an Iranian speaking cluster of tribes who totally envelop the Brahui. The Brahui do speak a Dravidian language, of a family dominant in South India and found in isolated regions of Central and Eastern India. There are two broad models for the existence of a Dravidian language in Pakistan. The first is that the Brahui are remnants of more widely spoken Dravidian languages which date back to the Indus Valley civilization. The second is that the Brahui arrived during the medieval period from another region of South Asia where Dravidian languages were more common. Assuming either model, it has long been presumed that their involution by the Baloch has had a strong impact on the Brahui genetically; the two groups are very close. This is evident in Dienekes’ results as well. But observe that the Baloch are the group which seems more cosmopolitan in ancestry than the Brahui. If the Brahui were Dravidians from deep in India it seems that they would have a greater residual component of India-specific ancestry (light blue and orange). This is not so. In fact the Baloch have more of the Indian ancestral component than the Brahui. The Brahui component is found across Pakistan, and into India, albeit at lower proportions. Naturally, the Baloch have the second highest fraction. I believe these results should shift us toward the position that the Brahui are indigenous in relation to the Baloch, and that the Baloch ethnic identity emerged through the shift of a Brahui substrate, as evidenced by the greater cosmpolitanism of the Baloch. Additionally, Dienekes observes that the Brahui have a lower proportion of the Dagestani component than most other Pakistani groups, and several Indo-Aryan groups in India proper.

The Burusho are event more interesting than the Brahui. Unlike the Brahui the Burusho are very isolated in the mountainous fastness of Baltistan in northern Pakistan. Additionally, their language, Burushashki, is a linguistic isolate. Others of the class are Basque and Sumerian. In general it is assumed that linguistic isolates were once part of broader families of languages which have gone extinct. Burushashki probably persists in large part because of the geography which its speakers inhabit. Mountainous areas often preserve ethnic and linguistic diversity because the terrain allows for the persistence of local variety. I believe it is plausible that the Burusho have been far more isolated than the Brahui. This seems to show up in the ADMIXTURE plot, the Burusho have a greater proportion of their modal ancestral component than the Brahui. Additionally, the Burusho have even an smaller component of Dagestani than the Brahui.

Below is a chart Dienekes constructed ordered by proportion of Dagestani for his South Asian populations. Next to it I’ve placed a chart from a PCA which has some of the same population samples. Compare & contrast:


The PCA is looking at between population variation in totality. So naturally the Dagestani component isn’t going to be predictive of that. Rather, it speaks to the possibility which Dienekes is mooting: that the Dagestani component spread in the India subcontinent with the Indo-Aryans specifically, overlying the local resident substrate. In South India this meant that Brahmins brought this, mixing with the indigenous Dravidian population. In Pakistan the Indo-Aryan, and Iranians, were overlain on a substrate which were the ancestors of the Burusho and Brahui. The dominant signal of genetic relationship has to do with the substrate, not the Indo-Aryans. So that’s what’s going to show up on the PCA. In other PCA plots the model where South Indian Brahmins are a linear combination of a Pakistani-like population and a Dravidian population becomes clearer. But when you look at ancestry using something like ADMIXTURE you have the potential to tease apart different components, and so uncover relationships which may have been obscured when looking at aggregate variation.

dieDienekes’ model seems to post three steps in rapid succession ~4,000 years ago. A background variable which must be mentioned is that one must account for the Mitanni, a dominant Syrian power circa 1500 BC where a non-Indo-European language was the lingua franca, and yet a definite Indo-Aryan element existed within the elite. Indo-Aryan specifically because the Indo-European element within the Mitanni was not Iranian, but specifically Indo-Aryan. An easy explanation for this is that the Indo-Aryan component of the Indo-Iranian branch of the Indo-European languages crystallized outside South Asia, and independently reached Syria and India. In Syria it went extinct, while in India it obviously did not. By Dienekes’ model the Mitanni would be rather closer to the urheimat of the Indo-Aryans.

An aspect of his model which I do not understand is why it has to be Indo-Aryan, instead of Indo-Iranian. The South Asian population which the Dagestani component is modal, the Pathans, are Iranian, not Indo-Aryan. Additionally, this model seems to not speak in detail to the existence of the Dagestani element among Europeans. Here is a sorting of European populations (with Iranians included) by the Dagestani component:

Population Dagestan
Urkarah 93
Lezgins 47.9
Stalskoe 38.7
Adygei 16.4
Orcadian (Orkney) 12.6
Georgians 12.4
White_Utahns 11.2
Iranian 10.9
Scandinavian_D 10.2
Armenian_D 9.9
German_D 9.1
Turks 8.8
Armenians 8.4
French 7.9
Hungarians 7.5
Russian_D 6.3
Spanish_D 4.6
North_Italian 4.5
Spaniards 4.4
Romanian 4.1
Finnish_D 4.1
Russian 4
Greek_D 3.8
Portuguese_D 3.6
Tuscan 3.5
Tuscans 3.4
Lithuanians 2.9
S_Italian_Sicilian_D 2.8
Belorussian 2.5
Cypriots 2
Sardinian 1.5
French_Basque 0.7

There is here a strange pattern of rapid drop off from the Caucasus, and a bounce back very far away, on the margins of Germanic Northwestern Europe. This to me indicates some sort of leapfrog dynamic. A well known illustration of this would be the Ugric languages. The existence of Hungarian on what was Roman Pannonia is a function of the mobility and power of Magyar horseman, and their cultural domination over the Romance and Slavic speaking peasantry (their genetic impact seems to have been slight). No one believes that Germanic languages are closely related to Indo-Aryan (rather, if there is structure in Indo-European beyond Indo-Iranian, Celtic, etc., it would place the Indo-Iranian languages with Slavic). So what’s going on? I think perhaps the Dagestani component is part a reflection of the common Indo-European origin in that region. For whatever reason that signal is diminished in much of the rest of Europe. Perhaps Southern Europe was much more densely populated when the Indo-Europeans arrived. Additionally, it seems highly likely that in places like Sardinia, much of Spain, and Cyprus, Indo-European speech came through cultural diffusion (elite emulation) and not population movement. Or perhaps we’re seeing the vague shadows of population admixtures on the Pontic steppe, where distinct Germanic and Indo-Iranian confederations admixed with a common North Caucasian substrate.

Going back to India, let’s revisit the model of a two-way admixture between “Ancestral North Indians,” who were genetically similar to Europeans and West Asians, and “Ancestral South Indians,” who were closer to, but not very close to, East Eurasians. The ANI & ASI. The ASI were probably one of the ancient populations along the fringe of southern Eurasia, all of whom have been submerged by demographic movements from other parts of Eurasia over the past 10,000 years, excepting a few groups such as the Andaman Islanders and some Southeast Asian tribes. The model was admittedly a simplification. But taking that model as a given, and accepting that the Dagestani element is in indeed Indo-Aryan, we can infer that the ANI were not Indo-European. It is notable that the South Indian Brahmins have elevated fractions of both the Brahui and Burusho modal components. This is probably indicative of admixture of the Indo-Aryan element in the Indus Valley, prior to their expansion to other parts of India. I assume one of the languages spoken was Dravidian, though if ancient Mesopotamia was linguistically polyglot at the dawn of history I would not be surprised if the much more geographically Indus Valley civilization was as well.

Aishwarya Rai

The irony is that today when someone refers to a “Dravidian” physical type, they’re not talking about someone who looks like a Pakistani. They’re talking about someone who looks South Indian, where most Dravidian languages are spoken. But combining the inference from Dienekes’ model and the previous two-way admixture model, you reach the conclusion that lighter skin and more West Asian features among South Asians may be more due to Dravidian-speaking ancestors in the Indus Valley, not Indo-Aryans! It goes to show the wisdom of differentiating linguistic classes from biological ones when discussing historical population genetics. Unfortunately wisdom most of us interested in these topics do not show, alas.

As I like to say, interesting times….

Note: If you leave a comment, please don’t be smarter-than-thou in your tone. I have stopped publishing those sorts of comments because the reality is that most of them have not been that smart or informed. At least by my estimation. If you actually are smarter than the average-bear, and impress me with your erudition and analysis clarity, I’ll probably let your comment through no matter your attitude. But I wouldn’t bet on it if I were you, so show some class and humility. Most of us are muddling through.

Image Credit: Georges Biard, iStockPhoto

(Republished from Discover/GNXP by permission of author or representative)
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I mentioned a few days ago that a friend was trying to get together some data to analyze the genetic variation of South Asians. By a strange coincidence Dienekes just published a more detailed analysis of South Asians…and uncovered something very interesting, though not that surprising. Some technical preliminaries:

A note of caution: The reduced marker set (~30k) means that a lot of noise is added in the admixture estimates. In particular, many individuals are likely to get low-level admixture from population sources that can be attributed to noise. But, as we will see, the small marker set does not really affect either the power of the GALORE approach, or of ADMIXTURE to infer meaningful clusters.

In addition to the various online sources of public data Dienekes got about a dozen South Asians. I was one of those South Asians, DOD075. In many ways I’m a rather standard issue South Asian, similar to Gujaratis, except that I have a substantial ‘East Asian’ component. More concretely, between 1/6 and 1/7 of my ancestry seems to be of eastern origin, far higher than the norm among South Asians. The rest of my ancestry was mostly South Asian specific, with a minor, but significant ‘West Asian’ component common across northern India.

Rerunning with more data with different samples Dienekes came out with a different set of ancestral components. Of particular interest to me he broke down the East Asian between East Asian proper and Southeast Asian. Below are a selection of populations with ancestral components + me. I’ve also renamed a few components. North Kannadi = Dravidian and Irula = Indian tribal. Indian = Generic Indian. Looking at the Fst it seems that Indian endogamy and population bottlenecks has had an effect…look at the North Kannadi distance from everyone else.


Remember that in the previous analysis I was very similar to a Gujarati, except with an East Asian element. My supposition that my ancestry has some connection to Burma seems to be supported by these results. Looking at my balanced ratio between East Asian and Southeast Asian, that is what one might expect from someone of a Burman ethnicity. I am not saying that I have recent Burman ancestry per se. Rather, Ahom, Mizo, Chakma, and a range of tribal populations from the liminal zone between South and Southeast Asia may suffice. The main other option is that I have a great deal of Munda ancestry. Not implausible in light of the likelihood that Munda brought rice agriculture to northeast South Asia, and pre-date Indo-Aryans, and possibly Dravidians, in Bengal. How would I distinguish these possibilities? I’ve ordered 23andMe kits for both my parents. The most likely candidate for recent Southeast Asian ancestry is my paternal grandfather. If the admixture event was recent, if I have a recent ancestor(s) of “hill tribe” origin, I would expect to see more linked regions of East/Southeast Asian origin than if the admixture was ancient (and so distributed more equitably across DNA strands due to recombination).

But the bigger point of Dienekes’ post is what he terms “Dagestani” ancestry across much of Eurasia. I’ll quote him:

The most exciting thing, however, is the fact that the origins of a part of the West Asian component of my previous analyses can be partially located: it is the purple component centered in Dagestan, i.e., among Northeast Caucasian speakers such as Lezgins, and the Dargins who inhabit Urkarah.

Readers of this blog may remember the surprising appearance of this Lezgin-specific component in the Balkans (but not Greeks) a few weeks ago. Now it has turned up as a substantial component in India as well.

Back then, I speculated that this component may derive from a prehistoric population that was spread in (but not limited to) the northern arc of the Black Sea from the Balkans to the Caucasus. Even in this analysis, you can see that both Romanians and Hungarians have some of it, and so do Lithuanians and Belorussians, while Tuscans (like the Greeks of my previous experiment) do not.

Hence, this component stretches from at least the Baltic to India, but is largely absent in southern Europe. I will go out on a limb and propose that this component is representative of a non-Indo-European component in the ancestors of the Indo-Iranians.

Paul Conroy observes that on this finer-grained analysis I don’t have any “West Asian” at all. What had previously been West Asian terms out to have been, in my case, a compound of Dagestani + European. I can’t say that I’m that surprised by this. Years ago I noticed that HGDP STRUCTURE analyses were always giving suggestive signs of a connection between West-Central Eurasia and South Asia.

Who were the Indo-Iranians? I lean toward the proposition that they do derive from the Andronovo culture of the Eurasian steppe. This would date the entrance and expansion of Indo-Aryans in northern India 3-4,000 years ago. I also contend that the dominant element of ancestry among modern South Asians is not Indo-Aryan. Rather, it is an ancient stabilized hybrid of pre-agricultural societies in the Indus valley and Neolithic farmers who originated from what is today western Iran and eastern Anatolia. Therefore, I posit that the “Aryanization” of the Indian subcontinent is properly modeled as the same processes which led to the emergence of an Anatolian and Rumelian Turkish identity; a small elite population which forces a identity shift among the majority.

Back to farming:

As I’ve remarked in the past, Eurasia can be broadly seen as the playground of three major groups of people: the Caucasoids of the West, the Mongoloids of the East, and a southern group of people which is most strongly represented in South Asia, but whose presence can be detected in Southeast Asia as well, although in the latter case it has been marginalized and/or absorbed by the arrival of Mongoloids.

This southern group of people has sometimes been called “Australoid” because of its perceived resemblance to Australo-Melanesians. Indeed, in my K=5 mega-analysis an affinity between Papuans/Melanesians and people of South and Southeast Asia is apparent. These “Australoids” are very old populations, probably stemming from the early Out-of-Africa coastal dispersal route, and we shouldn’t be tricked by their phenotypic similarity into thinking that different groups of them are particularly close genetically. Just as “black Africans” are not the same, neither are the “Australoids” and mixed-”Australoids” at the shores of the Indian Ocean.

It is probably the invention of agriculture that is responsible for their marginalization. In Africa, the Pygmies and Bushmen have been absorbed or pushed aside by the demographic Bantu juggernaut, with a few other language groups also hitching a ride on the agriculture/pastoralism economy. In West Eurasia, where agriculture was invented earliest, pre-agricultural populations left no traces. In East Eurasia, the agriculturalists could not expand to the far north where many relic populations exist, but they could (and did) move to the south where they assimilated or drove away pre-existing populations, leaving a few of thems, like the Taiwanese Atayal as partial remnants of the older population stratum.

The Irula are South Indian tribals, so they are the the closest one can get to South Asian autochthons, and yet even they presumably have a large minor component of “Ancestral North Indian.” The tribal groups in Reconstructing Indian Population History all exhibited proportions on the order of ~40% ANI. It seems that agriculture “stalled” in the Indus valley and the highlands to the west for thousands of years in South Asia. During this period of stalling I believe that the farmers absorbed a great deal of genetic material from the indigenous hunter-gatherers, and so produced a “distinctive” Indian genetic profile. More West Eurasian than not, but with a very large dollop of the ancient substrate of southern Eurasia which had a distant, but closer, affinity with that of East Asia. Once social and cultural forces allowed for the rapid expansion of farmers there was a wave of advance from the Indus valley east and south. In the east the proto-Indians would have encountered Mundari speaking groups drifting who practiced rice agriculture, which they also adopted. In the south the proto-Indians would have encountered more hunter-gatherers. Many of the tribal people in India are today facultative hunter-gatherers, herders, and extensive farmers. I believe that these marginal proto-Indian groups assimilated hunter-gatherers more easily than would have otherwise been the case because some of the proto-Indians reverted to a hunter-gatherer lifestyle in the agriculturally unsuitable highlands of the Deccan and Chota Nagpur. The social boundaries in the uplands of South India were such that the line between hunter-gatherer and farmer was more fluid than elsewhere, explaining the former’s greater genetic impact through intermarriage and assimilation.

This sort of general dynamic probably applies to Indo-Europeans. There is no reason why the original Indo-European tribes could not have been compounds who picked up different ancestral components in their peregrinations. Compare the various Turkic people, Anatolian Turks, Chuvash, and Yakut. All of them have affinities with nearby peoples, despite having a common Turkic culture and genetic component. One notable trend in Europe is that while the French have a minor, but significant West Asian component, the Basque have none of it. Dienekes’ sample is small, but it looks as if Scandinavians have more of this than the Finns. This West Asian component may not have been the dominant one among the Indo-Europeans, but I suspect it was a significant one. If the original speakers of proto-Indo-European did not have it, they likely absorbed early on, just as the West Asians absorbed a native South Asian element in the Indus valley.

Finally, as a general rule of thumb, I would now suggest that the primary way in which hunter-gatherer genes can persist is through an ecological stall on the part of farmers. During the stall gene flow naturally occurs, probably through exchange of females (coercive or not), or the integration of hunter-gatherer males into war-bands or as slaves. Over time the farmers on the frontier have changed genetically, so that when they start expanding rapidly due to a technological or cultural innovation, they share more with the hunter-gatherers whom they supersede than they otherwise would have.

(Republished from Discover/GNXP by permission of author or representative)
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modelhumanQuick review. In the 19th century once the idea that humans were derived from non-human ancestral species was injected into the bloodstream of the intellectual classes there was an immediate debate as to the location of the proto-human homeland; the Urheimat of us all. Charles Darwin favored Africa, but in many ways this ran against the cultural grain. The theory of evolution was birthed before the highest tide of the age of white supremacy and European hegemony, and Darwin’s model had to swim against the conviction that Africans were the most primitive of the colored races. After the waning of the ideological edifice of white supremacy, and the shock it received during and after World War II, the debates as to the origin of humanity still remained contentious and followed the same outlines (though without the charged normative inferences). But as the decades wore on many more researchers began to believe that Darwin was correct, and that the origin of humanity lay in the African continent. First, the deep origin of the human lineage in Africa was accepted, but eventually a more recent expansion out of Africa was argued for by one school. The turning point in these academic disputes was the popularization of the “mitochondrial Eve” theory of the 1980s.

What some paleontologists had long argued, that anatomically modern humans have their locus of origin in Africa, was supported now by research from genetics which indicated that Africans were the most basal clade of humans on a continental scale, so that non-Africans could be conceived of as a subset of Africans. From this originates the chestnut of wisdom that Africans have more genetic diversity than all other human populations combined. By the year 2000 one could say that the “Out of Africa” triumphalism had proceeded to the point where an almost exterminationist model had taken hold when it came to the relationships of anatomically modern H. sapiens, and other groups which had evolved outside of Africa over the past million or so years, such as the Neandertals. But the theoretical dichotomies were too coarse and absolute as it turns out. A division between multiregionalist phyletic gradualism, where H. sapiens evolved out of its hominin ancestors concurrently on a world wide scale, and a model of rapid expansion of one tribe in Africa to replace all others in totality, may have been warranted in the age of classical genetics and a morphometric analysis, but now we can look at the raw genomic material in a more fine-grained fashion. In fact, we can now look at the genomic patterns of variation among extinct hominins! Though there have long been hints that the expansion-and-replacement paradigm was too extreme from the genetic and morphological data, with the publication last spring in Science of a paper which made the claim for admixture between Neandertals and non-Africans in the range of 1-4% in all non-African groups based on a comparison of Neandertal and modern human genetic variation, one can dismiss absolutist expansion-and-replacement as self-evidently true orthodoxy. But one orthodoxy has no given way to another, and the shock to the old models presented by the data has not resulted in the coalescence of new robust paradigms. We live in a time of scientific troubles, so to speak.

One of the more notable results in the Science paper from last spring was that all non-Africans had about the same admixture in relation to the Neandertal reference genome, ~1-4%. This means from the Orkneys to New Guinea. Because Neandertals were distributed only in the western half of Eurasia this implies that the admixture was an early event. By the time of modern human expansion across Eurasia, Australasia, and the New World, it had become equally distributed across the individuals within the population. Recall the contrast between African Americans and Uyghurs. Among the Uyghurs the ancestral quanta are equitably distributed from individual to individual, but among African Americans there remains substantial intra-population variance. The reason is that African Americans are quite new, an order of magnitude younger than the Uyghurs in a genetic sense, and admixture is still occurring into the African American population from the ancestral groups. The Uyghurs as we known them today genetically are probably ~1,000-2,000 years old (though their cultural origins are both more and less ancient, as a matter of linguistics in the former, and ethnic self-conception as a Muslim East Turkic group in the latter). The implication here is clear: there was a pause in the Out of Africa movement, where the proto-non-Africans mixed with a Neandertal group, possibly in the Middle East, and only began a massive demographic expansion after an unspecified sojourn. A paper from last spring makes this all explicit:

A more likely explanation for the OoA bottleneck is that Eurasia was populated by a larger population that had been relatively isolated from other modern human populations for tens of thousands of years prior to the expansion. The first fossil evidence for modern humans outside of Africa is in the Middle East at Skhul and Qafzeh between 80,000-100,000 years ago, which is at least 20,000 years prior to the Eurasian diaspora. If a population of modern humans remained in the Middle East until the expansion into Eurasia, there would have been sufficient time for genetic drift to reduce heterozygosity dramatically before the Eurasia expansion. This “Middle East isolation” hypothesis provides a robust explanation for the relative homogeneity of European and Asian populations relative to African populations (see Figures 3A-B) and is supported by a recent maximum likelihood estimate of 140,000 years ago for the time of Eurasian-West African population separation . Interestingly, a recent study of the Neandertal genome suggests that the non-African individuals, but not the Africans, contain similar amount of admixture (1-4%) with the Neandertals . The authors suggest that the admixture must have happened between the Neandertals with an ancestral non-African population before the Eurasian expansion. Given the fossil, archaeological, and genetic evidence, the Middle East isolation hypothesis warrants rigorous evaluation as whole-genome sequence data become available.

Now the same group has published a follow up paper in Genome Biology which fleshes out the Deep Time aspect of human evolutionary history by looking closely at the genetic variation of an under-sampled population: South Asians. You may have noticed that the HGDP populations include Pakistani groups as South Asian exemplars. That’s apparently because during the Permit Raj era in India the government was wary of cooperating with the HGDP consortium. But more recently the barriers have come down in India, and one can viably supplement the data sets with Indian Americans. So the GIH sample in HapMap3 consists of Gujaratis from Houston. At ~1.25 billion, or nearly 20% of the world’s population, South Asians are a critical portion of the “big picture” when it comes to world wide genetic variation.

Genetic diversity in India and the inference of Eurasian population expansion:

To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100 kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90-110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans.

First, I want to put into the record that I think there are high enough uncertainties (evident in the confidence intervals in the paper itself) that we need to be careful about taking the divergence times from their results as values we’d bet the house on. Someone with a better knowledge of the fossils (e.g., John Hawks) or controversies about the mutational rates (e.g., Dienekes) can comment on the plausibilities of the dating. But, I think we can infer that there was a time lag closer to a 10,000 years order of magnitude than 1,000 years when it comes to the Middle Eastern sojourn of non-African humans.

The basic method here is that the research group zoomed in on a ~100 kb region of the genome, on chromosome 12, and surveyed their Indian populations, as well as the HapMap3 ones. This is important because the SNPs in the HapMap probably exhibit an ascertainment bias toward variants in European and other more widely surveyed groups. The fact 30% of the SNPs in the South Indian groups seem to not be found among the HapMap populations confirms this hunch. Before digging into the details of the paper, let’s note that the South Indian groups are from the state of Andhara Pradesh, Brahmins, a lower caste group (Yadava), Dalits (Mala/Madiga), and a tribe (Irula). This is a case where even more thorough coverage is necessary. There is some suggestion that South Asian groups have a long history of endogamy and genetic peculiarities, which would limit the usefulness of extrapolations from this sample. Even within the HapMap Gujarati sample there seems to be two clusters when the PCA is used with reference to the European samples.

There are basically three portions of the paper:

- A survey of conventional population genetic statistics,

θ = 4N eμ (N e = effective population, μ = mutation rate)
π = nucleotide diversity
H = heterozygosity
D = Tajima’s D

- Measures of genetic distance between contemporary populations, F st and PCA

- Finally, taking the genetic variance from the ~100 kb and plugging it into explicit models of human evolutionary history

Table 1 (I reformatted) shows the genetic statistics by “continent.” Indian includes some Gujarati individuals. They sampled out of the HapMap populations to equalize the numbers.


euro2Some of these results are striking. The general truism is that Africans are the most diverse population in the world, but some of the South Indian groups are very diverse indeed. Of particular interest though is that some Indian groups are not very diverse at all. What’s going on here? Here you have to look at the specifics of each group. It is likely that South Indian Brahmins are the result of a relatively recent population expansion, with some uptake of other genes through hypergamy. A paper from last year argued that all Indian populations can be modeled as a two-way admixture of different quantities from two ancestral groups, Ancient North Indians and Ancient South Indians. The heterozygosity values may be explained in such a fashion, though the relatively low values for Gujaratis and Andhara Pradesh Brahmins would still surprise. Frankly, I’m just mostly confused by the diversity statistics. Probably the substructure through endogamy and population bottlenecks are obscuring broader dynamics. We can, though, conclude that the idea that all non-Africans are uniformly homogeneous in comparison to Africans may not hold water. Figure 2 above illustrates this by plotting heterozygosity vs. distance from Africa.

Next, let’s move to genetic distance. There’s two ways you can look at this: a summary statistic like F st, which partitions between and within population variance, and PCA, which visualizes the largest dimensions of variations in the data set. So you have both below (reedited for reasons of space):


In the generality the results are expected, but there are weird details. For example, the Brahmins from Andhara Pradesh are on the margins, where you’d expect them to cluster with the Gujaratis. The Gujaratis are closer to the Chinese from Denver than Utah Whites? This is a provisional paper, so I’m almost wondering if there’s a typo or coding error here, as I don’t understand how the GIH can be so close to the Tuscans and Chinese from Denver, and much further from the Northern Europeans and Chinese from Beijing. The two European and Chinese samples are rather close in other analyses.

So let’s get to the real deal. The modified Out of Africa model where non-Africans take a “break” after they leave the mother continent:


I’ve mashed up the figures. The models were generated by looking at allele frequencies. They took the variants they found by sequencing the ~100 kb on chromosome 12, which was in a very gene-poor region so as to bias it toward neutrality, and plugged them into a few models in the ∂a∂i program. I’ll jump to the text here:

…the divergence time between African and the ancestral Eurasian population (88-112 kya, CIs: 63-150 kya) is much older than the divergence time among the Eurasian groups (27-39 kya, CI: 20-59 kya). The more recent divergence time and the low migration rate estimates among the current Eurasian populations support the “delayed expansion” hypothesis for the human colonization of Eurasia (Figure 5). Consistent with previous studies…these estimates indicate that a single Eurasian ancestral population remained separated from African populations for more than 40 thousand years prior to the population expansion throughout Eurasia and the divergence of individual Eurasian populations.

Manafi al-Hayawan, Adam and Eve

Take a good look at those confidence intervals. We know that some of those have to be false: the bones don’t lie. From what little I know a very young consensus date for the settlement of Australasia by modern humans is 40,000 years ago. That happens nicely to be their median, but the dispersion toward younger dates is probably not right, unless Aborigines are a separate population who are remnants of an earlier wave of migrants (or the current Aborigines replaced earlier waves). It is also hard to reconcile these dates for the diversification of non-African humanity with very old dates for Chinese fossils which exhibit some elements of modern morphology.

In the broad outlines I think we can accept that the model outlined in this paper may be correct. It would explain the uniform admixture of Neandertal in non-Africans, since they’d need time as a compact population before demographic expansion to integrate the Neandertal genes as part of their genetic background. But before the Neandertal genome came out there were plenty of papers which purported to show how there was no archaic admixture in modern humans, and plenty of papers which did claim there was evidence for such admixture. The point is that these computational models are sensitive to their inputs, and being models they simplify what really happened. In the discussion the authors repeatedly observe that migration between the various non-African demes doesn’t effect the outcome. That is fine, but there is modestly strong evidence that the Indian samples that they’re using are an admixed population of old. That would make me skeptical of claims about dating the separation of “Indians” when Indians are themselves possibly a compound between other groups.

Below is the model presented from Reconstructing Indian population history:


The teens of this century are going to be very exciting when it comes to reconstructing human evolutionary history. You’d be a fool to put bets on any horse at this time.

eurasicansAddendum: I need a term for non-African humanity. So I’m making up one right now: Eurausicans. From Eurasians, Australasians, and Americans.

Citation: Jinchuan Xing, W Scott Watkins, Ya Hu, Chad D Huff, Aniko Sabo, Donna M Muzny, Michael J Bamshad, Richard A Gibbs, Lynn B Jorde, & Fuli Yu (2010). Genetic diversity in India and the inference of Eurasian population expansion Genome Biology : 10.1186/gb-2010-11-11-r113

(Republished from Discover/GNXP by permission of author or representative)
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In the comments below a strange conversation grew out of the politicized nature of Pakistani identity, and its relationship to India the nation-state, and India the civilization. I assume that a typical reader, or more accurately commenter, on this weblog would be sanguine if they found out they were 10% chimpanzee. After all, it’s what’s between your ears that really matters, not who your ancestors were. I do understand that some readers have strong genealogical-nationalist interests in human population genetics, and that’s fine so long as you don’t presume that the rest of us share such priorities (this is a problem for some commenters, so please be aware that I get annoyed when you project this way, though it’s obviously not a banning offense).

But readers who come via search engines are a different case, and that’s why I’ve started to get worried about over-reading of PCA and such. Nevertheless, I do think PCA can answer the question of whether there is any real genetic discontinuity between Pakistanis and Indians. The answer is no. Page 19 of Reich et al. supplement 1 includes in the HGDP Pakistani populations in their plot of genetic variation of Indian groups. I’ve added some labels, but the top-line is rather clear. AP = Andhara Pradesh, UP = Uttar Pradesh, GUJ = Gujarat and RAJ = Rajasthan. I assume Ind. and Pak. abbreviations are self-evident.


Obviously it isn’t strictly true that Pakistanis are just like Indians. But, Pakistanis are pretty much exactly where you’d expect from their position in relation to India. There is only a small component of recent Persian or Central Asian ancestry, as evident by the relative closeness of Muslim Pakistanis with Hindu groups, who would presumably lack this component. The point of this post isn’t to vindicate or refute a particular political position, it’s to reinforce what’s been pretty clear from genetics over the past generation.

P.S. Just a small warning, if you leave a crazy comment, I’m not going to publish it!

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Genetics, India, Pakistan 
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The New York Times has a piece up, Defusing India’s Population Time Bomb, which reiterates what I was trying to get at yesterday, India’s demographic problems are localized to particular regions, not the nation as a whole. First, let’s review the world’s population growth & fertility rates:

Now let’s focus on a few nations:

China’s coercive policy is often held up as a great success of the power of government to change from on high. But did you see the world population growth correction in the early 1960s? That was China. If you don’t know what was going on in China then, read books (hint: if you don’t know much about the history of China, you don’t know much about the history of the world). My point is that China’s solution was in part a reaction to a pro-natalist drive encouraged by one of the most powerful crazy men in the history of the world. On pure pragmatic grounds one may say that China had to do something, but their actions in the early 1980s did not occur in a vacuum, and were a consequence of a sequence of earlier events particular to that nation.

Contrast China with South Korea, a culturally similar nation, which went through decades of authoritarian rule, but never imposed coercive family planning policies of the sort common in the People’s Republic. Like Japan and Taiwan South Korea’s fertility and population growth rates declined naturally through economic development. With abundant human capital (high literacy) to start out with these nations replicated, and in some ways exceeded, the trajectory of the European demographic transition concomitant with an increase in economic productivity and urbanization. In fact, their fertility rates are lower than that of China, probably because they’re economically more advanced. If it wasn’t for China’s three decade long dance with crazy Communism the coercive policies in relation to reproduction may never have been necessary.

Economic development isn’t the only way to staunch population growth. Iran has taken a different, and less optimal, but still not grossly coercive, path. Because of the lack of economic opportunity in Iran’s society there was an understanding at both the commanding heights and the grassroots that large families were simply not sustainable, at least not using the quality of life which people had become used to in the 1970s as a reference point.

As I noted yesterday, the problem within India is that there is a wide region-to-region variation. The southern cone of India is already verging toward sub-replacement fertility. A major difference I see between China and India though is that the economically and socially most backward area is the cultural heart of the latter. There may be vague analogies to Italy, where Rome is a government town in the center, while northern Italy is the economic motive force, and southern Italy serves as a vote-bank which reliably backs the party which makes the biggest cash transfer promise. A big difference between Italy and India: the backward region is numerically dominant in India, while it is not in Italy.

Here are two bubble plots which show the divide in India. The size of the bubbles are proportion to the population size of the state. The two ones to the top left are Uttar Pradesh and Bihar.

[nggallery id=4]

The fact is that South Asia is low on the human capital scale:


The only long term solution is to leverage the fact that other parts of the world are higher up on the human capital ladder, and still producing innovation and generating new ways to increase productivity. Matt Yglesias has a post up about Japan, from which I got this chart:


Because Japan’s population is shrinking its economy will decline over time. Additionally, because of the unfavorable demographics, with more older people than young workers, it will go through some decline in quality of life. But the average Japanese still consumes at a very high level, it’s not dystopia. Ultimately the Japanese are relying on innovation to buoy their economy. And that’s the real long term solution: without innovation we’re f**ked. Period. Demographic adjustments are really epiphenomena on the margins. That’s why the media can report on both sides of the ledger as if they are both positive and negative. It’s about quality of human capital and the innovation they’re producing, not the quantity of humans.

Image Credit: Wikimedia

(Republished from Discover/GNXP by permission of author or representative)
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In my post Pakistan ~10 years on I alluded to the fact that despite India’s robust economic growth of the past ~15 years or so in the aggregate there is a wide range of state-by-state variation. It is conventional in the media to point out the massive caste/class divisions in India, but because of the lack of familiarity with the geography of that nation there’s less reference to the regional gulfs. But if you look at the state-level data they’re rather large. The total fertility in the northern gangetic states of Uttar Pradesh and Bihar is ~4, while that in the southern states of Kerala and Tamil Nadu is ~2. Uttar Pradesh and Bihar are not trivial states, rather, they’re the two most populous! Additionally, they’re a meaty portion of the South Asian “Cow Belt”, the cultural heart of the subcontinent. The first great historic polities of South Asia, that of the Maurya and Gupta, had their focus in what is today Bihar, while later on the Muslim dynasts famously operated from a base around the region of Delhi in Uttar Pradesh. In the Indian cultural geography these states are the heart of Āryāvarta.

Wikipedia has a set of pages which rank the states of India by various metrics. The tables themselves are illuminating, but for non-Indian readers I thought a series of thematic maps would be better. Additionally, I added one scatterplot.

[nggallery id=3]

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Anthropology, Culture, Data Analysis, India 
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Frequency of lactose malabsorption among healthy southern and northern Indian populations by genetic analysis and lactose hydrogen breath and tolerance tests:

Volunteers from southern and northern India were comparable in age and sex. The LTT result was abnormal in 88.2% of southern Indians and in 66.2% of northern Indians…The lactose HBT result was abnormal in 78.9% of southern Indians and in 57.1% of northern Indians…The CC genotype was present in 86.8% and 67.5%…the CT genotype was present in 13.2% and 26.0%…and the TT genotype was present in 0% and 6.5%..of southern and northern Indians, respectively. The frequency of symptoms after the lactose load…and peak concentrations of breath hydrogen…both of which might indicate the degree of lactase deficiency, were higher in southern than in northern Indians.

The north Indian samples were from Lucknow on the mid-Gangetic plain, and the south Indian samples from Bangalore. The genetic variant conferring lactase persistence is the Central Asian one, T-1390. You can see the distribution of the genotypes by phenotype in the table to the left. These authors assume that the T allele was brought by the Indo-Aryans; this seems plausible seeing its clinal variation, as well the fact that this variant seems to be common in European and Central Asian populations. The frequency of the T allele in the Lucknow sample was 39%, and 13% in the Bangalore sample. Here are a selection of frequencies for the T allele in other populations:

17% – Saami
13% – Greeks (Athens)
82% – Scandinavians (Stockholm)
6% – Tuscans (Florence)
24% – Russians (Moscow)
73% – English (London)
66% – Basques
10% – Roma (Prague)
56% – Germans (Hamburg)
95% – North Irish (Enniskillen)
1% – Armenian (Yerevan)
5% – Uygur (Beijing)
10% – Mongolian (Beijing)
13% – Indians (Madras)
19% – Indians (New Dehli)
36% – Balochi (Islamabad)
51% – Pathan

You can see more here. This looks like a case of local adaptation.

(Republished from by permission of author or representative)
• Category: Science • Tags: India, Population Genetics 
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Razib Khan
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