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

September 14, 2018

Between the saffron and scimitar

Filed under: India,Islam,Islamicate — Razib Khan @ 10:10 pm

On my other weblog I have a post, On The Instrumental Uses Of Arabic Science, which reflects on the role that the idea of science, the Islamic world, and cultural myopia, play in our deployment of particular historical facts and dynamics. That is, an idea, a concept, does not exist on an island but is embedded in a cultural environment. Several different contexts.

My father is a professional scientist, and a Muslim who lives in the West. In our house there was always a copy of The Bible, the Qu’ran and Science: The Holy Scriptures Examined in the Light of Modern Knowledge. To those not convinced about the beliefs of Islam, as I never was, it was not a convincing book. But it played a particular role in my father’s life of the mind as both a Muslim and a scientist. Its arguments were less important in their detail than that a French scientist had written a book showing that Islam and science were compatible and that in fact, the Koran had prefigured scientific truths.

The intellectual achievements of medieval Islam, particularly the phase focused around the House of Wisdom, are a real thing in and of themselves. But more often they exist as tools for the implicit or explicit agendas of particular peoples with ends which are separate and distinct from an understanding of the past on its own terms.

For many Muslims, this period defines what Islam could have been. Should have been. More traditionalist Muslims will have a relatively understated take, and perhaps attribute the passing of this period due to external forces (e.g., the collapse of central authority by the end of the 9th century). More progressive Muslims will make a bolder claim, that Islam, that Muslims, made the wrong decisions internally (al-Ghazali often emerges as a villain).

A modernist, perhaps Whiggish, take would be that the 9th century of Islam was a “false dawn.” Illustrative of the acidic power of rationality, but an instance when it receded in the face of faith (the Mutazilites often become heroes in these tales). A more multiculturalist and contemporary progressive Western take would likely emphasize that Islamic cultural production was just as ingenious as that of the West, and its diminishment was due to the suffocating effect of colonialism.

But there are even more exotic takes one could propose. The shift from the Umayyads in Damascus to the Abbasids in Baghdad was a shift of the Islamic world from the west to the east. The prominence of Iranian culture during the latter period was palpable. The Caliph al-Mamun was half Iranian, and almost moved the capital of the Abbasids to Merv in Khorasan. The Barmakid family were ethnically Iranian, but also originally hereditary Buddhists. The historian of Central Asia, Christopher Beckwith, has alluded to an “Indian period” of Islamic civilization when the influence from Dharmic religion and Indian culture was strong. For example, Beckwith and others have argued that the madrassa system derives from that of Central Asian viharas.

But ultimately this post and this blog is not about Classical Islamic civilization and history. Rather, I want to pivot to the discussion of Islam and India.

This blog now gets in the range of the same amount of traffic as my other weblog. But a major difference is the source of traffic. About two times as many visitors to this weblog come from the USA as India. So Americans are dominant. But, on my other weblog, 15 times as many visitors come from the USA as India. Additionally, since this is a group weblog, I’m pretty liberal about comments, and so this weblog receives between 10 to 100 times as many comments as my other weblog. Obviously, since most people in the world are stupid, many of the comments are stupid. I try to ignore that.

Rather, let me focus on the “hot-button” issue of Islam and India, and how it impacts people here. In the comments of this weblog. Let’s divide the comment(ers) into two stylized camps. Or actually, one person and another camp. The person is commenter Kabir, who has taken it upon himself to defend the honor of Indo-Islamic civilization. On the face of it, that’s not a major problem, but he tends to take extreme offense and demand linguistic and topical policing that’s frankly rather obnoxious (this tendency extends beyond Islam, as he is a living personification of Syme). He’s a bully without the whip. Kabir is somewhat annoying, but I can honestly I can always just delete his comments. He’s one person.

In contrast, there are those who Kabir calls “Hindu nationalists.” This is a broad slur on his part, as it basically seems to include any person from a Hindu background who disagrees with any particular social-religious take he has in relation to the Indian subcontinent or Islam. If someone who was a Chinese Catholic lesbian left a common where their identity wasn’t clear, and they disagreed with Kabir’s take, he would no doubt accuse them of being a “Hindu nationalist.”

If you have a hammer, everything is a nail!

But, there are genuine Hindu nationalists who read this weblog of various stripes. I have friends who personally lean toward this direction in their politics, though they are cosmopolitan in their private life. On the other hand, there are others who are more backward and probably as crazy as Kabir depicts them. Honestly, I’ve never met these people in real life…most “Indian” people I meet are either coconuts like me or cosmopolitan blockchain engineers.

At this point, I should step back and reintroduce myself. Unlike many people from an Islamic background who are now rather frankly irreligious, I did not have a traumatic relationship with Islam. Or religion. My parents mostly raised me as a nominal Muslim, so my atheism came about naturally and at a young age. And, unlike some atheists from a Muslim background, I did not grow up in a Muslim community. Neither did I grow up in an immigrant community. I grew up in Ronald Reagan and Bill Clinton’s America as the token brown kid. I have only come to know other brown people of all religions and background as an adult. My stance is one of curiosity, and sometimes perplexment. I have a few memories of distaste when it came to attending masjid as a child because in hindsight it is clear I never believed in what they were saying and saw it as a massive waste of time and totally sterile.

But due to this perspective, I don’t have strong opinions on South Asian politics. I wish atheists and free-thinkers would get a little break in Bangladesh. Pakistan as a nation should go see a good therapist about its identity crisis. And in India, the saffron brigade should chill out on their paranoia on all things “foreign.” The British are gone. And the Muslims are a minority (also, I had a medium-rare hamburger with bacon today!).

Which brings me to the concerns of the Hindu nationalists, and their relationship to Islam. Their hatred of Islam. Their love of Islam. Their inability to quit Islam.

Imagine a beautiful bully. A bully with the social and interpersonal skills to hide their behavior. To get away with it. If Hindu nationalists were to personify the historical rage they feel, that seems to be their attitude toward Islam. What genetics is telling is that though South Asians are diverse, we’re a distinctive and recognizable branch of the human race that emerged out of particular social and historical dynamics that occurred between three and eight thousand year ago.

And yet Hindu nationalists see that one out of three South Asians now identifies as something distinct, part of an alienated (from South Asia) worldwide brotherhood. They used to be called Indians. What used to be called Hindus. But they are alienated from their own ancestral identity now. Their forenames are Ali or Pervez. Their surnames are Islam or Khan. Many of their sartorial choices and customs are dictated by the whims of a 7th century Arab and the norms of his community. Some even have the gall and conceit to claim to be scions of the Arab, Persian, or Turk, when their very faces give the lie to that claim.

As someone emotionally, personally, detached from the Indian subcontinent and its identities this is what I see. What I observe.

As a participant, even at the margins, my perspectives exist as well. Because the social norms in Islam outside of the West look dimly upon irtidāds, my general stance all things equal is to look where the Muslims stand, and take the opposite position. The mainstream view within Islam is that apostasy is punished due to its social and political implications. That is, it is treason. The punishment for treason is death.

Which brings me to reflect on attempting to understanding what Islam is, and why it is the way it is. Most atheists who have never been religious tend to have certain personalities. We’re not really intuitive people. We’re more analytic types. To understand a religion we believe that we should understand its doctrines.

This is easiest with Protestant Christianity, which in the United States of America is defined by a confessional individualistic orientation. That is, religious identity is fluid, and contingent on the freely given profession of faith in the doctrines of a particular sect. More liturgical forms of Christianity, such as Roman Catholicism and Eastern Orthodoxy, are somewhat different, but the overall emphasis on particularities of belief remains.

The landscape changes once one moves to Judaism and Islam, which are both orthopraxic religions. That is, traditional Judaism and Islam have highly developed tradition of religious law which apply to all believers, and not simply religious professionals. At least notionally. Though particular beliefs about the nature of God remain at the heart of customary Judaism and Islam, on the balance formulaic orthodoxy is not given as much overwhelming weight.

Whereas early Christians underwent conflicts over the precise nature of the Trinitarian doctrinal formula, early Muslims divided predominantly along lines of the nature of religious leadership.

When we move to the Dharmic traditions and Chinese and Japanese religion, the landscape alters again. I will forgo exploration of this topic since it is not germane to the post. Suffice to say I am well aware of the diversity and particularity across all these traditions.

Rather, let’s take a step back to Islam. The brutal bully whose life is charmed. The standard narrative is that Islam spread rapidly over a century, from the Indus to the shores of the Atlantic. It is a stupendous feat.

How did this happen? Naturally, Muslims will assert that it was the will of God himself. Islam succeeded in its audacity because it is true. Those of us who are not Muslim do not accept this viewpoint, because to us Islam is obviously not true.

So what explanation can we kaffirs give for this feat? A natural one adhered to by many is that Islam is by its doctrinal nature well suited to obtaining submission, and then in a sort of Stockholm Syndrome those who submit to conquest convert their own identity so they become partners in their own oppression and that of others. This model is one where the sons of pagans, Christians, and Hindus bow before Allah on High and smite the unbeliever in their own turn, in a devilish radius of conquest outward from the center.

And the blueprint is all there in the Koran and the Sunnah. All that one needs to do is to execute the plan was there in the beginning. All the snake had to do was uncoil.

To a great extent, this was my view 15 years ago. Because I was an atheist who had never been religious this made sense to me, because religion was about ideology, and the Islamic ideology was plainly one of submission. After all, Islam means “submission to God.”

Though I have never been a believer in a non-Muslim religion, my impression is that many non-Muslims find this also an easy way to understand Islam. Muslim majoritarianism has traditionally been brutal to non-Muslims, and it isn’t as if Muslims keep their doctrines and practices secret. Their contempt for kaffirs derives naturally from the nature of the religion, not some perverse heritable trait. Muslims are taught to have contempt for non-Muslims. They aren’t born with it.

Of course, there are those who disagree with this position for political and cultural reasons. These are the type of people who claim that Islam is a peaceful religion of tolerance. These people are either lying or deluded. Ultimately they don’t really care about Islam, they care about their own particular positions in culture wars fundamentally having nothing to do with Islam.

Over the years though I have come to revise my views about why Islam is the way it is and how it got to be the way it is. On the whole, I don’t really disagree with my earlier view that Muslims and Islamic societies tend to be characterized by intolerance and exclusion. These are not societies that I would ever want to be a member of. But, I have come to believe that this is less due to the fundamental nature of Islamic doctrine, and more due to historically contingent events. In other words, Islam and Muslim societies are the way they are for reasons that have nothing to do with the doctrines and scriptures of Islam.

This revision in my views has two broad sources. One is the cognitive anthropology of religion. This is a discipline which allows someone like me, who has never been religious, inside the minds of those who believe. Like many sciences, the findings of this field are confusing, startling, and often counter-intuitive. Glossing over the details, I will say though that they have convinced me that the logical consequences from doctrine given by the religious are almost always post facto rationalizations, and not a true inference via propositional logic. This applies to all religions. And it applies to Islam itself.

Consider that 2,000 years ago a poor and pacifistic Jewish preacher triggered a cultural revolution that led to the emergence of a world religion. That world religion eventually became the heart of a civilization that went on to commit the greatest quantity of acts of violent brutality on an aggregate basis in the history of our species. The line between the prince of peace and slaughtering heretics and enslaving Africans is peculiar indeed.

Second, contingent history matters. It will not here recapitulate revisionist scholarship about Islam, but I do not think it unreasonable to contend that much of what we know about Islam developed in the century after the conquest. In other words, the Arabs did not conquer as Muslims, the conquerors became Muslims. The shape of Islam then was defined by the reality that emerged within the context of being an imperial religion, just as the nature of Jews after the failure of the second rebellion against the Romans until the founding of the state of Israel was one of being a pacific and supine religion.

Many Indian commenters on this weblog promote a view of Islam, and the Abrahamic religions to a lesser extent, that is in line with my views from 15 years ago. It’s there right to hold these views, but I will object when individuals assume that these views are self-evidently true. Descriptively I tend to agree with Hindu nationalists that many Muslims of Hindu descent exhibit some level of Stockholm Syndrome, reveling in the brutal conquest of their black ancestors by Muslim Turks. But when it comes to the cause of the symptoms…that is a more complex thing than they are willing to credit in my opinion.

The ideological and missionary impulse of Islam is clearly a real doctrinal thing. And that makes it different from most streams of Hinduism. But there are far more contingent sequences of events than I think we often acknowledge.

Which brings me to the reality that contingent history that has happened cannot be unhappened. The history of Islam within India is a fact. 1,000 years of domination is a fact. Centuries of domination across much of the subcontinent by alien Muslim elites is a fact. It is a fact that the most glamorous ruling dynasty of the last 1,000 years in the Indian subcontinent was that of the Mughals. Though to some extent culturally and genetically assimilated, this ruling dynasty was of Turco-Mongol provenance, and always bowed down to a religion for which India was not holy.

Over the past few centuries, Indians have by and large shucked off Muslim domination. Those areas which are Muslim dominated are no longer India, being distinct nation-states. But the weight of history still hangs over the subcontinent. One could attempt to make the case that the 1,000 years when Muslim ghazis ran roughshod over the subcontinent was an aberration, a fever dream. But the very act of purifying languages of their Arabic and Persian words points to the reality that the serum of the aliens was injected into the veins of Indian civilization.

Pakistanis and Bangladeshis, and many Indian Muslims, especially those of the northern states, have their own deep identity crises. Many of them are raised with a deep and abiding contempt for the traditions and folkways of the non-Muslim peoples of the subcontinent, but on some level most must understand that these non-Muslims are the same people as their own were before the great change. Whereas the vast majority of Persians converted to Islam, and bent the knee to the Arabs for whom they had and still have so much contempt, the majority of South Asians remain non-Muslim. Witness to the cultural identity which Muslims in the subcontinent have turned their backs upon.

And yet many Hindus, envious of the vigor of the Muslims, noticing their international connections, and confused by the bizarre Islamophilic tendencies of the progressive West, may have to admit that the history of Islam is now also part of their history. The Sufi orders which were so instrumental to the spread of Islam served to buttress the great Indo-Islamic polities with their institutional heft, may themselves have been transmuted from Buddhist religious communities early Muslims encountered in eastern Iran and in Turan. If Islam is the snake, then part of the root of the serpent is ultimately Hindu, that is, Indian. It could be no other way, as Islam is the youngest of the great world religions. Constructed from preexistent modules perfected in other traditions. It was a computer assembled at home from commodity parts.

But even aside from older traditions’ roles in shaping Muslim thought, practice, and institutions, the educated Hindu of 1800 AD surely was influenced and impacted by the arrival and domination by Muslims in comparison to their precursor in 800 AD. Today in the West there are neopagans and other assorted post-Christian types who wish to recapture ancestral pre-Christian spirituality. The problem they always run up against is that that spirituality is passed down only due to the efforts of Christians, often clerics, who in the act of selection and modification likely reframed the old ways in more Christian terms. And, the lived pagan tradition was broken long ago, distributed and diffused through rural folk customs among unlettered peasants who transformed rapidly into modern urban Europeans just as the Romantic pagan awakening was beginning.

Obviously, Hinduism does not have such a great rupture. The tradition of Adi Shankara lives on. Religious reformers and innovators such a Chaitanya Mahaprabhu flourished even under Muslim Afghan rule. There is no need to reconstruct and resurrect Hinduism because it is a lived tradition. But Hinduism, Indian culture, Indian nationality, as it was before the Muslims arrived in large numbers is gone, transmuted and transformed into something new. But even if we can’t move backward, there is no shame in moving forward to better things.

Addendum: Muslim scholars, such as Shadi Hamid (and I believe our own Omar Ali), do sometimes claim that Islam is sui generis. That it may be ideologically, constitutively, resistant to secularism and the normal process of pacification of religion. This is not a crazy position and can be well argued, and to be frank, I am quite open to being convinced again of my old views.

September 10, 2018

The Muslim intrusion into India was probably inevitable

Filed under: India,Islam — Razib Khan @ 10:08 pm

Taking after Edward Gibbon it is often stated in some histories that the Islamicization of Europe was probably prevented by the defeat of the Muslim armies coming up from Spain by Charles Martel at the Battle of Tours.

This is probably wrong for several reasons. First, with hindsight, it seems clear that people like to anchor on salient contingent events which seem plausible bifurcations in our timeline. This is a cognitive bias. The fact is that sally north of the Pyrenees into Francia was probably simply a probing raid, not the precursor to a full-scale invasion. At least that is the impression given by the Muslim textual records, which barely mention this battle (in contrast to the second Siege of Constantinople, which had occurred a few decades earlier). A raid is not a campaign.

Additionally, Muslim armies and corsairs operated north of the Pyrenees and in what became southern France for several centuries after 732. The defeat at the Battle of Tours was simply another battle in the gradual rollback of Islamic depredations in the Western Mediterranean. Perhaps more important was the shift of the world-wide Islamic polity eastward with the emergence of the Abbasids in 750, and the detachment of western Muslim domains from Abbasid authority (a renegade Umayyad even reigned in Spain!).

Finally, limits of supply-lines and ecological constraints probably meant that a protracted campaign in Europe would have met difficulties that were less relevant for North Africa and Spain. The conquest of North Africa and Spain occurred in less than a generation (the conquest of the Maghreb was an opportunity opened during a period of tumult in Byzantium in the late 7th century) and were still recent when the Battle of Tours occurred. Additionally, ecologically North Africa and much of Spain were familiar to the Arabs, and in the latter case Berbers. This is not the case with Francia and much of Northern Europe. It is not well known, but Arab armies sallied north of the Caucasus into the territory of the Khazars for several centuries, but ultimately failed in permanent conquests, probably in part due to lack of preparation and experience with harsh cold (the lack of fitness of Arab armies for the harsh winters is noted in the texts).

Remember that the conquest of much of the more frigid regions of peripheral Europe occurred under the Ottoman Turks, who were culturally an Inner Asian people from Siberia.

Which brings us to India and the beginning of widescale Muslim intrusions under Mahmud of Ghazni. I immediately pointed out below that the true conquest, as opposed to raiding, did not occur until the late 12th century. But, to be honest, I think this is a minor detail, and the fact is that Muslim incursions were inevitable, and probably like to succeed to some extent, no matter the outcome of a particular battle.

The key here is less about Islam, and more about the period between 500 AD and 1500 AD, and what you see across Eurasia in terms of the balance of power between mobile people from Inner Asia, and the agricultural civilizations. In books as distinct as War! What Is It Good For? and Strange Parallels the authors observe that in the period after 500 AD, until the rise of “gunpowder empires”, pastoralists from the Inner Asian steppe were dominant, destructive, and overwhelming military forces (the Mongol conquests were the apotheosis, but not exceptional).

In Strange Parallels, the author reminds us that only a few societies among the Eurasian oikoumene polities avoided major shocks from pastoralists. Mainland Southeast Asia, Japan, and the far west of Europe were insulated from their depredations by and large.* The reason for this was almost certainly geography: Japan was separated by a sea from the mainland, while Southeast Asia and Western Europe were ecologically difficult for pastoralists to penetrate as well as distant. In “mainland Europe” the settlement of the Hungarian basin by repeated groups of steppe pastoralists, beginning with the Scythians and ending with the Magyars, is partly a function of the fact that its broad flat expanses were the westernmost suitable pastorage for large herds of horses typical on the Eurasian steppe.

In the centuries after 500 AD, most of the major civilizations of Eurasia were impacted by migrations of nomads seeking greener pastures. In China, the northern half of the country was occupied by various groups of Turkic origin between the Han and Sui-Tang. The southern half the country maintained local rule, in part because of the difficulty of penetration by pastoralists of the Yangzi basin. In the Near East, Persia was buffeted by both Inner Asians from the north, and Arabs from the southwest. The Arabs conquered Persia and severely diminished Byzantium. Like China, the persistence of part of Byzantium is probably due to geography: Constantinople occupied a strong position on the other side of Bosporus and could be provisioned by sea when encircled. The Persian heartland was much more exposed to the Arab advance (in contrast, the conquest of Turan took many centuries).

Which brings us to India. The pastoralist eruptions that impacted Persia also affected India. But, the initial impacts were of more political than cultural relevance. Groups like the Huna were absorbed into the South Asian cultural matrix.

The arrival of the Turks and Afghans after 1000 AD was different. These people, now Muslims, were not absorbed into the South Asian cultural matrix. The reason is obvious: with Islam, they had their own high culture, one which was assimilative insofar as native converts could be somewhat integrated into the ruling class, and unassimilable from the perspective of native elites due to its ideological and ritual predictions.

There is here a contrast to the Mongols who conquered China in the 13th century, and the Manchus who conquered it in the 17th century.

First, the raw numbers of Mongols and Manchus in comparison to Chinese was probably far less than the potential mobile Muslim populations which might have settled in India. In fact, Mongols who migrated west were eventually all assimilated into the Turkic or Persian cultural context due to the force of numbers (though they often retained genealogical awareness of part Mongol origins, as the Hazara and Timurids both did despite a Persian and Turkic cultural background).

Second, neither the Mongols or Manchus brought a hegemonic and oppositional high culture. The Mongols were predominantly shamanists, though a minority were Eastern Christians (Kubilai Khan’s mother was a member of the Church of the East, as was the norm among her tribe of Turks), and some were Muslims (the mass conversion of the Mongols to Buddhism occurred in the 16th century, prior to which they dabbled in Islam, Christianity, and Buddhism, as well as their dominant shamanism). The Manchus generally favored shamanism, or, as was the norm among northern border peoples in China, a form of Buddhism. Neither of these prevented assimilation to the Chinese substrate, a major problem for the Manchus over the centuries (like Mongol ancestry, in today’s China “Manchu” national origin is more a matter of genealogy than culture, as the Manchu language is now moribund, only a few thousand out of millions of Manchu speak it).

In regard to India I want to pinpoint a few key issues:

  1. Starting around 1000 AD the whole zone of pastoralist western Inner Asia began to adopt Islam as its standard religious ideology. To a great extent, West Asian Muslim societies were captured by Inner Asians, and they served Inner Asian aims and goals. Societies such as Egypt were ruled for a thousand years by Inner Asians, who created a Mamluk system which depended upon continuous migration and recruitment from Inner Asia.
  2. India was arguably more “exposed” to this culture than China due to geography. While Inner Asians adjacent to Muslim West Asia adopted Islam, those nearest to China tended to be shamanist or Buddhist (Magyars and Bulgars adopted Western and Eastern Christianity respectively).
  3. Mobile Inner Asians, of any religion, were “natural” soldiers (though to be fair, it seems a consistent pattern that Inner Asians, such as Mongols, who were shamanist were less “civilized” and often better soldiers than those who converted to “higher religions”). In the period between 500 AD and 1500 AD mobile mounted warriors had major advantages in continuous warfare against settled peoples. The main way that settled societies held the pastoralists in check was through bribery or co-option, or both. The Byzantines and Chinese deployed both, elevating frontier peoples with mobile fighting skill to their ruling castes, as well as paying nomadic groups tribute. By and large West Asian Muslim societies co-opted and were conquered by Turks (or their Caucasian federates).
  4. India was subject to the same dynamic as West Asian societies: pastoralists from Inner Asia continuously migrated into the subcontinent for opportunities of exploitation and domination down the early colonial period. Each wave of migrants was more “raw,” and brought alien and alienated sensibilities, to the subcontinent.

In discussions with individuals of South Asian origin, there is some exploration of the possibility that Indians, Hindus, were naturally a less vigorous and martial people than Muslims. That Islam was a muscular and masculine ideology, while Hinduism was feminine and passive (Hindu nationalism then emerging through some dialectical process as a superior synthesis; muscular, masculine, and Hindu).

I believe that this analysis suffers mostly from the issue of confounds. In the period after 1000 AD with the exception of the Mongols under Genghis Khan, the Inner Asian intruders were all Muslim because they were drawn from the broad zone of Inner Asia where Islam was the dominant high culture. The reality is that after 1000 AD Iranian speaking peoples also were dominated by numerically smaller groups of Inner Asians. Reza Shah in the 20th century was the first major ethnic Iranian founder of a dynasty to much of Iran since the Buyids and Samanids.

The difference between Iran and India is that the former eventually became majority Muslim, while the latter remained majority non-Muslim. Iran’s relative pliability can even be seen in sect, as the Turco-Kurdish Safavids forcibly converted the Persians from their predominant practice of Sunni Islam to Twelver Shia Islam in the 16th century. But of course, demographics is an important variable here. There were probably always an order of magnitude more Indians than Iranians. In Turan Turkic languages became dominant, and in Iran proper, they remain a substantial minority. In India, Turkic languages never took hold, presumably because the numbers were never sufficient. An analogy here might be made with Egypt, where the Mamluk caste drawn from non-Arabs eventually Arabicized in language and identity.

As a follow-up to my post, India as a hydra against Islam, I will suggest then a two things:

  1. India is not comparable to West Asia because it is a more robust civilization with more demographic heft. Like parts of Europe it “absorbed” the Islamic demographic impact without being totally captured. The difference here is not qualitative, but quantitative. There were so many more Indians than Iranians that erosion of indigenous culture took much longer and was never complete.
  2. Unlike parts of Europe which absorbed the Inner Asian shock, such as Russia, India never managed to reorganize and turn the tide. To some extent, the Russians adopted Inner Asian tactics with their Cossack bridges (some of the Cossacks were assimilated Muslim Tatars).

But, the emergence of the Maratha in the 18th century and the Sikh Empire in the 19th century, illustrate that a South Asian counter-reaction was occurring eventually. The reality is that this period saw the decline of Inner Asian military superiority because of mass mobilization of infantry with shock weapons (guns, artillery), which were finally decentering mounted warriors after nearly 1,500 years of supremacy. Though the later Mughals relied on cadres of Inner Asians, they were fundamentally a “gunpowder empire”, and the logic of mass mobilization means that it is unlikely that in the long term a culturally alienated elite could have persisted. The French republican armies’ defeats of rival powers showed European nation-states the power and necessity of mass mobilization.

Several years ago an Indian American friend of Hindu nationalist sympathies expressed to me the opinion that if it weren’t for the arrival of the British, the Marthas might have spearheaded the emergence of a new Indo-centric polity. At the time I was skeptical because Indians lacked access to horses, which gave Inner Asians an advantage. But now seeing the logic of massed infantry with guns, it does seem that the Inner Asian, and therefore Muslim, the advantage would eventually have given away to the force of numbers.

Of course, we’ll never get to see how history would have turned out. The British had different plans.

Note: This post was inspired by my reading of Imperial China 900-1800.

Addendum: I won’t tolerate stupid comments on this post in the beginning. Please understand that if I delete I think your comment was stupid. Perhaps you are smart, so try harder!

* The Mongol directed invasions of Japan, Burma, and Java, were arguably less a function of steppe pastoralism, than the militaristic Yuan co-opting and projecting the force capabilities of the Chinese state system.

July 15, 2018

India vs. China, genetically diverse vs. homogeneous

Filed under: China,China genetics,Human Population Genetics,India,India Genetics — Razib Khan @ 1:50 pm

About 36% of the world’s population are citizens of the Peoples’ Republic of China and the Republic of India. Including the other nations of South Asia (Pakistan, Bangladesh, etc.), 43% of the population lives in China and/or South Asia.

But, as David Reich mentions in Who We Are and How We Got Here China is dominated by one ethnicity, the Han, while India is a constellation of ethnicities. And this is reflected in the genetics. The relatively diversity of India stands in contrast to the homogeneity of China.

At the current time, the best research on population genetic variation within China is probably the preprint A comprehensive map of genetic variation in the world’s largest ethnic group – Han Chinese. The author used low-coverage sequencing of over 10,000 women to get a huge sample size of variation all across China. The PCA analysis recapitulated earlier work. Genetic relatedness among the Han of China is geographically structured. The largest component of variance is north-south, but a smaller component is also east-west. The north-south element explains more than 4.5 times the variance as the east-west.

Click to enlarge

Another dimension of the of the variation is that different parts of China are character by different levels of admixture between the Han and other groups. In Northwest China, there is gene flow from West Eurasian sources. In all likelihood, this is through proxy populations, such as Mongols, who are about ~10% West Eurasian. Also, during the period between the fall of the Han Dynasty and the rise of the Sui-Tang Dynasty much of northern China was dominated by barbarian groups from the steppe, and these groups settled down and were absorbed. In Northeast China, the source of admixture is from Siberian and Tungusic group. Again, this makes geographical sense.

In contrast in South China, the gene flow is from indigenous Chinese national groups, such as Dai. This is in keeping with the historical record, whereby South China became Han in the period between 0 and 1000 AD through migration, intermarriage, and acculturation.

Click to enlarge

I have my own small private dataset of Chinese individuals. Some with provenance. Some without. But using known populations I was able to divide China along the north to south cline.  Individuals from Guangdong in the south, those from Shaanxi in the north, and from Zhejiang to Sichuan in the center.

Using Punjabis as a West Eurasian outgroup I was able to plot these individuals on a PCA. If you click to enlarge you will see that a substantial minority of the Han_N sample is shifted to the left of the plot. This is toward the Punjabis. This is not because they have Punjabi ancestry, but because Punjabis are reasonable proxies for West Eurasians.

Click to enlarge

More importantly, I want to compare South Asia to China. To do that I created a small dataset that merged the Han with representative South Asian groups. The first PC, 1 and 2, illustrate the contrast. All three Chinese groups, sampled from the north to the south, occupy a very tight cluster, while the South Asians span PC 2. The Bengalis are shifted a bit to the Chinese, but most of the variance is due to within-South Asian genetic differences.

Click to enlarge

I ran PCA to 10 dimensions. Only at PC 10 did the Han Chinese separate along the north-south access. Most of the earlier PC’s separated out specific castes (e.g, Patels because if their large number in the Gujurati sample were PC 3). Here are the eigenvalues: 53.0682, 2.5641, 2.31876
1.97058, 1.90652, 1.88879, 1.7935, 1.69375, 1.61516, and 1.54207. The large value for PC 1 is what you’d expect, it’s a continental scale difference. PC 2 differentiates South Asia from north to south. It’s much more modest. The other PCs get progressively smaller, but within the data, it’s clear that the continental size difference is the big one. The variance between north and south China is a small one in a South Asian scale.

Click to enlarge

Pairwise Fst is more ambiguous. That’s probably because most of the South Asian samples have structure within them. Merging them into one pooled population just confuses the issue.

Using a South Asian dataset where groups are disaggregated makes a lot more sense, and you see the structure between the different groups.

Click to enlarge

Running Treemix gives similar results. The South Asian groups exhibit a fan-shaped topology, where the Han cluster tightly together. Since I removed Bengalis from Treemix adding migration edges doesn’t do anything between the two clusters, so I omitted those results.

Click to enlarge

Finally, of course I ran some admixture analysis. Using South Asians + Han Chinese, I thought K = 4 would be reasonable. Even if you don’t enlarge, the results are straightforward: the Han Chinese have very little diversity in unsupervised mode. A small South Asian-like component, which has affinities with Punjabis, is found in northern Han. This confirms other results with other methods that the northern Han have some West Eurasian gene flow.  Some of the southern and central Han have an affinity with one of the South Indian clusters. I think is artifactual, due to deep structure within Eastern Eurasian populations and affinities between those groups that the Han absorbed as they moved south.

This post doesn’t really shed new light on anything we didn’t know. Rather, it’s just a review of what jumps out at anyone who works with genotype data: there is not very much genetic diversity in China and there is a great deal of genetic diversity in India. Why? These are not questions genetics can really answer directly, though it can give us clues and support certain models over others.

Anyone who has read much about Chinese history knows that the cultural ideal of meritocracy is deeply ingrained, even if it is honored in the breach quite often. Chinese civilizations has been characterized by the domination of extended pedigrees (e.g., the Xianbei-Han ruling faction among the Tang), but those pedigrees never become ethno-religious castes. The exception occurred during the Yuan (Mongol) period where Kublai Khan entered into a divide-and-rule policy. But that was a short period which had no longer term cultural consequences.

In contrast, South Asia is characterized by long-term endogamy. This is not surprising to anyone who knows anything about South Asian history. The genetic evidence suggests that modern jati-barriers emerged around ~2,000 years ago. Not only do South Asian groups differ a great deal in biogeographic ancestry (deep ancestry), but historical endogamy has resulted in further drift between these groups.

April 16, 2018

Brown Pundits, big in India!

Filed under: Blog,India — Razib Khan @ 9:49 pm


I’ve mentioned this before, but I’ll reiterate something I’ve noticed recently: this website is getting bigger and bigger in India. More precisely, though traffic is increasing in the USA, traffic is increasing from Indian IPs even faster.

Here is the breakdown for the last month:

Country % Users
United States 35%
India 29%
UK 6%
Canada 5%
Pakistan 5%
Australia 2%
Germany 1%
France 1%
UAE 1%
Bangladesh 1%

In terms of where the traffic is coming from, the map above shows the cities.

I’m of two feelings about this.

  1. This is going to cause issues because of cultural differences. Educated Indians speak English, but norms and idioms differ. In general, my personal strategy is to hegemonically impose American norms.
  2. Over the past few years I have become bearish on the United States, and bullish on India and China. I’m very curious what people in Asia think, because I think the Asian future is coming at us more quickly than I’d anticipated just a few years ago (American decline, rather than Asian ascension being a cause).

April 1, 2018

The quiz show contestant

Filed under: India — Razib Khan @ 11:56 pm

The above click is “going viral.” One of the things that crosses my mind: would a guy who looks like this ever get a shot in Bollywood, or more generally Indian, film industry as a leading man? Is skin color an issue for men as well as women? The only leading men I know off the top of my head are relatively fair to medium, as opposed to dark (I can think of three or four, hardly any, I don’t follow Indian media).

March 31, 2018

The maturation of the South Asian genetic landscape

Filed under: Dravidian,Human Population Genetics,India,Indo-Aryan — Razib Khan @ 9:39 pm


The above is a stylized map from the preprint, The Genomic Formation of South and Central Asia. In broad strokes, it says some things that are very expected, and some things that are not so expected.

The abstract is long, but I’ll reproduce it in full:

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

First Turk Empire

Though the abstract is focused on South Asia, the preprint actually has quite a bit about Inner Asia, because of the provenance of the samples. We often view the typical person in the past as a peasant in an agricultural society, and therefore relatively immobile over their lifetime. The story we like to tell ourselves is that non-elites in premodern societies, on the whole, had narrow horizons, delimited by their home village, or the neighboring network of villages.

But results from this work and others show that mobile populations where individuals spanned vast areas of Eurasia across their lifetimes, were not that uncommon for pastoralists. We know this historically, as empires such as that of the Turks and Mongols were defined by a ruling elite whose writ extended from eastern to western Eurasia. The Sintashta samples, which exhibit genetic heterogeneity, with some individuals very different from the norm in their settlement, is exactly what you’d expect from a social and political culture which was united in some fashion over huge distances.

As the sample sizes for ancient DNA have increased it seems rather clear that demographic dynamics that we see in later historical expansions of Inner Asian polities extends back to the Bronze Age. With expanding populations across the ecologically friendly landscape, the ancient proto-Indo-Europeans seem to have mixed with the local substrate wherever they went, just as Turks did later. As they moved west, they mixed with late Neolithic Europeans, as they went east, they mixed with Siberian populations, and as they conquered south they mixed with descendants of West Asian farmers.

One of the primary aspects that I think one needs to keep in mind is that one can’t just imagine that this was defined by simple diffusion dynamics. Historically the boundary between pastoralists and peasants could be fluid, but when political resistance collapses pastoralists have been able to use their military prowess to swarm across the lands of agriculturalists. In other words, centuries of gradual inter-demic gene flow might be interrupted by a rapid “pulse” admixture. There’s no reason that pre-literate polities couldn’t exist. The Inca were one such example, the homogeneity of the Uruk civilization in the 4th millennium BC is strongly suggestive of an imperial hegemony or paramountcy.

Another dynamic is that pastoralists are highly mobile, and so may leapfrog over territory which is unsuitable. Or, they may move so rapidly that there isn’t much mixing with populations in between point A and point B.

This is apparently the case with the Bactria–Margiana Archaeological Complex. These people were mostly descended from people related to the eastern farmers of West Asia, those in modern day Iran. Some of their ancestry had affinities with Anatolian farmers, and there is some evidence even of Siberian admixture in this region. But there are three important takehomes of this preprint in relation to this area 1) the BMAC did not contribute much genetically to South Asia at all, 2) steppe ancestry, related to that of the Yamna culture of the Pontic region, only shows up in BMAC ~2000 3)  there is actually evidence of South Asian (Indus valley?) migration into the BMAC.

The fact that Yamna-like ancestry shows up in the BMAC region so late is a strong reason to suspect that Indo-Iranian peoples did not move to Iran and India until after 2000 BC. In earlier comments on this issue, I was rather vague about timing, because the Corded-Ware people show up in Europe before 2500 BC, and I was going along with the parsimonious idea that this was part of one single cultural and social revolution.

I was wrong. Going back to the Turkic analogy, there were multiple waves of migration and folk wandering by Turkic pastoralists. By different Turkic groups. One of the major ones occurred due to the rise of the Mongols, and the Mongols were not even Turks. The same seems to be true of Inner Eurasian Indo-European groups.

Moving on to South Asia, there are two primary constructs which come out of this preprint. “Indus Periphery” and “Ancient Ancestral South Indians.” I’ll call the former InPe and the latter is termed AASI. To some extent these complement and replace the earlier terms “Ancestral North Indian” and “Ancestral South Indian” (ANI and ASI). The AASI are the ancient hunter-gatherers of the Indian subcontinent. The authors suggested that divergence of this group from other eastern Eurasians occurred very early, that the division between the ancestors of the Papuans, Onge, and AASI was even polytomic (that basically separated very quickly without discernible structure).

The InPe samples are from eastern Iran and the BMAC. They’re unique in having AASI ancestry, at variable fractions (indicating contemporaneous admixture). They also resemble samples from Swat Valley which date to 1200 BC and later, with one major difference: the Swat Valley samples have steppe ancestry.

There are no samples from the Indus Valley proper, so the authors suggest that the InPe are reasonable proxies. Additionally, they assert that ASI can best be modeled as a mixture between InPe and AASI. In other words, there were two admixture events. Their Pulliyar samples are actually pretty good proxies for the resultant ASI, while the Kalash of Pakistan are good proxies for the ANI, who are presumably now modeled as a mixture of steppe populations with the InPe.

This resolves the enigmatic result that Priya Moorjani reported to me last year: less than 4,000 years ago “pure” ANI and ASI people existed. She was presumably going off admixture timing estimates. These results suggest that in some form ANI and ASI still exist, and the first admixture occurred with the creation of InPe.

Using a new method the authors contend that InPe emerged 4700-3000 BC. If this is true then the Indus Valley Civilization (IVC) was a compound of AASI and Iranian agriculturalists (sampled from the eastern end of the cline of admixture with Anatolians, that is, they had none of that ancestry). They also post the first arrival of agriculture to Mehrgarh by 2,000 years at the least. I suspect that it will turn out there were earlier admixtures, which are not being detected. For various ecological reasons the West Asian cultural complex was portable only to the northwest fringe of South Asia, and there it persisted for ~4,000 years. This served as a natural eastern limit for cultures which were migrating out of the West Asian zone, and a point where AASI hunter-gatherers constantly mixed into the local population.

As the IVC sites begin to get sampled in the future I predict that instead of a homogeneous transect of admixture over time and space we’ll see a lot of heterogeneity.

In the Swat samples, the authors see two correlated trends, an increase in steppe ancestry, and an increase in AASI ancestry. No doubt this dates to the “great admixture” which occurred between 2000 BC, and some time before 1000 AD (the Bengali admixture with East Asians dates to between 0 and 1000 AD, as does that of Brahmins who left the North Indian plain and mixed with local populations elsewhere).

Finally, the authors detect a skew toward steppe ancestry among some populations, in particular, Brahmins. The skew is in relation to Iranian farmer ancestry, the two being the primary constituents of ANI ancestry. In Who We Are and How We Got Here David Reich says some of the ANI admixture is much more recent than the rest, judging by tract length. And also going by the BMAC and Swat samples it seems that the time period for when Indo-Aryans arrived in South Asia has to be in the interval between 2000 BC and 1200 BC.

There’s another aspect of the preprint which allows for dating. The arrival of Austro-Asiatic people in South Asia probably has to postdate the expansion of the same group in Vietnam about 4,000 years ago (though not necessarily obviously). But the Munda Austro-Asiatic people of northeast India exhibit curious genetic patterns. They clearly have East Asian ancestry related to other Austro-Asiatic populations in Southeast Asia, but they have a lot less “West Eurasian” in their ANI/ASI mix. The authors resolve this by suggesting that the Munda arrived in South Asia when there was still heterogeneity among the ASI, and unadmixed AASI.

After 2000 BC the IVC went into decline. Various groups of Indo-Aryans were expanding and admixing. From the other end of the subcontinent arrived rice cultivators from Southeast Asia. At some point, they ran into an ASI population that had some Iranian admixture, but not as much as typical. All of this probably occurred in the period between 2000 BC and 1000 BC. I know that some researchers have argued that the Gangetic plain was inhabited by Munda speaking peoples before it was inhabited by Indo-Aryans. The main issue I’ve had with this is that modern Munda peoples are very genetically distinctive, and there’s no evidence of East Asian ancestry in most populations of the Gangetic plain (the main exceptions are those which have experienced Tibetan influence/contact).

So here is my interpretation of the genetic and historical evidence:

1) IVC emerges out of a matrix that was a synthesis of West Asian farmers and indigenous hunter-gatherers. I would not be surprised if later genetic work recapitulates the findings in Europe of an initial period of separation, and then a “resurgence” of indigenous ancestry as the barriers between the two groups break.

2) The period between 2000 BC and 1000 BC is the beginning of the transformation of the South Asian genetic and ethnolinguistic landscape, with the intrusion of two different groups from different directions, Indo-Aryans to the west and Austro-Asiatics from the east. Austro-Asiatic rice culture was superior to western wheat culture because rice is more delicious than wheat, but the Indo-Aryans ultimately established cultural supremacy across South Asia by the Iron Age.

3) The situation in South India is more complicated and confused. The admixture of groups like Pulliyar from InPe and AASI into the classic ASI configuration seems to be more recent than 2000 BC (their low bound dates go as late as 400 BC). The admixture may have occurred in various places, not just in South India. The evidence from this paper suggests that the Andronovo/Sintashta cultural zone was characterized by some genetic heterogeneity due to variation in admixture with neighboring peoples, and the same could be said for the IVC then. I would not be surprised if northern IVC locations had more AASI than southern IVC, as the latter were more insulated from the east due to the Thar desert (the results are consistent with earlier work that suggest modern populations in the lower Indus basis have less Indo-Aryan and more Iranian, with less AASI).

4) We need to be careful about assuming that everything here is a linear combination of distinct and separable atomic units of cultural integrity and wholeness. What I mean is that though Brahmins and some other North Indian groups are enriched for steppe ancestry, it is not only their purview. Rather, it may be that these upper caste groups simply mixed less with the other populations with Iranian and AASI ancestry. The statistics in this paper do not detect enrichment of steppe ancestry in South Indian Brahmins. I believe this is simply an artifact of the reality that South Indian Brahmins mixed with Iranian-enriched elites, like Reddys, when they emigrated to the south.

Though the model outlined in the preprint is much more complicated than a simple ANI/ASI mix, it still simplifies the demographic histories of many populations. For example, own survey of the data suggests that Brahmins who left the Indo-Gangetic plain mixed with local elites wherever they went (Bengali Brahmins have East Asian ancestry, just as South Indian Brahmins have more Iranian-like ancestry).

5) Language is important but is not determinative. R1a1a-Z93 arrived in South Asia relatively late with groups from the steppe. Its frequency is highest in the northwest, and among upper castes. That is, it is correlated in a coarse manner to steppe ancestry. But R1a1a-Z93 is pervasive throughout South Asia irrespective of caste and region. Even in Dravidian speaking southern populations, some groups have quite a bit of R1a1a-Z93.

The analogy that presents itself here is Southern Europe, where some groups with high frequencies of R1b, such as the Basques and Sardinians, are clearly descended in the main from pre-steppe populations. What this suggests is that a broad social-culture prestige network mediated by males extended itself into regions where its cultural hegemony was not assured. Additionally, the autosomal genetic impact was modest, even if privileges given to particular male lineages allowed them to sweep other groups out of the gene pool.

Tamil history precipitates out only a little later than that of North Indian Indo-Aryan civilization. I suspect that this is not a coincidence, that South Asia after the collapse of the IVC and the arrival of the Indo-Aryans and Mundas, could be thought of as a brought mixing cauldron genetically and culturally. In many regions, Dravidian languages persisted in the face of the expansive Indo-Aryan, but there was a cultural influence, likely reciprocal. This is why once Indian civilization reemerged its coherent unity set against peoples to the west and east was not strange despite the linguistic gap between the north and the south.

The only exception here might be the Munda. As I have said, R1a1a-Z93 is pervasive. But it is nearly unfound among the Munda, who tend to carry relatively exotic Southeast Asian Y lineages such as O. I believe that the Munda were in some way losers in a cultural conflict, but they maintained themselves in the hills above the Gangetic plain.

Finally, two reflections, one navel-gazing, one big picture. Genome bloggers in the years around 2010 actually anticipated many of these results. There’s some hindsight bias here because you remember the times you are right and not the times you were wrong. We were right that there was more than one ANI pulse. Additionally, we were looking at the ratio between “Eastern European” and “West Asian” ancestry years ago and noticing the skewed patterns, with North Indian Brahmins biased toward the former and South Indian elite non-Brahmins skewed toward the latter. Chaubey 2010 suggested to us that something was different about the Munda not only in their East Asian ancestry but in their ANI/ASI ancestry. They just didn’t seem to have any Indo-European ancestry (steppe), and a lot of ASI. Over the past few years I’ve been suggesting that Dravidian languages were not primal to South India, but the product of a recent expansion (though part of this is due to scientific publications).

The truth was out there. It just took ancient DNA and the analytic chops of the Reich group and their collaborators to prune the tree of possibilities so that we could zero in on a few precise and likely models.

In the general, I wonder about the role of clines, diffusions, and pulses. The models that the foremost practitioners of the science of ancient DNA utilize tend to assume pulse admixtures, rather than isolation-by-distance gene flow. This isn’t always a crazy assumption. But there was a discussion in the paper of a west-east admixture cline between Anatolian farmers and Iranian farmers. Is this cline due to admixture, or was it always there? A paper from a few years ago implied that early farmers were highly structured, structure that broke down later.

Also, the polytomy at the base of the eastern Eurasian human family tree, where all the major lineages diverge rapidly from each other, makes me wonder about gene flow vs. admixture. It seems possible that the polytomy may mask a phylogenetic tree topology which had gradually bifurcating nodes, if periodically a single daughter population replaced all its sister lineages in a local geographic zone. Much of history in human meta-populations may be characterized by isolation-by-distance and gene flow, erased by the extinction of most lineages and expansion of a favored lineage.

November 28, 2017

The Elephant, dragon and eagle

Filed under: Asia,China,Economics,India — Razib Khan @ 12:24 am


The relationship between China and India is clearly one-sided: India is obsessed with a China which is approaching lift-off toward becoming on the verge of a developed nation within a generation (certain urban areas are already basically developed, albeit not particularly wealthy in comparison to Hong Kong or Singapore).

Often when I see interviews with regular Chinese about their opinions of the other country the fixation is upon the manifest Third World nature of India, which seems to be changing much more slowly than their own nation. For me GDP is less important that vital statistics like child mortality or life expectancy. And it is in these sorts of statistics where you see the gap opening up between the two nations. India is developing…. but China is leading, and converging faster with developed nations.

It is in this context that this piece in The New York Times jumped out at me, Amazon, in Hunt for Lower Prices, Recruits Indian Merchants:

While Amazon.com has sellers hailing from many countries, Mr. Cheris said that India and China are the two most important places for Amazon to recruit new merchants since both nations are sources of cheap manufactured goods.

Unlike China, where local companies dominate e-commerce, India is also a huge domestic market for Amazon. Although most of India’s commerce is conducted offline, Indians are coming onto the internet at a rapid clip through their smartphones. Amazon’s chief executive, Jeff Bezos, views India and its 1.3 billion residents as vital to his company’s future, and he has vowed to spend at least $5 billion building up his India operations.

a, I was aware that Amazon really hadn’t gotten any traction in the Chinese market. I did not know that Amazon was so competitive in India, though Flipkart is still dominant there.

The story outlined seems to be part of a bigger trend whereby India is on a very different path from China in its relationship to the rest of the world. China’s economy is big enough and insular enough that it sees the world as either an export market or a source of commodities. It is quickly taking back its place of old as a lumbering hegemon. India, in contrast, seems to be developing a more integrative relationship with large economies such as the United States, despite its command and regulatory economy legacy.

Of course, the India-USA relationship is nothing like “Chimerica” in terms of magnitude, but the Sino-American relationship strikes me as very transactional. Despite the recent tendency of Indian society to espouse a stronger Hindu nationalist line, which is at odds with the West, it seems that there is more cultural exchange between elite Indians and Western societies in the deep sense of values, than has occurred with the Chinese and the West. And, yoga and aspects of spirituality notwithstanding, most of the cultural exchange seems to be toward cosmopolitan elites Indians assimilating to global values which draw from the mode of the West.

Ultimately all of this seems to have geopolitical implications. I’m assuming smarter people than me are keeping track of these trends….

July 17, 2017

Castes are not just of mind

Filed under: Caste,Human Genetics,India — Razib Khan @ 8:31 pm

Before Nicholas Dirks was a controversial chancellor of UC Berkeley, he was a well regarded historian of South Asia. He wrote Castes of Mind: Colonialism and the Making of Modern India. I read it, along with other books on the topic in the middle 2000s.

Here is Amazon summary from Library Journal:

Is India’s caste system the remnant of ancient India’s social practices or the result of the historical relationship between India and British colonial rule? Dirks (history and anthropology, Columbia Univ.) elects to support the latter view. Adhering to the school of Orientalist thought promulgated by Edward Said and Bernard Cohn, Dirks argues that British colonial control of India for 200 years pivoted on its manipulation of the caste system. He hypothesizes that caste was used to organize India’s diverse social groups for the benefit of British control. His thesis embraces substantial and powerfully argued evidence. It suffers, however, from its restricted focus to mainly southern India and its near polemic and obsessive assertions. Authors with differing views on India’s ethnology suffer near-peremptory dismissal. Nevertheless, this groundbreaking work of interpretation demands a careful scholarly reading and response.

The condensation is too reductive. Dirks does not assert that caste structures (and jati) date to the British period, but the thrust of the book clearly leaves the impression that this particular identity’s formative shape on the modern landscape derives from the colonial experience. The British did not invent caste, but the modern relevance seems to date to the British period.

This is in keeping with a mode of thought flourishing today under the rubric of postcolonialism, with roots back to Edward Said’s Orientalism. As a scholar of literature Said’s historical analysis suffered from the lack of deep knowledge. A cursory reading of Orientalism picks up all sorts of errors of fact. But compared to his heirs Said was actually a paragon of analytical rigor. I say this after reading some contemporary postcolonial works, and going back and re-reading Orientalism.

To not put too fine a point on it postcolonialism is more about a rhetorical posture which aims to destroy what it perceives as Western hegemonic culture. In the process it transforms the modern West into the causal root of almost all social and cultural phenomenon, especially those that are not egalitarian. Anyone with a casual grasp of world history can see this, which basically means very few can, since so few actually care about details of fact.

Castes of Mind is an interesting book, and a denser piece of scholarship than Orientalism. Its perspective is clear, and though it is not without qualification, many people read it to mean that caste was socially constructed by the British.

This seems false. It has become quite evident that even the classical varna categories seem to correlate with genome-wide patterns of relatedness. And the Indian jatis have been endogamous for on the order of two thousand. From The New York Times, In South Asian Social Castes, a Living Lab for Genetic Disease:

The Vysya may have other medical predispositions that have yet to be characterized — as may hundreds of other subpopulations across South Asia, according to a study published in Nature Genetics on Monday. The researchers suspect that many such medical conditions are related to how these groups have stayed genetically separate while living side by side for thousands of years.

This is not really a new finding. It was clear in 2009’s Reconstructing Indian Population History. It’s more clear now in The promise of disease gene discovery in South Asia.

Unfortunately though science is not well known in any depth in the general public. The ascendency of social constructionism is such that a garbled and debased view that “caste was invented by the British” will continue to be the “smart” and fashionable view among many elites.

June 24, 2017

Indian genetic history: before the storm

Filed under: Genetics,History,India — Razib Khan @ 2:52 pm

Over at Brown Pundits I’ve mentioned the continuing simmer of controversy over a recent piece, How genetics is settling the Aryan migration debate. This has prompted responses in the Indian media from a Hindu nationalist perspective. One of these notes that the author of the piece above cites me, and then goes on to observe I was fired from The New York Times a few years ago due to accusations of racism (also, there is the implication that I’m just a blogger and we should trust researchers with credibility like Gyaneshwer Chaubey; well, perhaps he should know that Gyaneshwer Chaubey considers me “unbiased” according to an email exchange which I had with him last week [we all have biases, so I think he’s wrong in a literal sense]).

I was a little surprised that a right-wing magazine would lend legitimacy to the slanders of social justice warriors, but this is the world we live in. Those who believe that everything written about me in the media, I invite you to submit your name and background to me. I have contacts in the media and can get things written if I so choose. Watch me write something which is mostly fact, but can easily misinterpreted by those who Google you, and watch how much you value the objective “truth-telling” power of the press.

There’s a reason so many of us detest vast swaths of the media, though to be fair we the public give people who don’t make much money a great deal of power to engage in propaganda. Should we be surprised they sensationalize and misrepresent with no guilt or shame? I have seen most of those who snipe at me in the comments disappear once I tell them that I know what their real identity is. Most humans are cowards. I have put some evidence into the public record to suggest that I’m not.

Perhaps more strange for me is that the above piece was passed around favorably by Sanjeev Sanyal, who I was on friendly terms with (we had dinner & drinks in Brooklyn a few years back). I asked him about the slander in the piece and he unfollowed me on Twitter (a friend of Hindu nationalist bent asked Sanjeev on Facebook about the articles’ attack on me, but the comment was deleted). It shows how strongly people feel about these issues.

I’m in a weird position because I’m brown and have a deep interest in Indian history. But that interest in Indian history isn’t because I’m brown, I’m pretty interested in all the major zones of the Old World Oikoumene. Aside from some jocular R1a1a chauvinism I don’t have much investment personally (I just told said Hindu nationalist friend who turns out to be R2 to clean my latrine; joking of course, though I’m sure he resents that I’m descended on the direct paternal line from the All-Father & Lord of the Steppes and he is not!).

In the aughts I accepted the model outlined in 2006’s The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations. But to be frank it always struck me as a little confusing because the tentative autosomal data we had suggested that many South Asians were closer to West Eurasians than deep divergences dating to the Last Glacial Maximum would suggest. Since I’ve written something like 5 million words in 15 years, I actually can check if I’m remembering correctly. So here’s a post from 2008 where I express reservations of the idea of long term deep heritage of Indians separate from other West Eurasians. The reason I was so impressed by 2009’s Reconstructing Indian Population History is that it resolved the paradox of South Asian genetic relatedness.

To recap, Reich et al. proposed that modern Indians (South Asians) could be modeled as a two way mixture between two distinct populations with separate evolutionary genetic histories, Ancestral North Indians and Ancestral South Indians (ANI and ASI). How distinct? ANI were basically another West Eurasian population, while ASI was likely nested in the clade with Eastern Non-Africans. Additionally, there was a NW-to-SE and caste admixture cline. In other words, the higher you were on the caste ladder the more ANI you had, and the further your ancestors were from the north and west, and more ANI you had. The difference between Y and mtDNA, male and female, could be explained by sex-biased migration.

But there were still aspects of the paper which I had reservations about. After all, it was a model.

  • Models are imperfect fits onto reality. The idea of mass migration seemed ridiculous to me at the time, because even by the time of the Classical Greeks it was noted that Indian was reputedly the most populous land in the world (to their knowledge). But ancient DNA has convinced me of the reality of mass migrations.
  • I wasn’t sure about the nature of the closest modern populations to the ANI. The researchers themselves (in particular, Nick Patterson) told me that the relatedness of ANI to Europeans was very close (on the order of intra-European differences). But modern Indians do not look to be descended from a population that is half Northern European physically. Again, ancient DNA has shown that there was lots of population turnover, and it turns out that Europeans and ANI were likely both compounds and mixed daughter populations of common ancestors (also, typical European physical appearance seems to emerged in situ over the past 5,000 years).
  • The two way admixture modeled seemed too simple. I had run some data and it struck me that North Indian populations like Jats had something different than South Indian groups like Pulayars. In 2013 Priya Moorjani’s paper pretty much confirmed that it was more than a two way admixture along the ANI-ASI cline.

This March BMC Evolution Biology published Silva et al’s A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. It has made a huge splash in India, arguably triggering the write up in The Hindu. But for me it was a bit ho-hum. If you read my 2008 post it is pretty clear that I suspected the most general of the findings in this paper at least 10 years back. It is nice to get confirmation of what you suspect, but I’m more interested to be surprised by something novel.

Nevertheless A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals has come in for lots of repeated attack in the right-wing Indian press. This is unfair, because it is a rather good paper. I suspect that it wasn’t published in a higher ranked journal because most scientists don’t consider the history of India to be that important, and they didn’t really apply new methods, as opposed to bringing a bunch of data and methods together (in contrast, the 2009 Reich et al. paper was one of the first publications which showed how to utilize “ghost populations” in explicit phylogenetic models with relevance to human demographic history).

As it happens I will be writing up my thoughts in detail in an article for a major Indian publication (similar circulation numbers as The Hindu). This has been in talks for over six months, but I’ve been busy. But a month or so ago I thought it was time that I put something into print for the Indian audience, because I felt there was some misrepresentation going on (i.e., the Aryan invasion theory has been been refuted by genetics, but this is what many Indians assert).

For any years people have told me there are certain topics that shouldn’t be talked about. I have offended people greatly. There are many things people do not want to know. I have come to the conclusion this is not an entirely indefensible viewpoint (though if you accept this viewpoint, I think acceptance of authoritarianism is inevitable, so I hope people will toe the line when the new order arrives; knowing their personalities I think they will conform fine). But my nature is such that I continue to have nothing but contempt for the duplicitous and craven manner in which people go about these sorts of private conversations. I assume that as someone with the name “Razib Khan” I will be attacked vociferously by Hindu nationalists, who will no doubt make recourse to the Left-wing hit pieces against me to undermine my credibility. The fact that these groups are fellow travelers should tell us something, though I will leave that as an exercise for the reader.

I will write my piece that reflects the science as I believe it is, without much consideration of the attacks. That is rather easy for me to do in part because I live in the United States, where denigrating the deeply held views and self-esteem of Hindu nationalists is not sensitive or politically protected (unlike say, Muslims). And Hindu nationalists are less likely to kill me by orders of magnitude than Muslim radicals, and they have far less purchase in this nation then the latter (though you may be interested to know that very conservative Muslims follow me on Twitter; they’re actually more open-minded than many SJWs to be entirely honest).

Let me go over some general points that I see coming up over and over on the relationship between Indian (pre)history and genetics in the critiques .

One of the major critiques has to do with the nature of R1a-Z93 and its subclades. Basically this Y chromosomal haplogroup, the greatest that has ever been known, exhibits a strong signature of very rapid expansion over the past 4,000 years or so. It is divided from Z282. While Z93 is found in South Asia, Central Asia, and Siberia, Z282 is European, with its dominant subclade the one associated with Eastern Europeans. Both of these clades of R1a have gone through massive expansion. In the Altai region R1a is 40% of the heritage of peoples who are now predominantly East Eurasian today. But they are Z93. Additionally, ancient DNA from the Pontic Steppe dated ~4,000 years ago from Srubna remains is Z93, as are Scythian remains from the Iron Age.

Much of the argument comes down to dating, and citing papers that give deep coalescence numbers between difference branches of R1a1a. Hindu nationalists and their fellow travelers point to recent papers which give dates >10,000 years ago, and so place the origin of Z93 plausibly in the Pleistocene. The problem is that Y chromosomal coalescence dating is something of a mug’s game. Often they use microsatellite data whose mutational rates are highly uncertain. In contrast, using SNP data, which has a slower mutation rate but requires a lot more data, you get TRMCA (common ancestry) between Z93 and Z282 around ~5,800 years ago. But coalescence estimates often have wide confidence intervals of thousands of years. And even with these intervals, the assumptions you make (e.g., mutation rate) strongly influence your midpoint estimate.

The Y chromosomal data is powerful, but its interpretation is still buttressed upon other assumptions. The really big picture framework is the nature of ancient genome-wide variation across Eurasia. Lazaridis et al. 2016 condition us to a prior where much of Eurasia was subject to massive population-wide genetic changes since the Holocene. Therefore, I am much less surprised if there was massive genetic change in India relatively recently. The methods in Priya Moorjani’s paper and in other publications make it obvious that mixture was extensive in South Asia between very distinct groups until about ~2,000 years ago. In fact, Moorjani et al. using patterns of variation across the genome to come at a number of two to four thousand years ago as the period of massive admixture.

Though we don’t have relevant ancient DNA from India proper to answer any questions yet, we do have ancient DNA from across much of Europe, Central Asia, and the Near East. What they show is that Indian populations share ancestry from both Neolithic Iranians and peoples of the Pontic steppe, who flourished ~5 to ~10,000 years ago. To some extent the latter population is a daughter population of the former…which makes things complicated. Conversely, no West Eurasian population seems to harbor ancient signals of ASI ancestry.

One scientist who holds to the position that most South Asian ancestry dates to the Pleistocene argued to me that we don’t know if ancient Indian samples from the northwest won’t share even more ancestry than the Iranian Neolithic and Pontic steppe samples. In other words, ANI was part of some genetic continuum that extended to the west and north. This is possible, but I do not find it plausible.

The reasons are threefold. First, it doesn’t seem that continuous isolation-by-distance works across huge and rugged regions of Central Eurasia. Rather, there are demographic revolutions, and then relative stasis as the new social-cultural environment crystallizes. This inference I’m making from ancient DNA and extrapolating. This may be wrong, but I would bet I’m not off base here.

Second, it strikes me as implausible that there was literally apartheid between ASI and ANI populations for the whole Holocene right up until ~4,000 years before the present. That is, if Northwest India was involved in reciprocal gene flow with the rest of Eurasia over thousands of years I expect there should have been some distinctive South Asian ASI-like ancestry in the ancient DNA we have. We do not see it.

Third, one of the populations with strong affinities to some Indian populations are those of the Pontic steppe. But we know that this group itself is a compound of admixture that arose 5,000-6,000 years ago. Because of the complexity of the likely population model of ANI this is not definitive, but it seems strange to imagine that ANI could have predated one of the populations with which it was in genetic continuum as part of a quasi-panmictic deme.

Finally, many of the critiques involve evaluation of the scientific literature in this field. Unfortunately this is hard to do from the outside. Citing papers from the aughts, for example, is not wrong, but evolutionary human population genomics is such a fast moving field that even papers published a few years ago are often out of date.

Many are citing a 2012 paper by a respected group which argues for the dominant model of the aughts (marginal population movement into South Asia). One of their arguments, that Central Asian migrant should have East Asian ancestry, is a red herring since it is well known that this dates to the last ~2,000 years or so (we know more now with ancient DNA). But the second point that is more persuasive in the paper is that when they look at local ancestry of ANI vs. ASI in modern Indians, the ANI haplotypes are more diverse than West Eurasians, indicating that they are  not descendants but rather antecedents (usually the direction of ancestry is from more divers to less due to subsampling).

There are two points that I have make here. First, local ancestry analysis is difficult, so I would not be surprised if they integrated ASI regions into ANI and so elevated the diversity in that way (though they think they’ve taken care of it in the paper). Second, if the ANI are a compound of several West Eurasian groups then we expect them to be more diverse than their parents. In other words, the paper is refuting a model which is almost certainly incorrect, but the alternative hypothesis is not necessarily the one they are supporting within the paper.

But there are many things we do not know still. Many free variables which we haven’t nailed down. Here are some major points:

  • Y chromosomal lineages have a correlation with ethno-linguistic groups, but the correlation is imperfect. R1b and R1a seems correlated with Indo-European groups, but both these are found in high proportions in groups which are putatively most “pre-Indo-European” in origin (e.g., Basques, Sardinians, and South Indian tribals and non-Brahmin Dravidian speaking groups). Also, haplogroups like I1 in Europe expands with Indo-Europeans locally, suggesting there was lots of heterogeneity in Indo-Europeans as they expanded. In other words, Indo-European expansion in relation to powerful paternal lineages did not always correlate with ethno-linguistic change.
  • There are probably at minimum two Holocene intrusions from the northwest into South Asia, but this is a floor. The models that are constructed always lack power to detect more complexity. E.g., it is not impossible that there were several migrations of Indo-Europeans into South Asia which we can not distinguish genetically over a period of a few thousand years.
  • If one looks over all of South Asia it may be that ASI ancestry in totality is >50% of the total genome ancestry. I haven’t have a good guess of the numbers. If this is correct, perhaps most South Asian ancestors 10,000 years ago were living in South Asia (though the fertility rate are such in Pakistan that ANI ancestry is increasing right now in relative rates).
  • But, this presupposes that ASI were present in South Asia in totality 10,000 years ago, rather than being migrants themselves. If ancient DNA confirms that ANI were long present in Northwest India, I hold then it is entirely likely that ASI was intrusive to South Asia! The BMC Evolutionary Biology Paper does a lot of interpretation of deep structure in haplogroup M in South Asia. I’m moderately skeptical of this. Europe may not be a good model for South Asia, but there we see lots of Pleistocene turnover.

So where does this leave us? Ancient DNA will answer a lot of questions. Pretty much all scientists I’ve talked to agree on this. My predictions, some of which I’ve made before:

  1. The first period of admixture is old, and dates to the founding of Mehrgarh as an agricultural settlement. The dominant ANI component dates to this period and mixture event, all across South Asia. The presence in South India is due to expansion of these farming populations.
  2. A second admixture event occurred with the arrival of steppe people. Those who argue for the Aryan invasion model posit 1500 BCE as the date. But these people probably were expanding in some form before this date.
  3. We still don’t know who the antecedents for the Indo-Aryans were. Probably they were a compound of different steppe groups, and also other populations which were mixed in (by analogy, in Europe it is obvious now that there was some mixture with the local European farmers and hunter-gatherers as Europeans expanded their frontier westward; the same probably applies for Indo-Aryans are the BMAC).

June 19, 2017

Indian genetics, the never-ending argument

Filed under: Genetics,India,Indian Genetics,Indo-Europeans,science — Razib Khan @ 10:44 pm

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The second paper is very confused (or confusing):

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

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

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

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

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

May 24, 2017

Across the chasm of Incommensurability

Filed under: China,Epistemology,India — Razib Khan @ 11:23 am

The Washington Post has a piece typical of its genre, A Chinese student praised the ‘fresh air of free speech’ at a U.S. college. Then came the backlash. It’s the standard story; a student from China with somewhat heterodox thoughts and sympathies with some Western ideologies and mores expresses those views freely in the West, and social media backlash makes them walk it back. We all know that the walk back is insincere and coerced, but that’s the point: to maintain the norm of not criticizing the motherland abroad. The truth of the matter of how you really feel is secondary.

Tacit in these stories is that of course freedom of speech and democracy are good. And, there is a bit of confusion that even government manipulation aside, some of the backlash from mainland Chinese seems to be sincere. After all, how could “the people” not defend freedom of speech and democracy?

Reading this story now I remember what an academic and friend (well, ex-friend, we’re out of touch) explained years ago in relation to what you say and public speech: one can’t judge speech by what you intend and what you say in a descriptive sense, but you also have to consider how others take what you say and how it impacts them. In other words, intersubjectivity is paramount, and the object or phenomenon “out there” is often besides the point.

At the time I dismissed this viewpoint and moved on.

Though in general I do not talk to people from China about politics (let’s keep in real, it’s all about the food, and possible business opportunities), it was almost amusing to hear them offer their opinions about Tibet and democracy, because so often very educated and competent people would trot out obvious government talking points. In this domain there was little critical rationalism. One could have a legitimate debate about the value of economic liberalization vs. political liberalization. But it was ridiculous to engage with the thesis that China was always unitary between the Former Han and today. That is just a falsehood. Though the specific detail was often lacking in their arguments, it was clearly implied that they knew the final answer. I would laugh at this attitude, because I thought ultimately facts were the true weapon. The world as it is is where we start and where we end.

Or is it? From the article:

Another popular comment expressed disappointment in U.S. universities, suggesting without any apparent irony that Yang should not have been allowed to make the remarks.

“Are speeches made there not examined for evaluation of their potential impact before being given to the public?” the commentator wrote.

“Our motherland has done so much to make us stand up among Western countries, but what have you done? We have been working so hard to eliminate the stereotypes the West has put on us, but what are you doing? Don’t let me meet you in the United States; I am afraid I could not stop myself from going up and smacking you in the face.”

Others were critical not of Yang’s comments but of the venue in which she chose to make them.

“This kid is too naive. How can you forget the Chinese rule about how to talk once you get to the United States? Just lie or make empty talk instead of telling the truth. Only this will be beneficial for you in China. Now you cannot come back to China,” @Labixiaoxin said.

There is a lot of texture even within this passage. I do wonder if the writers and editors at The Washington Post knew the exegetical treasures they were offering up.

To me, there is irony in the irony. Among the vanguard of the intelligensia in these United States there is plenty of agreement with the thesis that some remarks should not be made, some remarks should not be thought. Especially in public. The issue is not on the principle, but specifically what remarks should not be made, and what remarks should not be public. That is, the important and substantive debates are not about a positive description of the world, but the values through which you view the world. The disagreements with the Chinese here are not about matters of fact, but matters of values. Facts are piddling things next to values.

So let’s take this at face value. Discussions about Tibetan autonomy and Chinese human rights violations cause emotional distress for many Chinese. I’ve seen this a little bit personally, when confronting Chinese graduate students with historical facts. It’s not that they were ignorant, but their views of history were massaged and framed in a particular manner, and it was shocking to be presented with alternative viewpoints when much of one’s national self-identity hinged on a particular narrative. Responses weren’t cogent and passionate, they were stuttering and reflexive.

Now imagine the psychic impact on hundreds of millions of educated Chinese. They’ve been sold a particular view of the world, and these students get exposed to new ideas and viewpoints and relay it back, and it causes emotional distress. Similarly, for hundreds of millions of Muslims expressing atheism is an ipso facto assault on their being, their self-identity. This is why I say that the existence of someone like me, an atheist from a Muslim background, is by definition an affront to many. My existence is blasphemy and hurtful.

And the Chinese view of themselves and their hurt at insults to their nationhood do not come purely from government fiction. There’s a factual reality that needs to be acknowledged. China was for thousands of years was one of the most significant political and cultural units in the world. But the period from 1850 to 1980 were dark decades. The long century of eclipse. China was humiliated, dismembered, and rendered prostrate before the world. It collapsed into factious civil war and warlordism. Tens of millions died in famines due to political instability.

In the late 1950s and early 1960s between 20 to 50 million citizens of the Peoples’ Republic of China starved due to Mao’s crazy ambitions. This is out of a population of ~650 million or so. Clearly many Chinese remember this period, and have relatives who survived through this period. A nation brought low, unable to feed its own children, is not an abstraction for the Chinese.

On many aspects of fact there are details where I shrug and laugh at the average citizen of China’s inability to look beyond the propaganda being fed to it. And I am not sure that the future of the Chinese state and society is particularly as rosy as we might hope for, as its labor force already hit a peak a few years ago. But the achievement of the Chinese state and society over the past generation in lifting hundreds of millions out of grinding poverty have been a wonder to behold. A human achievement greater than the construction of the Great Wall, not just a Chinese achievement.

But it is descriptively just a fact that nations which have been on the margins and find themselves at center stage want their “time in the sun.” The outcomes of these instances in history are often not ones which redound to the glory of our species, but it is likely that group self-glorification and hubris come out of a specific evolutionary context.

There are on the order of ~300 million citizens of the United States. There are 1.3 billion Chinese. If offense and hurt are the ultimate measures of the acceptance of speech than an objective rendering might suggest that we lose and they win. There are more of them to get hurt than us.

But perhaps the point is that there is no objectivity. There is no standard “out there.” Once the measuring stick of reality falls always, and all arguments are reduced to rhetoric, it is sophistry against sophistry. Power against power. Your teams and views are picked for you, or, through self-interest, or, your preferences derived from some aesthetic bias. Sometimes the team with the small numbers wins, though usually not.

Discourse is like a season of baseball. At the end there is a winner. But there is no final season. Just another round of argument.

Ten years ago I read Alister McGrath’s The Twilight of Atheism. I literally laughed at the time when I closed that book, because the numbers did not seem to support him in his grand confidence about atheism’s decline. And since the publication of that book the proportion of people in the United States who are irreligious has increased. Contrary to perceptions there has been no great swell of religion across the world.

But on a deep level McGrath was correct about something. Much of the book was aimed at the “New Atheism” specifically. A bold and offensive movement which prioritized the idea of facts first (in the ideal if not always the achievement), McGrath argued that this was a last gasp of an old modernist and realist view of the world, which would be swallowed by the post-modern age. He, a traditional Christian, had a response to the death of reason and empiricism uber alleles, his God of Abraham, God of Isaac, and the God of Jacob. Primordial identities of religion, race, and nationality would emerge from the chaos and dark as reason receded from the world.

With the rise of social constructionism McGrath saw that the New Atheists would lose the cultural commanding heights, their best and only weapons, the glittering steel of singular facts over social feelings. On the other hand, if facts derive from social cognition, than theistic views have much more purchase, because on the whole the numbers are with God, and not his detractors.

And going back to numbers. The Washington Post is owned by Jeff Bezos. And China is a massive economic shadow over us all. Anyone who works in the private sector dreams of business in China. Currently Amazon is nothing in China. What if the Chinese oligarchs made an offer Bezos couldn’t refuse? Do you think The Washington Post wouldn’t change its tune?

When objectivity and being right is no defense, then all that remains is self-interest. Ironically, cold hard realism may foster more universal empathy by allowing us to be grounded in something beyond our social unit. In the near future if the size of social units determines who is, and isn’t, right, than those who built a great bonfire on top of positivism’s death may die first at the hands of the hungry cannibal hordes. Many of us will shed no tears. We were not the ones in need of empathy, because we were among the broad bourgeois masses.

In the end the truth only wins out despite our human natures, not because of it.

April 20, 2017

Aryan marauders from the steppe came to India, yes they did!

Filed under: Genetics,Genomics,History,India — Razib Khan @ 10:21 pm

Its seems every post on Indian genetics elicits dissents from loquacious commenters who are woolly on the details of the science, but convinced in their opinions (yes, they operate through uncertainty and obfuscation in their rhetoric, but you know where the axe is lodged). This post is an attempt to answer some questions so I don’t have to address this in the near future, as ancient DNA papers will finally start to come out soon, I hope (at least earlier than Winds of Winter).

In 2001’s The Eurasian Heartland: A continental perspective on Y-chromosome diversity Wells et al. wrote:

The current distribution of the M17 haplotype is likely to represent traces of an ancient population migration originating in southern Russia/Ukraine, where M17 is found at high frequency (>50%). It is possible that the domestication of the horse in this region around 3,000 B.C. may have driven the migration (27). The distribution and age of M17 in Europe (17) and Central/Southern Asia is consistent with the inferred movements of these people, who left a clear pattern of archaeological remains known as the Kurgan culture, and are thought to have spoken an early Indo-European language (27, 28, 29). The decrease in frequency eastward across Siberia to the Altai-Sayan mountains (represented by the Tuvinian population) and Mongolia, and southward into India, overlaps exactly with the inferred migrations of the Indo-Iranians during the period 3,000 to 1,000 B.C. (27). It is worth noting that the Indo-European-speaking Sourashtrans, a population from Tamil Nadu in southern India, have a much higher frequency of M17 than their Dravidian-speaking neighbors, the Yadhavas and Kallars (39% vs. 13% and 4%, respectively), adding to the evidence that M17 is a diagnostic Indo-Iranian marker. The exceptionally high frequencies of this marker in the Kyrgyz, Tajik/Khojant, and Ishkashim populations are likely to be due to drift, as these populations are less diverse, and are characterized by relatively small numbers of individuals living in isolated mountain valleys.

In a 2002 interview with the India site Rediff, the first author was more explicit:

Some people say Aryans are the original inhabitants of India. What is your view on this theory?

The Aryans came from outside India. We actually have genetic evidence for that. Very clear genetic evidence from a marker that arose on the southern steppes of Russia and the Ukraine around 5,000 to 10,000 years ago. And it subsequently spread to the east and south through Central Asia reaching India. It is on the higher frequency in the Indo-European speakers, the people who claim they are descendants of the Aryans, the Hindi speakers, the Bengalis, the other groups. Then it is at a lower frequency in the Dravidians. But there is clear evidence that there was a heavy migration from the steppes down towards India.

But some people claim that the Aryans were the original inhabitants of India. What do you have to say about this?

I don’t agree with them. The Aryans came later, after the Dravidians.

Over the past few years I’ve gotten to know the above first author Spencer Wells as a personal friend, and I think he would be OK with me relaying that to some extent he was under strong pressure to downplay these conclusions. Not only were, and are, these views not popular in India, but the idea of mass migration was in bad odor in much of the academy during this period. Additionally, there was later work which was less clear, and perhaps supported an Indian origin for R1a1a. Spencer himself told me that it was not impossible for R1a to have originated in India, but a branch eventually back-migrated to southern Asia.

But even researchers from the group at Stanford where he had done his postdoc did not support this model by the middle 2000s, Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists. In 2009 a paper out of an Indian group was even stronger in its conclusion for a South Asian origin of R1a1a, The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system.

By 2009 one might have admitted that perhaps Spencer was wrong. I was certainly open to that possibility. There was very persuasive evidence that the mtDNA lineages of South Asia had little to do with Europe or the Middle East.

Yet a closer look at the above papers reveals two major systematic problems.

First, ancient DNA has made it clear that there has been major population turnover during the Holocene, but this was not the null hypothesis in the 2000s. Looking at extant distributions of lineages can give one a distorted view of the past. Frankly, the 2009 Indian paper was egregious in this way because they included Turkic groups in their Central Asian data set. Even in 2009 there was a whole lot of evidence that Central Asian Turkic groups were likely very different from Indo-European Turanian populations which would have been the putative ancestors of Indo-Aryans. Honestly the authors either consciously loaded the die to reduce the evidence for gene flow from Central Asia, or they were ignorant (the nature of the samples is much clearer in the supplements than the  primary text for what it’s worth).

Second, Y chromosomal marker sets in the 2000s were constrained to fast mutating microsatellite regions or less than 100 variant SNPs on the Y. Because it is so repetitive the Y chromosome is hard to sequence, and it really took the technologies of the last ten years to get it done. Both the above papers estimate the coalescence of extant R1a1a lineages to be 10-15,000 years before the present. In particular, they suggest that European and South Asian lineages date back to this period, pushing back any possible connection between the groups, and making it possible that European R1a1a descended from a South Asian founder group which was expanding after the retreat of the ice sheets. The conclusions were not unreasonable based on the methods they had.  But now we have better methods.*

Whole genome sequencing of the Y, as well as ancient DNA, seems to falsify the above dates. Though microsatellites are good for very coarse grain phyolgenetic inferences, one has to be very careful about them when looking at more fine grain population relationships (they are still useful in forensics to cheaply differentiate between individuals, since they accumulate variation very quickly). They mutate fast, and their clock may be erratic.

Additionally, diversity estimates were based on a subset of SNP that were clearly not robust. R1a1a is not diverse anywhere, though basal lineages seem to be present in ancient DNA on the Pontic steppe in some cases.

To show how lacking in diversity R1a1a is, here are the results of a 2016 paper which performed whole genome sequencing on the Y. Instead of relying on the order of 10 to 100 SNPs, this paper discover over 65,000 Y variants worldwide. Notice how little difference there is between different South Asian groups below, indicative of a massive population expansion relatively recently in time which didn’t even have time to exhibit regional population variation. They note that “The most striking are expansions within R1a-Z93 [the South Asian clade], ~4.0–4.5 kya. This time predates by a few centuries the collapse of the Indus Valley Civilization, associated by some with the historical migration of Indo-European speakers from the western steppes into the Indian sub-continent.

(BEB = Bengali, GIH = Gujarati, PJL = Punjabi, STU = Sri Lanka Tamil, ITU = Indian Telugu)

The spatial distribution of Z93 lineages of R1a is as you can see to the left. There are branches in South Asia, Central Asia, and in the Altai region. Ancient DNA from the Bronze Age Mongolia has found Z93. Modern Mongolians clearly have a small, but appreciable, fraction of West Eurasian ancestry. Some also carry R1a1a. Z93 has also been found in North-Central Asian steppe samples that date to ~4,500 years before the present.

Today with ancient DNA we’re discovering individuals who lived around the time of the massive  expansion alluded to above. What are these individuals like? They are a mix of European, Central Eurasian, Near Eastern, and Siberian. Many of them share quite a bit of ancestry with South Asian populations, in particular those from the northwest of subcontinent, as well as upper castes more generally.

A new paper using ancient DNA from Scythians (Iranian speakers) also shows that they carried Z93. Some of them had East Asian admixture. These were the ones from the eastern steppe. So not entirely surprising. In the supplements of the paper they have an admixture plot with many populations. At K = 15 in supplementary figure 14 you see many ancient Central Eurasian populations run against modern groups. At this K there is a South Asian modal cluster which is found in South Asians as well as nearby Iranian groups from Afghanistan.

It is not light green or dark blue. You see see that this salmon color is modal in tribal South Indian populations, or non-Brahmin South Indians. It drops in frequency as you move north and west, and as you move up the caste ladder. Observe that is present even among the relatively isolated Kalash people of Chitral.

Outside of South Asia-Afghanistan, this salmon component is found among Thai and Cambodians. From talking to various researchers, and recent published findings, it seems clear that this signature is not spurious, but is indicative of some migration from South Asia to Southeast Asia in the historical period, as one might infer based on cultural affinities. It is also found at lower frequencies among the Uyghur of Xinjiang. This is not entirely surprising either. This region of the Tarim basin was connected to Kashmir across the Pamirs. The 4th century Buddhist monk from the Tarim basin city of Kucha, who was instrumental in the translation of texts into Chinese, Kumārajīva, may have had a Kashmiri father.

Even before Islam much of Northwest India and Central Asia were under the rule of the same polity, and after Islam there is extensive record of the enslavement of many Indians in the cities of the eastern Islamic world, as well as the travel of some Indian merchants and intellectuals into these regions.

And yet this South Asia cluster is not present in the ancient steppe samples carrying R1a1a-Z93. None of them to my knowledge. Many ancient samples share ancestry with South Asians. For example it seems that many ancient West Asian samples from Iran share common history as evident in genetic drift patterns with many South Asians. And, there is good evidence that a subset of South Asians, skewed toward northwest and upper caste groups, share drift with steppe Yamna samples. But South Asians are often clearly composites of these exogenous populations and an indigenous component with affinities with Andaman Islanders, and more distantly Southeast Asians and other eastern non-Africans.

How can you reconcile this with migration out of South Asia? The path is found in publications such as Genetic Evidence for Recent Population Mixture in India. Here you have a paper which models mixing between Ancestral North Indians (ANI) and Ancestral South Indians (ASI). The ANI would be the source population for the ancestry shared with West Eurasians. And, they would lack ASI ancestry because the mixing had not occurred. The admixture dates the paper are between two and four thousand years before the present.

There is a problem though. These methods detect the last admixture events. Therefore, they are a lower bound on major mixing events, not a record of when there was no mixing. Secondarily, but not less importantly, recent work indicates that because of the pulse admixture simplification these methods likely underestimate the time period of admixture.

Another issue for me is the idea that ANI and ASI could be so separate within India. If ANI is the source of gene flow into other parts of Eurasia from South Asia, then I believe that ASI is intrusive to the subcontinent. I don’t think that ASI being intrusive is so implausible. Southeast Asia has undergone massive genetic changes over the Holocene, and it may be that there was much more ASI ancestry in placers like Burma before the arrival of Austro-Asiatic rice farmers. The presence of Austro-Asiatic languages in northeast India and central India shows a precedent of migration from Southeast Asia into the subcontinent.

In sum, the balance of evidence suggests male mediated migration into South Asia from Central Asia on the order of ~4-5,000 years ago. There are lots of details to be worked out, and this is not an assured model in terms of data, but it is the most likely. In the near future ancient DNA will clear up confusions. Writing very long but confused comments just won’t change this state of affairs. New data will.

Addendum: Indian populations have finally been relatively well sampled, thanks to Mait Mepsalu’s group in Estonia, David Reich’s lab and, the Indian collaborators of both, and the 1000 Genomes (HGDP gave us Pakistanis). Additionally, Zack Ajmal’s Harappa website did some work filling in some holes in the early 2010s.

* A Facebook argument broke out about one of my posts where one interlocutor asserted that he leaned on papers from the late 2000s, not all the new stuff. That’s obviously because the new stuff did not support his preferred position, while the old stuff did. I would prefer that faster-than-light travel were possible, so I’ll just stick to physics before 1910?

April 18, 2017

Women hate going to India

Filed under: Anthroplogy,Genetics,Human Genetics,India,Parsi — Razib Khan @ 9:11 pm


For some reason women do not seem to migrate much into South Asia. In the late 2000s I, along with others, noticed a strange discrepancy in the Y and mtDNA lineages which trace one’s direct male and female lines: in South Asia the male lineages were likely to cluster with populations to the north an west, while the females lines did not. South Asia’s females lines in fact had a closer relationship to the mtDNA lineages of Southeast and East Asia, albeit distantly.

One solution which presented itself was to contend there was no paradox at all. That the Y chromosomal lineages found in South Asia were basal to those to the west and north. In particular, there were some papers suggesting that perhaps R1a1a originated in South Asia at the end of the last Pleistocene. Whole genome sequencing of Y chromosomes does not bear this out though. R1a1a went through rapid expansion recently, and ancient DNA has found it in Russia first. But in 2009 David Reich came out with Reconstructing Indian population history, which offered up somewhat of a possible solution.

What Reich and his coworkers found that South Asia seems to be characterized by the mixture of two very different types of populations. One set, ANI (Ancestral North Indian), are basically another western or northwestern Eurasian group. ASI (Ancestral South Indian), are indigenous, and exhibit distant affinities to the Andaman Islanders. The India-specific mtDNA then were from ASI, while the Y chromosomes with affinities to people to the north and west were from ANI. In other words, the ANI mixture into South Asia was probably through a mass migration of males.

But it’s not just Y and mtDNA in this case only. A minority of South Asians speak Austro-Asiatic languages. The most interesting of these populations are the Munda, who tend to occupy uplands in east-central India. Older books on India history often suggest that the Munda are the earliest aboriginals of the subcontinent, but that has to confront the fact that most Austro-Asiatic language are spoken in Southeast Asia. There was no true consensus where they were present first.

Genetics seems to have solved this question. The evidence is building up that Austro-Asiatic languages arrived with rice farmers from Southeast Asia. Though most of the ancestry of the Munda is of ANI-ASI mix, a small fraction is clearly East Asian. And interestingly, though they carry no East Asian mtDNA, they do carry East Asian Y. Again, gene flow mediated by males.

The same is true of India’s Bene Israel Jewish community.

A new preprint on biorxiv confirms that the Parsis are another instance of the same dynamic: The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection:

Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present novel genome-wide autosomal, Y-chromosome and mitochondrial data from Iranian and Indian Zoroastrians and neighbouring modern-day Indian and Iranian populations to conduct the first genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we show that Zoroastrians in Iran and India show increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we show that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690-1390 CE and providing strong evidence that the migrating group was largely comprised of Zoroastrian males. By exploiting the rich information in DNA from ancient human remains, we also highlight admixture in the ancestors of Iranian Zoroastrians dated to 570 BCE-746 CE, older than admixture seen in any other sampled Iranian group, consistent with a long-standing isolation of Zoroastrians from outside groups. Finally, we report genomic regions showing signatures of positive selection in present-day Zoroastrians that might correlate to the prevalence of particular diseases amongst these communities.

The paper uses lots of fancy ChromoPainter methodologies which look at the distributions of haplotypes across populations. But some of the primary results are obvious using much simpler methods.

1) About 2/3 of the ancestry of Indian Parsis derives from an Iranian population
2) About 1/3 of the ancestry of Indian Parsis derives from an Indian popuation
3) Almost all the Y chromosomes of Indian Parsis can be accounted for by Iranian ancestry
4) Almost all the mtDNA haplogroups of Indian Parsis can be accounted for by Indian ancestry
5) Iranian Zoroastrians are mostly endogamous
6) Genetic isolation has resulted in drift and selection on Zoroastrians

The fact that the ancestry proportion is clearly more than 50% Iranian for Parsis indicates that there was more than one generation of males who migrated. They did not contribute mtDNA, but they did contribute genome-wide to Iranian ancestry. There are wide intervals on the dating of this admixture event, but they are consonant oral history that was later written down by the Parsis.

So there you have it. Another example of a population formed from admixture because women hate going to India.

Citation: The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection.
Saioa Lopez, Mark G Thomas, Lucy van Dorp, Naser Ansari-Pour, Sarah Stewart, Abigail L Jones, Erik Jelinek, Lounes Chikhi, Tudor Parfitt, Neil Bradman, Michael E Weale, Garrett Hellenthal
bioRxiv 128272; doi: https://doi.org/10.1101/128272

March 28, 2017

How Indians are a lot like Latin Americans

Filed under: Anthroplogy,Genetics,India — Razib Khan @ 5:45 am


Pretty much any person of Indian subcontinental origin in the United States of a certain who isn’t very dark skinned has probably had the experience of being spoken to in Spanish at some point. When I was younger growing up in Oregon I had the experience multiple times of Spanish speakers, probably Mexican, pleading with me to interpret for them because there was no one else who seemed likely. It isn’t a genius insight to conclude I was most likely South Asian…but it wasn’t out of the question I was Mexican. This applies even more to lighter skinned South Asians. In the Central Valley of California, where there are many Sikhs from Punjabi and Mexicans, this confusion occurred a lot for some Indian kids.

Of course biogeographically there isn’t that much connection between South Asia and the New World. But it isn’t crazy that Christopher Columbus labelled the peoples of the New World “Indian.” After all, they were a brown-skinned people whose features were not African, East Asian, or West Eurasian. And, it turns out genetically there is a coincidence that connects the New World and South Asia: the mixed peoples of Latin America with Amerindian and European ancestry recapitulate an admixture which resembles what occurred in South Asia thousands of years ago. It looks as if about half the ancestry of South Asians is West Eurasian and half something more like eastern Eurasians.

On principles component analysis that means that South Asian and Mexican and Peruvian samples often overlap. This is somewhat curious because the non-West Eurasian ancestors of South Asians and Amerindians diverged in ancestry on the order of 25 to 45 thousand years before the present. And the Iberian ancestry of the mixed people of the New World is almost as far from the character of South Asian West Eurasian ancestry as you can get (in the parlance of this blog, lots of EEF, less CHG, not too much ANE).

A new paper, A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals, highlights another similarity: massive bias in biogeographic ancestry by sex. More precisely, the rank order of West Eurasian ancestry in South Asia is skewed like so: Y chromosome > whole-genome > mtDNA (as is evident in the above figure).

I actually began writing about this in the late 2000s, when the fact that South Asian mtDNA was very different from West Eurasian mtDNA, and South Asian Y chromosome was mostly West Eurasian, was obvious. Then work using genome-wide data sets began to point to massive intra-Eurasian admixture between very diverged lineages. The paper is not revolutionary, but worth reading for its thoroughness and how it brings together all the lines of evidence.

Finally, no ancient DNA. That’s probably for the future, but I don’t expect any surprises.

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

August 29, 2012

The future of the three “Pakistans”

Filed under: Data Analysis,Demographics,India,Pakistan,Population — Razib Khan @ 9:55 pm

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, ...

The future of the three “Pakistans”

Filed under: Data Analysis,Demographics,India,Pakistan,Population — Razib Khan @ 9:55 pm

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, ...

May 27, 2012

Genetics’ random truths

Filed under: Anthroplogy,India,Indian — Razib Khan @ 12:05 am

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 ...

February 25, 2012

Men on the move and women in place?

Filed under: Anthroplogy,Human Genetics,Human Genomics,India — Razib Khan @ 7:22 pm

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.

December 31, 2011

The South Asian libertarian newspaper of record

Filed under: India,The New York Times — Razib Khan @ 12:00 pm

As I’ve joked before, The New York Times always seems to be pushing free market private sector solutions in South Asia. Many of India’s Poor Turn to Private Schools:

For more than two decades, M. A. Hakeem has arguably done the job of the Indian government. His private Holy Town High School has educated thousands of poor students, squeezing them into cramped classrooms where, when the electricity goes out, the children simply learn in the dark.

Parents in Holy Town’s low-income, predominantly Muslim neighborhood do not mind the bare-bones conditions. They like the modest tuition (as low as $2 per month), the English-language curriculum and the success rate on standardized tests. Indeed, low-cost schools like Holy Town are part of an ad hoc network that now dominates education in this south Indian city, where an estimated two-thirds of all students attend private institutions.

“The responsibility that the government should shoulder,” Mr. Hakeem said with both pride and contempt, “we are shouldering it.”

The issue seems to be that in terms of what it provides the masses India’s public sector is an unmitigated joke verging on disaster. What India needs is greater federalism, as it seems that coordination from the center is just not possible with all the special interests tugging at it.

October 16, 2011

Don’t overgeneralize about 2.5 billion people

Filed under: China,Data Analysis,India — Razib Khan @ 3:40 pm

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.

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