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

September 30, 2018

Open Thread, 9/30/2018

Filed under: Open Thread — Razib Khan @ 9:17 pm

A new shirt, Vaccines Cause Adults. I think that’s pretty funny. Since I don’t have that sort of human, it wasn’t my idea. Obviously, Photo 51 t-shirts are still on the  DNAGeeks website.

Patrick Wyman does not recommend The Silk Roads: A New History of the World. The killer observation for me is that whenever Patrick knew a lot about the topic the author was kind of wrong or off. This is an incredibly important sign for me. If you don’t have this still, you probably need to get to a point where you know enough about a topic. Just pick one, any topic. Additionally, he observes that 40% of the book deals with 20th and 21st century history. That’s also a big no-no for me. Contemporary history is well covered in our society. We have a presentism bias.

On the other hand, I would recommend Empires of the Silk Road. Christopher I. Beckwith is kind of cranky, but he’s learned and interesting.

Valerie Hansen’s The Silk Road: A New History is one I’d also recommend. It’s more focused on archaeology and the earlier period before 1000 AD. Hansen also lacks the long narrative ambition of Beckwith’s treatment, but if you want to know how Sogdian merchants rolled during the Tang dynasty, this is for you.

Buddhism and Islam on the Silk Road is also a good book, though its focus is rather narrow.

Lee Jussim asked on Twitter what counts as “white” today since so much social justice discourse (SJD) revolves around the concept. My response is basically “white” is what is necessary for you to win an argument (though another element now is that if you are Muslim you are not white, no matter how white you look, just like if you have a Spanish surname, you are not white either somehow). Here is how it works:

Italians are white: the ancient Romans were white people who oppressed and executed a marginalized person of color, a brown Palestinian named Jesus.

Italians are not white: Until after World War II Italians were actually not viewed as white, and had to “become white” (or, they had to become people who think they are white). They were even lynched!

The takeaway is that sophism is a feature, not a bug. That’s why I’m so good at faking this discourse.

He’s trolling us.

Global alliances and wheels within wheels. Talking about the concern that American Leftists have about Hindu nationalism. Though they seem sanguine about Islamism.

John Horgan interviews Bob Trivers in Jamaica. As usual with Trivers, it’s crazy. Though if you read his autobiography, Wild Life, there’s a lot that’s similar.

Of all Trivers’ books though, I would really recommend Natural Selection and Social Theory: Selected Papers of Robert Trivers. There’s a lot of science and biography in that work. Anecdotes about W. D. Hamilton in particular I enjoyed.

Variation in actual relationship as a consequence of Mendelian sampling and linkage.

What’s China’s new luxury status symbol? A curvy butt. Had a conversation with a friend who is a businessman in China. His female employees have butt-workout apps.

Gen­ome-edit­ing scis­sors will re­volu­tion­ise plant breed­ing, yet a pro­fessor fears EU countries will get side-tracked.

Margins – Save, annotate and share your papers with anyone.

An Empirical Demonstration of Unsupervised Machine Learning in Species Delimitation. The title is kind of weird. STRUCTURE? Also, I don’t really believe in automatic species delimitation. But it’s an effort.

Common genetic variants contribute to risk of rare severe neurodevelopmental disorders.

Reproductive Longevity Predicts Mutation Rates in Primates.

Stronger and higher proportion of beneficial amino acid changing mutations in humans compared to mice and flies. I think I’ll blog this.

Reihan Salam has a new book out, Melting Pot or Civil War?: A Son of Immigrants Makes the Case Against Open Borders. The title is a bit overwrought, but Reihan is not. Obviously we share a lot in terms of our backgrounds and our opinions. And on questions regarding assimilation we’ve been on the same page for a long time.

Sexual selection, environmental robustness and evolutionary demography of maladapted populations: a test using experimental evolution in seed beetles.

The Blank Slateism of the Right. This is really about the Anglo-Right. American conservatives who come out of the liberal tradition are big fans of John Locke. That should tell you all that you need to know.

Robert Plomin’s Blueprint: How DNA Makes Us Who We Are is coming out soon. To be honest it looks like an updated version of Judith Rich Harris’ The Nurture Assumption.

Greg Cochran wrote up a review in Quillette with the expected title, Forget Nature Versus Nurture. Nature Has Won. Nathan Comfort in Nature wrote Genetic determinism rides again.

Stuart Ritchie was not happy with Comfort’s review:

The review is as bad as you’d think. He doesn’t seem to know the science, but that’s a feature, not a bug, for the sort of review he’s going to give. It’s useful for me because I can note who retweets and “likes” the review, as these are people who I will ignore on all things genetics indefintely.

A bigger question that I asked a few liberal academic friends: with all the concern over eugenics where’s the widespread objection among the usual hand wringers about noninvasive prenatal testing and widespread abortion of fetuses that test positive for Down Syndrome? In the Nordic countries nearly 100% of fetuses which test positive are aborted. In France about 75%. In the United states 70%.

My personal suspicion is that academics are much more concerned about future and vague eugenical specters. Not those activities done freely and through the proactive choice of people of their own class and likely liberal politics. Burn a few Robert Plomin’s at the stake, but make sure you don’t jeopardize your colleagues’ dreams of having a “healthy” baby.

Overlooked factors in the analysis of parole decisions. Basically it looks like the old result that judges are harsher before lunch is an artifact of who is seen before lunch (prisoners without attorneys tended to be seen before lunch).

Unless I have looked at the original study, I’m starting to just shy away from retelling results published through peer review. Studies really need to have sample sizes in the title. Small sample sizes are OK in some contexts, but so often they are used to get away with stuff.

The shadow of the Ice Age

Filed under: paleontology,Wolves — Razib Khan @ 1:55 pm

As ancient DNA becomes a more standard part of archaeological science it’s going really yield up some doozies. You’ve probably read Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, and how it’s upended old paradigms. But with the human past we probably have a better idea of the range of possibilities. When it comes to other organisms it’s going to be a weirder and wilder ride I predict.

This is why a new preliminary result does not shock me, Ancient Japanese wolf may be rare remnant of ice age wolves:

The wolf’s DNA more closely resembled that of a long-extinct wolf that lived in Siberia more than 35,000 years ago than that of living Eurasian and American wolves, Niemann reported here on Friday at the International Symposium on Biomolecular Archaeology. Most ancient wolves went extinct when the ice sheets that covered the Northern Hemisphere began to melt more than 20,000 years ago and the large mammals the wolves hunted, such as mammoth, died off. But some of their DNA lived on in the Honshū wolf, which could offer a new window on the evolution of wolves as well as dogs, says paleogeneticist Mikkel Sinding of the Greenland Institute of Natural Resources in Nuuk, who extracted the DNA.

Unfortunately the last Honshu wolves were killed more than a century ago. But for the purposes of DNA extract that’s basically yesterday.

From everything I can see the “megafauna” that inhabit the Palearctic ecozone seem to have through a lot of mass extinctions over the last 50,000 years. This extends from Neanderthals, to mammoths, to large canids and felids. Some lineages, such as that of humans and wolves, also underwent expansions from the remaining branches of the phylogenetic tree. But it’s reasonable that various relic groups of earlier diversifications might persist here and there.

Global alliances and wheels within wheels

Filed under: Politics — Razib Khan @ 11:36 am

Over ten years ago I read Adam K. Webb’s Beyond the Global Culture War with some skepticism. In it, Webb outlined the future revitalization of non-Western societies and cultures and their ultimate face-off with global liberalism.  It’s a really strange book, which talks positively about the Iranian Revolution and Rabindranath Tagore.

But I think elements of the thesis are coming to fruition in ways I couldn’t have imagined. For example, the Western Left has a very strong animus against Hindu Nationalism. case in point, the Western (mostly American) feminist website, Feministing, has published a piece documenting a protesting a Hindu meeting in Chicago: Why These Activists are Protesting Hindu Nationalism in Trump’s America.

Here’s a thought experiment: can you imagine left-wing activists protesting an Islamic Society of North American meeting? Curiously, the atheist ex-Muslim activist Armin Navabi, who was at the meeting in Houston this summer, observed that the people who were most hostile to the ex-Muslims were not the Muslims themselves (most of whom were curious), but philo-Islamic Communist activists. These activists were apparently shouting Islamic slogans at right-wing anti-Islamic demonstrators.

Navabi even reported that the Muslim attendees talked to him and seemed disturbed and confused by the specter of hammer & sickle brandishing Communists, and could not understand why or how they were pro-Islam.

September 29, 2018

China is what you get if your civilization never gets amnesia

Filed under: China — Razib Khan @ 9:26 pm

The author of Early China: A Social and Cultural History occasionally engages in asides which analogize his own domain of study to other societies and histories. In the process, he illustrates how China is in some ways nonpareil.

When discussing the emergence of philosophical thinking during the Spring and Autumn Period there is a connection made to the same process occurring in India and Greece. It is suggested that during this period the memories of the older Bronze Age world were fading, and in the chaos, new ideas and strictures were arising. The problem is that in fact there is no analogy between the Chinese recollection of their own past, and that of India and Greece.

Homer and Hesiod both lived in the period after the Greek Dark Ages, which lasted from about 1100 to 800 BC. Though the oral history did preserve important fragments of knowledge from the Mycenaean period (e.g., the importance of the Argolid and the distinctive boar’s head helmets), enough was forgotten that the Greeks were not entirely clear that the citadels constructed during the Mycenaean period were in fact constructions of their ancestors. The loss of literacy meant there was no institutional connection to the past, and when Linear B was deciphered most archaeologists were surprised that it was an archaic form of Greek.

For India, the connections are even more tenuous and vague. The Mycenaeans seem to have created a synthetic civilization, repurposing Minoan high culture toward their own ends. But, they were also clearly Greek, with many of their gods being the same gods that we recognize from the Classical era. In Early China the author implies that the people of 6th century India may have had some memory of the Indus Valley Civilization. Though it is likely some elements of culture were passed down from that period, no institutional memory seems to have persisted, in large part because of the likely cultural shock of the arrival of Indo-Aryans around 1500 BC.

The contrast with China here is strong. In Early China the author talks about the Doubting Antiquity School, which was skeptical of the veracity of Chinese historical memory before the Qin period 2,300 years ago. Today, due to archaeology, analysis of inscriptions on bronze vessels, as well as the famous oracle bones, it is clear that historians such as Sima Qian had access to cultural memory that went back at least 1,000 years. The Shang dynasty, once thought to be legend, clearly existed. Names of kings retrieved from the oracle bones matche those provided by classical sources, including their sequence of reigns.

We know that in 1046 the Zhou defeated the Shang. Because of a planetary alignment anomaly the month and date are even remembered.

Which brings us to the Erlitou culture. This archaeological culture flourished in broadly the same region as the Shang dynasty polity, but earlier. The author of Early China contends that this was likely the Xia dynasty. Though we will never be able to validate this in all likelihood, as there are no known forms of writing from this society, we can assume just as with the Shang the legends of the Xia probably have some basis in fact (eventually ancient DNA will accept or reject demographic continuity).

Though I’m not sure where I read it, though probably John King Fairbanks’ book, it has been asserted that China from the Han dynasty down to fall of the Imperial system in 1912 exhibited such a strong cultural continuity that an official in the Former Han might find the bureaucracy of 1900 comprehensible. But wait, there’s more here. As outlined in Early China many of the broad outlines of Han culture which crystallized under the Qin-Han, actually date back to the Zhou dynasty of 1000 BC. The Shang even earlier clearly prefigure the importance of ancestor worship in Chinese culture.

The contrast with the other end of Eurasia is stark. A book like 1177: The Year Civilization Collapsed has a hyperbolic title which totally ignores the fact that that date passed without much tumult in East Asia, where the Shang were ascendant on the plains of the Yellow river. In fact, the curious thing to observe is that the periodic phases of political disunity and cultural turmoil never resulted in a sharp and distinct rupture in Chinese self-identity. Chris Wickham’s Framing the Early Middle Ages: Europe and the Mediterranean, 400-800 outlines the argument that the difference between Rome and the post-Roman polities assembled by the Germans is that the latter lost control of taxation and so dissolved the bureaucratic state. The mature and more self-confident Europe of the High Middle Ages was very different from Classical Rome. It was created de novo. In contrast, Song China was not that different from Han China.

Perhaps a better analogy would be with the Byzantine Empire. Though it is hard to justify it being much of an “Empire” by 1100, in 1000 AD it was a powerful and expansive state, pushing into the Levant. Though very different from the Classical Empire, the Byzantines did engage in extensive preservation of that heritage (most of the humanistic works of the Greeks are preserved thanks to the efforts of 10th century Byzantine copyists). But Byzantium was eventually swallowed by the Turks. The institutional continuity with the ancient world of the West disappeared.

Some of the reviewers of Early China: A Social and Cultural History complained that there was too much discussion of Shang dynasty floor plans. That’s fair enough, but the sections on the Western Zhou and the Spring and Autumn are the meat of the book. I could have done without the precis on the Han, as that is covered extensively elsewhere. But this book definitely is an essential update to the scholarship on the roots of Chinese civilization.

The sons of Japeth divide the world between them

Filed under: Ancient DNA,Spain — Razib Khan @ 5:22 pm

Most “old hands” in the discipline of historical population genetics remember when grand narratives were constructed out of Y chromosomal haplogroup distributions. One of the most distinctive ones is that of haplogroup R1b, which exhibits very high frequencies in the west of Europe, as high as more than 80% among the Basques. Because the Basques are the only non-Indo-European population which exists today in Western Europe, it was presumed that they are more ancient than other groups. And, their high frequency of R1b (along with other peculiarities such as a high frequency of Rh-), was taken to indicate that they reflected the genetics of Europe’s aboriginal hunter-gatherers when farming arrived.

This turned out to be wrong in a lot of details. Genetically the Basques are quite like the European farmers from Anatolia who replaced the original hunter-gatherers. Less so than the Sardinians, but more so than their neighbors in Iberia. Instead of being the language of European hunter-gatherers, it seems plausible that the Basque language descends from that of the Cardial culture.

Distribution of R1a

So what about R1b? Well, it turns out that the particular branch of R1b that is very common in Europe is not found in the Neolithic farmer populations. Rather, its arrival in places like Britain and Iberia is associated with cultures with original origins in the Eurasian steppe. In the eastern half of Europe and in Central Asia and South Asia, R1a expanded in the period after 2000 BC.

New Scientist is now quoting David Reich has having asserted that this population turnover in Iberia occurred ~4,500 years ago. Reich, in particular, is emphasizing the disruption in the Y chromosomes. I don’t know if Reich’s group is coming out with new data, but we do have some evidence on this in Iberia from earlier publications.

This figure from Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia basically says it all. Around the transition between the Iberian Neolithic and the Bronze Age a new element came into the Iberian peninsula with affinities with populations to the north and east. The samples are not dense enough in terms of time to give a precise date, but this paper seems to suggest somewhere between 4,000 and 4,500 years as the most likely interval. The Reich group probably has more samples and so can date it more precisely. Interestingly, ~4,500 years ago is exactly when R1b bearing males arrived, and there was massive genetic turnover, in the British Isles. Perhaps the correlation between these two regions being overrun at the same time is not coincidental?

Please remember that the post-steppe Corded Ware people had settled in Central Europe by 2900 BC. Time elapsed between this period, and the later expansion west and south. And, I wouldn’t be surprised if the arrival on the eastern steppe of people with ancestry from Europeans (that is, they had some ancestry from Neolithic Europeans) was also due to changes in Central Europe around 2500 BC.

With the demographic superstructure getting really into place for Europe, it’s really time that archaeologists, cultural evolutionists, and anthropologists, start to think about how these processes occurred.

Muslims are not a People of the Book

Filed under: Cognitive Science,Islam,Religion — Razib Khan @ 1:29 pm

Recently I became a patron of the Secular Jihadists podcast. Ten years ago this wouldn’t be a big deal, but as a “grown-up” with three kids I’m much more careful to where I expend my discretionary income. So take that as a stronger endorsement than usual. I think Secular Jihadists is offering a nonsubstitutable good today. By which I mean a robust, but not cliched or hackneyed, critique of the religion of Islam. For various reasons the modern-day cultural Left has become operationally Islamophilic in public, while the political Right isn’t really too concerned with details of fact and nuance when they level critiques against Islam.

On this week’s episode, the hosts talked about the life of Muhammad, focusing some of the rather unpalatable aspects of his biographies as they’ve been passed down in tradition (in the Hadiths), or as can be found in the Koran. Armin Navabi points out that the prophet of Islam married Safiyya bint Huyeiy Ibn Akhtab on the day her father and husband were killed by his forces. Therefore Navabi’s interpretation, which is entirely in keeping with our modern values, is that Muhammad raped a woman on the day her father and husband were killed.

Of course, this behavior is not shocking in the pre-modern world. In the Illiad Hector’s widow, Andromache, eventually becomes the concubine of Neoptolemus. He is the son of Achilles, who killed Hector. And, in many traditions, Neoptolemus is the one who kills Andromache’s infant son by Hector, Astyanax. Eventually, the son of Neoptolemus by Andromache inherits his kingdom.

Obviously, the Illiad plays things up for drama, but I think it correctly reflects the values of a pre-modern tribal society. One of my favorite books is Jonathan Kirsch’s The Harlot by the Side of the Road: Forbidden Tales of the Bible. Like the Illiad, the Hebrew Bible has within in stories that reflect values of pre-modern societies very different from ours. Moses, like Muhammad, was a military and political leader as well as a religious prophet, and so it is entirely unsurprising that he was a participant in and director of what we would today term war crimes.

The question from the perspective of the hosts of the Secular Jihadists podcast is how Muslims will react to the fact that in the Koran itself, which most Muslims take to be the literal recitation of the words of God through Muhammad, documents the founder of the religion engaging in sex and war crimes. I think the truth though is that most Muslims won’t be very impacted by these revelations, because for most Muslims Islam is not reducible to the revelation within the Koran.

“Higher religions” tend to have scriptures and texts which serve as the scaffold for their intellectual superstructure. But most people who believe in these religions never read these texts. That’s because most people don’t read much, period. The organized institutional and multi-ethnic religions which have emerged over the last 3,000 years have a complex division of labor among the producers of religious “goods and services”, as well as among the consumers and identifiers. A minority are highly intellectualized, and these are the types who will record the history of the religion.

Nearly 2,000 years after his death we know a great deal about the life and times, and ideas, of the great Christian theologian Origen. We know far less about the life and times of the average believer. But I believe that the structure, organization, and folkways of the Christian church in the first half of the 3rd century were arguably far more instrumental in the religion’s success in the 4th century than the particular philosophical arguments which Origen so brilliantly expounded.

Of course from the perspective of many nonbelievers, this seems perverse. Islam, for one, makes a book the very foundation of the religion. And yet ultimately religion persists not because of specific books and beliefs, but general intuitions and cultural phenomena which are evoked by those intuitions. Many people have strong intuitions about “how the world works.” The beliefs of some indigenous tribes about the role of animistic forces may seem bizarre and strange in the particularity, but in the generality, they are totally comprehensible.

Within Islam, it is commonly asserted that Muhammad was the perfect human being. Ergo, a perfect model of how to behave. Additionally, most Muslims accept that the Koran is a literal and straightforward rendering of the facts of Muhammad’s life. The logical implication of this is that the perfect human being had no compunction making use of sex slaves.

But I think a focus on logic misses the mark in understanding most human cultural phenomena, which have cognitive roots. Our reasoning faculties are slow and faulty. Other aspects of our psychology, often habitual, rule our day to day lives. Of course this varies by person to person. Perhaps the greatest lesson we need to take from the last generation of cognitive science is that those who live by ratiocination more than reflex are a very small and peculiar minority, no matter how they unconsciously rewrite history (because they’re the ones doing the writing).

September 27, 2018

Do the northern Chinese have Scythian ancestors?

Filed under: China,Historical Population Genetics,Scythian — Razib Khan @ 2:32 pm

There was some question regarding possible Scythian admixture into the early Zhou below. This is possible because of the Zhou dynasty, arguably the foundational one of Chinese imperial culture (the Shang would have been alien to Han dynasty Chinese, but the Zhou far less so), may have had interactions with Indo-European peoples to their north and west. This has historical precedent as the Tang dynasty emerged from the same milieu 1,500 years later, albeit the Tang were descended from a Turkic tribe, not Indo-Europeans.

I looked at some of my samples and divided the Han into a northern and southern cluster based on their position on a cline (removing the majority in between). I also added Lithuanians, Sardinians, Uyghurs, Mongols, and Yakut. As you can see on the PCA the Mongols are two clusters, so I divided them between Mongol and Mongol2.

Running ADMIXTURE after some outlier removal you see that the northern Han are distinct because they share ancestry from the Yakut modal cluster. In contrast, the Mongols and Uyghurs have ancestry from the Lithuanian modal cluster. Uygurs also have quite a bit of ancestry from the Druze modal cluster, which is West Asian. Also notice that the Mongol2 cluster, which shares more ancestry with the Yakuts also has more Lithuanian modal cluster ancestry. Two of the Mongol2 individuals are labeled as Khalkha.

Using some of the Sarmatian/Scythian samples from David Reich’s lab, I ran ADMIXTURE again. These ancient samples need to be interpreted with caution, as usual. But notice again that the northern Han obtain their minor ancestry from the Yakut. The Iron Age nomadic modal ancestry is found at low levels in the Mongols and Uygurs. I think this is a real effect. The presence of Alans with the hordes of the Mongol Empire is well attested, though the admixture is almost certainly earlier.

I ran some three population tests. This is what was notable.

  1. Han_N looks like it is mixed somewhat with Yakut
  2. Mongol has gene flow from Mongol2
  3. Mongol2 has gene flow from Lithuanians and Iron Age nomads

I literally spend an hour on this assembling the data. But I think the easiest conclusion to draw is that the “West Eurasian” shift in modern Chinese (north) is probably mediated through Turkic people.

September 26, 2018

Vietnamese are not that much like the Cambodians

Filed under: Cambodia,Historical Population Genetics,Vietnam — Razib Khan @ 11:45 pm

A comment below suggested another book on Vietnamese history, which I am endeavoring to read in the near future. The comment also brought up issues relating to the ethnogenesis of the Vietnamese people, their relationship to the Yue (or lack thereof) and the Khmer, and also the Han Chinese.

Obviously, I can’t speak to the details of linguistics and area studies history. But I can say a bit about genetics because over the years I’ve assembled a reasonable data set of Asians, both public and private. The 1000 Genomes collected Vietnamese from Ho Chi Minh City in the south. I compared them to a variety of populations using ADMIXTURE with 5 populations.

Click to enlarge

You can click to enlarge, but I can tell you that the Vietnamese samples vary less than the Cambodian ones, and resemble Dai more than the other populations. The Dai were sampled from southern Yunnan, in China, and historically were much more common in southern China, before their assimilation into the Han (as well as the migration of others to Southeast Asia).

Curiously, I have four non-Chinese samples from Thailand, and they look to be more like the Cambodians. This aligns well with historical and other genetic evidence the Thai identity emerged from the assimilation of Tai migrants into the Austro-Asiatic (Mon and Khmer) substrate.

Aside from a few Vietnamese who seem Chinese, or a few who are likely Khmer or of related peoples, the Vietnamese do seem to have some Khmer ancestry. Or something like that.

Narrowing the populations, and using Indians as an outgroup, I wanted to test the Vietnamese against a few select populations. In the graph to the right you see that they are on the same branch as the Dai, and there is gene flow from the Dia into the Cambodians, and from the Cambodians into the Vietnamese. These results actually suggest that the Cambodians have had more gene flow in than the Vietnamese.

If you check the ADMIXTURE plot though you notice that there is a huge range of variation in the Cambodians in terms of their ancestry. The Mon kingdoms to the west of Cambodia fell to the Tai, but Cambodia itself did not. It probably absorbed a fair amount of Tai ancestry though, even if it retained its cultural distinctiveness and character.

A PCA shows that the Vietnamese are a distinct cluster. Different from both the Dai and South Chinese. Some of the samples in the 1000 Genomes are shifted toward the Cambodians and others toward the Chinese.

Finally, I ran a three population test. Here are some results of interest:


India is eternal but Indians are not

Filed under: History,India,science — Razib Khan @ 10:18 pm

This week’s episode of The Insight dug deeply into the current scientific understanding of the genetic origins of the peoples of the Indian subcontinent. Recent publications and media coverage have caught the science in midstream, as scholars have to deal with the clamor for new information in the face of the need to be careful and cautious when presenting new results.

Steppe Chariot

The show notes linked extensively to the scientific literature which documents the interface between cutting-edge genomics, modern population genetics and computation, and finally the abstruse lab science of ancient DNA. Or, just go to the preprint, The Genomic Formation of South and Central Asia.

The general outline of what we know so far is straightforward. Over the past 10,000 years, the Indian subcontinent has been a great vortex, sucking in peoples from various corners of Eurasia. The overwhelming proportion of the ancestry of any given person in the Indian subcontinent, from Punjab to Tamil Nadu, from the Arabian Sea to the Bay of Bengal, binds together the heritage of three peoples. First, the longstanding residents of South Asia who were descended from the original migrants out of Africa. Second, farmers and pastoralists from the hills of western Iran. And finally, Indo-Aryan peoples who arrived in chariots and drove their cattle before them.

Meenakshi Temple, South India

As noted on the podcast, the slippery and sometimes sloppy usage of labels can mislead as much as illuminate. The term “Indian” can refer to many things, whether it’s a geographic landmass, or, people. More esoteric but still widely used terms such as “Indo-Aryan” are properly linguistic, but they have gained ethnic connotations. A shorthand that communicates, and sometimes, distorts.

In some of the scholarly literature, and on the podcast, you may hear terms such as “Iranian farmer” without context. By this, we do not mean the farmers of modern Iran, but the people nearly 10,000 years ago who lived in what became Iran, and began to herd goats and grow wheat. These people then migrated eastward, eventually to India. Of the great farming cultures of the Middle East that arose with agriculture, these were the easternmost extension.

Obviously, the same caveat applies to the “steppe ancestry”, which is associated with likely Indo-European peoples, from the early Yamnaya to the successor Corded Ware, Andronovo and Sintashta cultures. The fact is that there were different peoples on the steppe before these cultures arose, and there were, and are, people on the steppe after they left the stage of history. But, in the context of Indian history what we mean by “steppe ancestry” are these particular cultures, and the genetic imprint we see on the steppe between the Volga and the Aral Sea, and later among the peoples of India after 2000 BC. The term is not genetic, but specific.

Indra atop his mount, an elephant

The latest genetic work aligns with earlier theories that the Indo-Aryans arrived in India after the decline of the Indus Valley Civilization. All signs point to their connection to peoples on the Eurasian steppe, whose origins are themselves a melange of West Asian, European and Siberian. This has led some commentators to suggest that the Indo-Aryans were “alien invaders.”

In sharp contrast, Indian nationalists have long been keen to point out that the earliest texts written down from the oral epics of the Indian Aryans do not seem to record a memory of a land outside of South Asia. In the Vedas, the oldest of the memories of the Indo-Aryan tribes, the Thunder God Indra sits atop an elephant, an Indian beast if there ever was one.

Though the origin of the Indo-Aryans was likely outside of the continent, it is important to remember that their cultural and historical identity as we understand them today seem to have been forged in the Indian subcontinent. The Vedas themselves bear the imprint of non-Aryans words, indicating that by the time the warlike and pastoralist tribes began to fashion the seminal epics which defined their identity, they had already become of the soil of the subcontinent in a deep sense.

Diversification of the Dravidian languages 4,500 years ago

One of the major dichotomies in the prehistory of South Asia on the edge of the history, from the arrival of Alexander the Great in the north to the Sangam period flourishing in the south, is between Indo-Aryan and Dravidian. Often, the Indo-Aryans are posited to be newcomers, while the Dravidians are aboriginals. But new research in linguistics and archaeology is pointing to the conclusion that Dravidian languages themselves diversified in the period after 2,500 BC. In other words, not very much earlier than when the Indo-Aryans arrived in the subcontinent.,

Though the Dravidian populations of the south often lack the ancestry from the Eurasian steppe, so common among Brahmins, in particular, they invariably show signs of being descended from the ancient Iranian farmers. Like Indo-Aryan speaking peoples, the Dravidians are themselves likely a fusion of newcomers from the north and west, and indigenous hunter-gatherers. The linguistic evidence, along with the start of the South Indian Neolithic in 2,500 BC, indicates that Dravidian-speaking peoples forded the path for the Indo-Aryans that came after them.

What genetics has told us over the past generation is that most of the world’s populations are mixes between very different groups of people. 10,000 years ago no one lived in the world who looked much like modern Indians. Or Northern Europeans. Or, likely Southeast Asians. And so on.

Underneath all the statistics, the new science and old history, the final truth is that in the game of precedence and indigeneity, no one really comes out ahead. It’s been a long and complicated dance between many different peoples, and everyone’s ancestry leads to both outsiders and insiders.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!

India is eternal but Indians are not was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

The Insight Show Notes — Season 2, Episode 3: ANI, ASI, IVC and The Genetics of India

Filed under: Genetics,History,India,science — Razib Khan @ 3:49 pm
A scene from an ancient Indian epic

This week on The Insight (Apple Podcasts, Stitcher and Google Play) we discussed how the genetics of 25% of the world’s population, the people of South Asia, came to be. It’s a journey of thousands of years.

We cited the preprint, The Genomic Formation of South and Central Asia.

Additionally, we cite a chapter in David Reich’s Who We Are and How We Got Here, where he discusses the genetics of India, and how it’s analogous to Europe.

A cover story from India Today, 4500-year-old DNA from Rakhigarhi reveals evidence that will unsettle Hindutva nationalists, was also referenced. Please read with caution! The research has not been published, and there are likely going to be changes based on new results (actually, probably certainly from what I have heard)….

There was a discussion of some technical, but important, statistical genetic tests to infer admixture. The paper in Genetics, Ancient Admixture in Human History, outlines these methods in detail. The three and four population tests, as well LD decay estimates of admixture time are all discussed in this paper. All are alluded to or discussed in the podcast.

Linguistic families in South Asia

There was extensive discussion of the various language families in India, in particular, Indo-Aryan, Dravidian, and Munda. We discussed the results of a recent, paper A Bayesian phylogenetic study of the Dravidian language family, which indicates a recent expansion of this language family in South Asia. Also, a new preprint on Munda, The genetic legacy of continental scale admixture in Indian Austroasiatic speakers suggests that the Munda emerged around the same time as the Dravidians.

A lot of ethnographic terms were thrown around with deeper exploration. If you want to follow-up, Elamites from ancient Iran, Indo-European Sintashta culture, and the Bactria-Margiana culture of Central Asia.

We talked about ANI and ASI. The 2009 paper, Reconstructing Indian Population History, introduced these terms and constructs. The Kalash and Pulayar people of Pakistan and southern India respectively were mentioned as modern-day exemplars of ANI and ASI.

Distribution of R1a1a

The distribution of R1a1a in India and Eastern Europe was also discussed, and how it is associated with expanding steppes. Also, caste and its antiquity were discussed, in particular, that modern boundaries between groups seem to have emerged around 2,000 years ago, after several thousand years of admixture between disparate Indian groups. The promise of disease gene discovery in South Asia is a preprint that explores the relevance of this endogamy today for health risks.

Linguistic isolates Burusho and Nihali were mentioned. And, the development of the “Yankee” identity, which Razib analogized to Indo-Aryans!

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!

The Insight Show Notes — Season 2, Episode 3: ANI, ASI, IVC and The Genetics of India was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

September 25, 2018

The lineage of the ancient sage kings

Filed under: China genetics — Razib Khan @ 9:27 pm

After recording the “India genetics” podcast for The Insight and reading Early China: A Social and Cultural History, I wonder what surprises we’re going to get from China from ancient DNA when it comes online. If there is one thing we are learning by looking closely at DNA, modern and ancient, it’s that at least for humans there are very few ‘primal’ populations from the “Out of Africa” event which haven’t been threaded together from pulse admixtures of continuous gene flow across the landscape.

Early China makes it clear that Erlitou culture which dates from ~1900 to 1500 BC was almost certainly the legendary Xia dynasty. This means that the ethnogenesis of the modern Han Chinese probably dates to the latest ~4,000 years ago. This is centuries before the Indo-Aryans were likely arriving in South Asia, and around the same time that Indo-European groups were pushing into peninsular Southern Europe.

The Y chromosome data does not indicate a Bronze Age ‘star phylogeny’ expansion in East Asia that I know of, so the dynamics were not entirely similar to Western Eurasia. But, it seems quite plausible that the Han themselves are not a chrysalis from the late Pleistocene.

A cursory examination of the SNP data makes it clear that there is a north-south cline whereby the peoples north of the Yangzi have more West Eurasian admixture than those to the south. In fact, if you look at the PCA and admixture plot you notice that the Japanese have no West Eurasian ancestry. The Yayoi ancestry dominant among the Japanese probably arrived from southern Korea ~2,500 years ago. And, positioned away from the Chinese “mainland” southern Korea was relatively shielded from Inner Asian migrations (I am aware of Korea’s association with Manchuria and the extent of those early kingdoms).

In Empires of the Silk Road, Christopher Beckwith argues strongly for the role of Indo-Europeans in the ethnogenesis of the early proto-Han, through the influence of the Rong, Di, and Qiang. The Qiang were probably proto-Tibetan, but the genetically attested presence of people with overwhelmingly West Eurasian ancestry in areas like Dzungaria during the Bronze Age is well known. Y chromosome R1a1a is found at levels of a few percents among the northern Han, and perhaps as high as ~10% among the Mongolians (though R1b is found among many Uygurs, which is rare for Central Asia).

Beckwith points to the spread of chariot technology from Inner Asia ~1200 BC as strong evidence that Indo-Europeans were somehow involved with the rise of the Shang or Zhou, and so ties them into the emergence of Sinic civilization. Though it is clear that early Chinese chariots were originally derived from Inner Asian exemplars, as Egyptian chariots were, I think it is not unreasonable to suppose this was a case of genuine cultural diffusion and emulation of a useful weapon of war. Consider how quick native peoples in the New World adopted firearms and horses.

Within the next few years, we will have ancient DNA from a wide transect of Chinese history. Unlike some peoples the Chinese are highly historical people, so the genetics will not be stepping into the breach. We even have census records going back 2,000 years, and attempts of scholars to trace migrations based on the changing distribution of the taxable households (though note that some variation in the census count is due to tax dodging during times of political weakness).

I’ll hazard a prediction that most of the West Eurasian admixture into the North Chinese will be seen to be a function of the period after the fall of the Han dynasty and before the Sui-Tang, as well as the influx of Sogdians during the Sui-Tang, and later the arrival of large numbers of Muslims with the Mongolian Yuan. In other words, the shape of modern China on the edges came into being between 300 AD and 1300, as a small proportion of very exotic West Eurasian ancestry became the norm on the North China plain, while a large proportion of far less exotic and quite similar non-Chinese people were instrumental in the development of a distinctive southern Han people, based around particular localities and dialects.

The more interesting story will probably be in the Neolithic, around the time of the rise of agriculture on the North China plain (and in the Yangzi basin).

This is America

Filed under: Immigration — Razib Khan @ 8:19 pm

As you may know, Reihan Salam, who I would consider a friend (albeit, one I see in person three years or so!), has a new book out, Melting Pot or Civil War?: A Son of Immigrants Makes the Case Against Open Borders.

It won’t be a surprise to know that I generally agree with him on a lot of issues relating to immigration. The first time I met him in person in 2007 we actually talked about the positive externalities of high skill immigration streams. Since then my views haven’t changed much, though my faith in these United States has declined some to be honest.

I will pass along this interview with Reihan today, A Son Of Immigrants Makes The Case For Tighter Immigration Policy. Reihan, as you may know, is the son of Bangladeshi immigrants who arrived in the late 1970s. The woman interviewing him happens to be ethnically Bengali herself (though her family is from India), raised in Oregon around the same time I was (we’re about the same age).

This is America 2018. An American of Bengali ethnic extraction writes a book and happens to be interviewed by happenstance by another Bengali American. Definitely not a world we could have imagined in the 1980s.

Open Thread

Filed under: Open Thread — Razib Khan @ 12:22 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

A clash of civilizations along the lower Mekong

Filed under: Cambodia,Mainland Southeast Asia,Southeast Asia,Vietnam — Razib Khan @ 12:16 am

The lower Mekong region is a fascinating zone from the perspective of human geography and ethnography. Divided between Cambodia and Vietnam, until the past few centuries it was, in fact, part of the broader Khmer world, and historically part of successive Cambodian polities. Vietnam, as we know it, emerged in the Red River valley far to the north 1,000 years ago as an independent, usually subordinate, state distinct from Imperial China. Heavily Sinicized culturally, the Vietnamese nevertheless retained their ethnic identity.

Vietnamese, like the language of the Cambodians, is Austro-Asiatic. In fact, the whole zone between South Asia and the modern day Vietnam, and south to maritime Southeast Asia, may have been Austro-Asiatic speaking ~4,000 years ago, as upland rice farmers migrated from the hills of southern China, and assimilated indigenous hunter-gatherers.

But the proto-Vietnamese language was eventually strongly shaped by Chinese influence. This includes the emergence of tonogenesis. Genetically, the Vietnamese are also quite distinct, being more shifted toward southern Han Chinese and ethnic Chinese minorities such as Dai. My personal assumption is that this is due to the repeated waves migration out of southern China over the past few thousand years, first by Yue ethnic minorities, and later by Han Chinese proper. Many of these individuals were culturally assimilated as Vietnamese, but they clearly left both their biological and cultural distinctiveness in what was originally an Austro-Asiatic population likely quite similar to the Khmer.

As I have posted elsewhere it is also clear to me that Cambodians have Indian ancestry. Because unlike Malaysia Cambodia has not had any recent migration of South Asians due to colonialism, the most parsimonious explanation is that the legends and myths of Indian migration during the Funan period are broadly correct. There is no other reason for fractions of R1a1a among Cambodian males north of 5%. Depending on how you estimate it, probably about ~10% of the ancestry of modern Cambodians is South Asian (the Indian fraction is easier to calculate because it is so different from the East Asian base).

This is present in a few Vietnamese (Kinh) samples I have seen, but it is at a lower frequency. The reason for this Indian ancestry is that southern Vietnam became Vietnamese only in the last 500 years, and more intensively only in the last 200 years. The Vietnamese with Indian ancestry are almost certainly people who are from the southern part of the country with Khmer, or Cham, heritage.

Viet Nam: A History from Earliest Times to the Present is divided into three broad periods. The first is the development of the Vietnamese people as a synthesis of external elements from the north, and the Austro-Asiatic “sons of the soil.” Roughly from the Trung sisters down to the emergence of an independent Vietnamese state in the decades before 1000 AD. This is a narrative of perseverance. Unlike the Yue people of Guangdong and Fujian (and parts further north), the Vietnamese maintained their ethnic identity through long periods of Chinese rule. Transformed and reshaped by the Chinese rule, they emerged from it inflecting Sinic cultural elements within their own traditions.

The second phase is one of conquest. To some extent to an American who is used to seeing the Vietnamese as being catspaws in 20th-century geopolitics, it is painful to read about the drive south of the Vietnamese, and their extermination and assimilation of the earlier peoples and polities. Though they did not use a word such as “Manifest Destiny,” with hindsight it was clear that the Vietnamese were going to push along the coast southward until someone stopped them by force. As it happened, the rise of Vietnam coincided with the decline of Cambodia.

In the 18th and early 19th centuries, Vietnam and Siam (what became Thailand) fought over Cambodia in a manner analogous to occurred with Poland in the same period. The Vietnamese rule of Cambodia, especially in the first half of the 19th century, was concurrent with a drive toward more punctilious Confucianization of Vietnamese society along with a drive to forcing Buddhism into the private domain. This Confucianization entailed reinforcement of patriarchal rules, as well as attention to matters of uniform dress. The Vietnamese monarchy was attempting to create a Confucian society ruled by virtuous bureaucrats, overseeing a populace aware of and cognizant of the proper civilized forms.

Though never as extreme as Korea, Vietnamese Confucianism during this period was probably more pervasive than it ever became in Japan (where formal Confucianism tended to be the purview of the samurai class during the Tokugawa age). As part and parcel of civilizing Cambodia, making it Vietnamese, the conquerors attempted to do with the Khmer what they had done to their own people. Diminish the role and prominence of institutional religion, in this case, Theravada Buddhism, and educate the populace so that they could begin to produce their own virtuous bureaucrats.

One of the most interesting and curious aspects of the Vietnamese rule of the Cambodians is that the comments by the ruler of Vietnam and his subordinates clearly show some deep lack of the understanding of the distinctive nature Khmer culture as opposed to Vietnamese, in particular, northern Vietnamese, culture. They complain that though the Khmer maintain outward forms of proper decorum, they seem not to internalize the forms in a manner that would indicate they are sincerely civilized. The Vietnamese ruler marvels that the Cambodians have 1,200 years of history, but lack precise dates on their origins, and have vague dynastic periods (this is, to be frank, a very Indian feature). Additionally, the Khmer seemed obstinately attached to their Theravada Buddhist religion. When they rebelled against their Vietnamese overlords with the aid of Siamese invaders they declared that they did so to defend the Three Jewels of Buddhism. As is common in China, Vietnamese Buddhist sects periodically rebelled. But these rebellions were sectarian. In Cambodia Buddhism was not a sect, to be a Cambodia was to be a Theravada Buddhist.

In frustration, the Vietnamese ruler declared that “moral suasion” simply does not work with the Khmers! Though his regime was brutal, he was ultimately a Confucian who assumed exhortation would win out in the end.

Though the Vietnamese were aware of the cultural differences between themselves and the Khmer, they were not prepared for the task of swallowing a whole civilization distinct from their own.

This brings to mind comments of Victor Liberman, a scholar of mainland Southeast Asia, that Vietnamese Sinic Confucian statecraft was qualitatively different from the “solar polities” to its west. In his book Strange Parallels Southeast Asia in a Global Context, he outlines what he believes to be the features of these societies which allowed them to emerge in the early modern period with nation-states in a manner recognizable to Europeans. Over most of Southeast Asia Indian high culture spread in the period before 1000 AD (in fact, it was dominant in the southern two-thirds of modern Vietnam before 1500 AD). This meant the emergence of relatively politically loose societies around the charismatic figure of a monarch whose legitimacy was fundamentally religious and metaphysical. Southeast Asian kings aspired to be cakravartin. The turners of the wheel of history.

In contrast through steps and starts the Vietnamese developed a society which was in many ways a miniature shadow of that of China to the north. Instead of a divinely sanctioned monarchy, Vietnam produced subordinate kings to the emperor of China or in some cases a ruler who declared he was an emperor himself.  Their rule was sanctioned not by gods or priests, but impersonal Heaven and its mandate.

Whereas other Southeast Asian monarchs had court brahmins, bhikkhus, and later in the Malayan world ulema, the Vietnamese monarchs often put away the Buddhist monks and priests and hid any religious devotion from public view. On the Chinese model, the Vietnamese drove religion away as a helpmate, and subordinated religious impulse as ancillary to state functions and transformed it primarily to something that was a matter of popular enthusiasm and private devotion. Like the Chinese, the Vietnamese polity aimed to recruit and produce a large and broad class of virtuous administrators, many drawn from the agricultural populace itself to main social order and proper state function.

Liberman observes that the Chinese model necessarily requires greater coordination, concentration, and mobilization. Additionally, there naturally develops a cultural chasm between the simple peasant, and the educated bureaucrat, in such a society. In contrast in solar polities, the king and high nobility may be distant from the people as symbols, but the vast mass of peasants and clerics interact and engage on a popular level. Religious truths and ideals often can propagate on a dimension closer to the masses than the culture of the Confucian literati. While efficient and constitutive mobilization of the resources of solar polities is low at any given time, mass enthusiasm may be easy to trigger in punctuated bursts of activity around charismatic figures and exigent circumstances.

September 24, 2018

Podcast on South Asian genetics this week

Filed under: Genetics — Razib Khan @ 10:07 am

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

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

September 23, 2018

Open Thread, 9/23/2018

Filed under: Open Thread — Razib Khan @ 10:56 pm

Curious how many readers recognize the reference on the shirt to the left? You probably know if you’ve read The Double Helix. On the DNAGeeks website now.

Salon is stiffing freelancers of $150. I think this is more a commentary on the market for freelancers than Salon‘s always tenuous finances. The market-clearing price for a lot of web journalism/commentary is pretty low. Salon does this because it knows freelancers will tolerate and accept this behavior more often than not.

This long article from Huffington Post (and boosted on the editor in chief’s Twitter), Everything You Know About Obesity Is Wrong, is being widely shared on Facebook (I haven’t seen it much on my Twitter, but that’s because I follow mostly scientists).

Of course it’s really really light on the science of nutrition. Or should I say “science”? Because the truth is that nutrition science has a lot of problems, so there is space to criticize it. But that being said, this piece is being shared by people who seem to think that there is a conspiracy make it seem like being obese is unhealthy. But most of the article is about how cruel people are to the obese, especially medical professionals. There’s really little evidence presented that being obese doesn’t cause issues with morbidity and mortality. Quotes like this are representative: “But individuals are not averages: Studies have found that anywhere from one-third to three-quarters of people classified as obese are metabolically healthy.” That’s a huge interval. Why?

Ultimately the article should have been titled Everyone Is Cruel to Obese People and That is Wrong and Ineffective.

If you want some real nutrition science, What I learned about weight loss from spending a day inside a metabolic chamber.

I bought Early China: A Social and Cultural History. A lot of archaeology. But that’s what you get! I figure I should know more about Zhou China though. I think next I’ll try to read up on Neo-Confucianism, a topic I’ve been lax in because of my leaning toward “Han learning.”

Highly recommend Viet Nam: A History from Earliest Times to the Present. Most of the book does not deal with the Vietnam War. One curious thing I learned: the Vietnamese identity in the period around 0 AD was strong influenced by the influx of Yue people from southern China, as they imparted their culture and statecraft on the proto-Vietic populace. Of course on top of that came later Chinese migration, which resulted in the emergence of Vietnamese as a tonal language.

Though you’ll probably really want Phở as you read the book….

Also, I knew this, but Viet Nam makes it clear in all the gory details that the Austronesian Cham people of central and southern coastal Vietnam were undergoing the same shift to Islam from Hinduism that was occurring further south in the period after 1500. It seems rather clear that the emergence of a Cham sultanate on the model of Mataram or Johor never occurred because the Vietnamese conquered the Cham kingdom, and then assimilated or exterminated most of the natives. Many Cham fled to Cambodia, where they form the Muslim minority of that nation.

But, a small minority of Cham remain in Vietnam, and amongst these are a substantial Saivite Hindu community. It seems entirely possible that if the Cham had retained their independence as a nationality one would have seen total Islamicization, as occurred among the Malays. As is this, this process was retarded by Vietnamese conquest, and so some Chams still remain Hindu (the same process applies to the Philippines, where the native population was influenced by Hinduism first, and was in the first stages of Islamicization, when the Spaniards conquered the archipelago).

Indonesia: Peoples and Histories is worth a quick read. Not as dense and informative as Viet Nam: A History from Earliest Times to the Present.

Change in sexual signaling traits outruns morphological divergence in a recent avian radiation across an ecological gradient. Not a surprising result I guess.

This AJ+ video about “white feminism” is getting a lot of attention. Mostly because AJ+ is backed and owned by a conservative Salafist regime which runs an oligarchic state on the backs of dark-skinned South Asian indentured labor. I’ve spent a week in Qatar at a really nice hotel. I’ve never encountered service staff as solicitous and courteous in the United States. At some point I may write about how certain organizations and institutions use political movements as instruments…but I always feel this is so obvious.

Digging Into the Genetics of Drug Targets. Derek Lowe, the science blogger who has been blogging for the longest time. This is why it’s worth reading him.

Next week on The Insight we’ll be talking about Indian genetics, again. Partly in anticipation of the ancient DNA paper, which should drop any day now (I have no inside information). Question suggestions welcome.

Quantifying Heterogeneity in the Genetic Architecture of Complex Traits Between Ethnically Diverse Groups using Random Effect Interaction Models

Evolution and Selection of Quantitative Traits has finally been published in book form. It’s a good value on a pound-for-pound basis….

Individual selection leads to collective efficiency through coordination. The last sentence of the abstract is key: “This finding reveals a general principle that could play a role in nature to smoothen the transition to efficient collective behaviors in all games with multiple equilibriums.” You need to figure out ways to get to cooperation.

Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. It seems within the Near East farming spread mostly through cultural diffusion. My suspicion is that that is due to the fact that it didn’t provide that huge of a demographic boost in its primitive form. Once the various farmer groups perfect their toolkit, they expanded into areas dominated by hunter-gatherers, not other farmers.

The Austronesian expansion actually makes me consider the possibility that we may never understand why the modern humans in the Near East ~55,000 years ago “broke out” and absorbed all the other hominin groups.

Cornell Just Found Brian Wansink Guilty Of Scientific Misconduct And He Has Resigned. If Wansink hadn’t become famous through his self-promotion, he could have continued on with his career. What he’s guilty of lots of people are guilty of, and the media and the public are complicit by demanding sexy and practical results.

Detecting archaic introgression using an unadmixed outgroup.

How Connected Is Your Community to Everywhere Else in America? This is incredible data journalism.

Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast.

Large-scale investigation of the reasons why potentially important genes are ignored.

Polygenicity of complex traits is explained by negative selection.

The effects of demography and genetics on the neutral distribution of quantitative traits.

When I’m working sometimes I listen to the Men of the West YouTube channel. It’s run by a Tolkienist who does some serious work in this area.

Tracing the paths of Noah’s sons

Filed under: Population genomics — Razib Khan @ 10:40 pm

The above admixture graph is from a new preprint, Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry. To be honest, if you read the supplementary text there’s almost no point in reading the main preprint, as it is far more in depth when it comes to the methodology as well as spotlighting a variety of particular results. It’s hard to know where to begin with such a preprint so I want to highlight the “this is a simplified model” portion in the figure above. That’s actually the truth. Remember, no admixture graph is the Truth, it is an attempt by humans to capture concisely and informatively the major features of our species’ population history dynamics. The reality was never as clear and distinct as stylized graphical representations would have you think, and the researchers are aware of this.

In any case, if you want to really get at how they arrived at the conclusions they did, really read the supplementary section SI 2, “An admixture graph model of Upper Paleolithic West Eurasians.” The authors have so many potential combinations of ancestral populations that they can’t simply manually and intuitively posit admixtures. Rather, they have to explore a huge number of combinations (trees/graphs)…at which point they run into computational limits. This section explicitly lays out computationally efficient ways to automatically traverse the possibility space, and arrive at the best fitting set of models, within reason.

The title of the preprint says it all, but let me quote the abstract in full:

The earliest ancient DNA data of modern humans from Europe dates to ~40 thousand years ago, but that from the Caucasus and the Near East to only ~14 thousand years ago, from populations who lived long after the Last Glacial Maximum (LGM) ~26.5-19 thousand years ago. To address this imbalance and to better understand the relationship of Europeans and Near Easterners, we report genome-wide data from two ~26 thousand year old individuals from Dzudzuana Cave in Georgia in the Caucasus from around the beginning of the LGM. Surprisingly, the Dzudzuana population was more closely related to early agriculturalists from western Anatolia ~8 thousand years ago than to the hunter-gatherers of the Caucasus from the same region of western Georgia of ~13-10 thousand years ago. Most of the Dzudzuana population’s ancestry was deeply related to the post-glacial western European hunter-gatherers of the ‘Villabruna cluster’, but it also had ancestry from a lineage that had separated from the great majority of non-African populations before they separated from each other, proving that such ‘Basal Eurasians’ were present in West Eurasia twice as early as previously recorded. We document major population turnover in the Near East after the time of Dzudzuana, showing that the highly differentiated Holocene populations of the region were formed by ‘Ancient North Eurasian’ admixture into the Caucasus and Iran and North African admixture into the Natufians of the Levant. We finally show that the Dzudzuana population contributed the majority of the ancestry of post-Ice Age people in the Near East, North Africa, and even parts of Europe, thereby becoming the largest single contributor of ancestry of all present-day West Eurasians.

Shared drift with Dzudzuana

Longtime readers know that I hate the American racial term “Caucasians.” It’s pretentious when you could just say “white European,” because that’s what people really mean, judging by the fact that the real people from the Caucasus are marginally Caucasian in the eyes of many Americans. The genealogical origin of the term goes back to Johann Friedrich Blumenbach. And yet this paper takes these two samples, and finds that a lot of the ancestry of modern groups can be attributed to them! (also, a religion interpretation of the results is in the title of the post)

To be fair, they caution that these ancient Caucasian samples are representative of a particular thread of human heritage, not that the center of this thread was necessarily in the Caucasus. This does make me wonder about ascertainment bias in the Near East toward samples from mountainous areas which were colder. But, at the granularity they are attempting to understand human population history, it’s probably not that big of a deal. Ultimately, they conclude that this Paleo-Caucasian population contributes “~46-88% of the ancestry” of modern Europeans, Near Easterners, and North Africans. That’s kind of a big deal.

There are so many results in this preprint, so I think we need to back to the “beginning” of the non-African branch. The Paleo-Caucasian sample is of note in part because it is from before the Last Glacial Maximum, and, about halfway back to the massive diversification of most non-African populations around 55,000 years ago.  Using the Paleo-Caucasian samples’ affinities this preprint reinterprets results from last spring on ancient DNA from Northwest Africa. In that paper, the authors conclude that Paleolithic North Africans were a mix between an unspecific Sub-Saharan population and Natufians. Here though the authors suggest that the Natufians and Yoruba both received gene flow from Paleolithic North Africans. And, these Paleolithic North Africans were themselves mixed between something similar to the Paleo-Caucasians (a mix between an ancient West Eurasian ancestry and “Basal Eurasian”), and a “Deep” ancestry which diverged from other non-Sub-Saharan Africans before the Basal Eurasians did.

The reason that the Paleo-Caucasian sample is so important is that it allowed the researchers to see that the early Holocene Near East, where Anatolian and Iranian farmers, as well as Natufians in the Levant, were ancestral to many later groups, was subject to many genetic changes from before the Last Glacial Maximum. The Natufians seem to be well modeled as having ancestry from the Paleolithic North Africans as one of the major ways they are distinctive from the Paleo-Caucasians. This presents us with a reasonable model for the west to east movement of haplogroup E, and, the Afro-Asiatic languages. The gene flow of Paleolithic North African also explains the non-trivial level of Neanderthal admixture which is found in the Yoruba population. This is mediated through the presumed back migration of Paleo-Caucasians from the Near East at some point in the Pleistocene, contributing some Neanderthal ancestry to the genetic background of Paleolithic North Africans.

Additionally, the distinction between western (Anatolian/Levant) and eastern (Iran) farmers during the early Holocene can now be understood as a product of later admixture into eastern proto-farmers of basic Paleo-Caucasian stock. The relative closeness of Anatolian farmers to the Paleo-Caucasian samples is indicative of the fact that there was an “Ancestral North Eurasian” (ANE) admixture cline into the Near East during the Pleistocene, which meant that some populations to the east became rather different from the pre-LGM samples. Probably after the Last Glacial Maximum proto-Siberian ancestry became prominent in the zone between the Caucasus and Iran (additionally, some of the models imply there was eastern Eurasian ancestry). This is in keeping with the fact that ANE ancestry does seem to have been found in places like Khorasan before the expansion south of steppe populations after 2,000 BC.

As noted in the abstract, Paleo-Caucasians had Basal Eurasian ancestry ~30,000 years ago. This increases the likelihood that Basal Eurasians weren’t recent migrants from deep inside Africa. Additionally, for various reasons, the authors are now positing a Deep ancestry which diverged even further into the past. Both Basal Eurasians and Deep populations seem to lack Neanderthal admixture. The authors also repeatedly suggest that Basal Eurasians were part of the Out of Africa bottleneck event. In Who We Are and How We Got Here David Reich presents the model that this bottleneck population had a low effective population size for a long time. This seems plausible because the genetic homogeneity that you see in non-Africans is pretty striking vis-a-vis Sub-Saharan Africans. On the other hand, this work confirms earlier results that imply that Basal Eurasians did not admix with Neanderthals, and also indicates that the divergence has to be greater than 60,000 years before the present from other non-Africans, who diversified more recently.

In contrast, the Deep ancestry group, which nevertheless forms a clade with the new Eurasian lineages (Basal and non-Basal), does not clearly seem to have undergone the bottleneck event according to this preprint. It’s more a matter of what they don’t say, rather than what they say in this case.

The big picture needs to be integrated I think with the new “modern humans emerged through a multi-regional process” within Africa. If you think of modern humans as emerging across an African range which shifted in the Near East based on oscillating climatic conditions, the ancestors of the “non-African” lineages can be thought of as one of the main deeply rooted lineages, probably in the northeast of the continent. During the Pleistocene, the Sahara was even more brutal than today during many periods, so it is not implausible that some of these marginal populations on the edge of Africa were subject to long periods of very small effective population sizes. Most of them presumably went extinct. But one population was probably far enough north and east that it had a little more margin to play with. This population was probably connected along the Mediterranean littoral at some point with the Deep component in North Africa, which had higher effective population sizes because the mountainous terrain of the Atlas region was always going to remain more clement through dry phases.

At some point one a group of the bottlenecked population mixed with some Neanderthals, and began to break out of containment in southwest Asia. If I had to bet money, I suspect there were already other related groups, probably somewhat admixed with local hominin lineages, further east. That is, I believe the archaeological results in Southeast Asia, and think that those in Australia are credible. But these groups were probably small in number, and totally absorbed by the later migration wave.

Also, the timing of the separation of Africans and “non-Africans” is such that I wouldn’t be surprised Qafzeh-Skull people were somehow ancestral to, or closely related to, the ancestors of non-Africans.

Finally, let’s remember that the authors were focusing on North Africa and Western Eurasia in this preprint. Things will get more complicated as East Asia and Africa come “online” in terms of these analyses. Of course, we are going to be helped by the reality that human genetic variation is not arbitrarily and randomly distributed, but reflects real constraints in our evolutionary history and the forces of geography as well as contingency. The non-African story is made simpler in part because of the great bottleneck, and especially the common descent of most peoples from the population that mixed with Neanderthals. The modeling of effective population size changes over time in Sub-Saharan groups does not lead us to believe that it will be so simple in that continent.

Related papers: The genetic history of Ice Age Europe, Tales of Human Migration, Admixture, and Selection in Africa, and Genomic insights into the origin of farming in the ancient Near East.

September 22, 2018

The great human migrations (coming in waves)

Filed under: Migrations,Population genomics — Razib Khan @ 8:53 pm

The figure above is from a new paper, Estimating mobility using sparse data: Application to human genetic variation, which uses genomic data from late Pleistocene to the Iron Age in western Eurasia, and then infers migration rate considering both spatial distribution and the variable of time (remember that samples apart in time should also be genetically different, just as those apart in space often are).

The empirical results are shown above, but they validated their method first by running some simulations. Interestingly they modeled the migration as a Gaussian random walk. Which is fine. But I wonder how true this is for a lot of the Eurasian migrations of the last 10,000 years. Perhaps the the distribution of distances from the place of birth would turn out be multi-modal, with a minority of individuals tending to make “long jumps”?

With that out of the way, it’s fascinating that migration peaks around the Neolithic transition, the Bronze Age, and then the Iron Age. If you read a book like 1177 BC, you know that there was a major regression in the 13th century BC across the Near East, and for several centuries the region was in a “Dark Age.” In The Human Web William H. McNeill argues that one of the reasons for the length and depth of this Dark Age is that the network of complex societies exhibited less density and so less redundancy to failure.

The authors conclude:

We find that mobility among European Holocene farmers was significantly higher than among European hunter–gatherers both pre- and postdating the Last Glacial Maximum. We also infer that this Holocene rise in mobility occurred in at least three distinct stages: the first centering on the well-known population expansion at the beginning of the Neolithic, and the second and third centering on the beginning of the Bronze Age and the late Iron Age, respectively. These findings suggest a strong link between technological change and human mobility in Holocene Western Eurasia and demonstrate the utility of this framework for exploring changes in mobility through space and time.

Earlier they say:

We find strong support for a rise in mobility during the Neolithic transition in western Eurasia, likely corresponding to a well-established demic expansion of farmers, originating in the Middle East and resulting in the spread of farming technologies throughout most of Western Eurasia

One of the main findings of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past is that oftentimes change is not gradual. Consider the transition to the Corded-Ware society in Northern Europe.

The “demic diffusion” model is an easy one because it relies on the mass-action of individuals and family-groups as they expand in space through high fertility rates. And yet one thing that I think it misses is the socio-political context of that demic diffusion. For prehistoric periods we don’t have writing, and so no socio-political context. This is why in War Before Civilization the author focused on ethnographies of historical societies which came into contact with literate cultures which recorded their organization and folkways. The short summation is that these societies were often very aggressive and well organized for war. Additionally, hunter-gatherers themselves were keen on expanding farmers, and it seems clear they too could mobilize for violence.

The upshot is we need to think of the rise and expansion of strong states and expansionist polities as the context for an increase in the rate of migration. The reality of low migration rates in Pleistocene Europe was pretty evident even before this formal analysis. The pairwise genetic difference due to drift, and therefore low migration rates, for some nearby populations in the Pleistocene and early Holocene indicates that small-scale societies tend to be quite insulated from each other. In contrast, the Iron Age has witnessed a great deal of admixture, as large states and polities, as well as meta-ethnic identities, have broken down genetic barriers.

A regression around 1000 BC correlates neatly with reduced migration, This was almost certainly due to the fact that without larger states much of West Eurasian society, such as in Greece, had disintegrated into smaller tribal units.

Future historians and geneticists will notice that in the period between 1500 and 2000 the distribution of the Y chromosome lineage R1b1a1a2 expanded far beyond Western Europe. They will also understand the political context for this expansion of the lineage…

Where readers come from

Filed under: Admin — Razib Khan @ 2:34 am

I looked at traffic from Jan 1 of 2018. Here are the top 30 cities, standardized by the # of users from the 30th, Indore:

CityUser #
New Delhi4.3
San Jose4.3
New York4.1
Mountain View2.4
San Francisco1.9
Los Angeles1.4

The average session form San Jose lasts more than 10 minutes and people look at 4+ pages. This is in contrast to all readers who are closer to 5 minutes. Also, I find it funny that we have more readers from Mountain View than San Francisco. I don’t think it’s just Google crawlers, the sessions average nearly 7 minutes.

If readers want to they can use this as an “unlurk” post too. Basically, you can say who you are if you are so inclined.

September 21, 2018

The Munda arrived in India 4,000 years ago (probably)

Filed under: India Genetics,Indian Genetics — Razib Khan @ 8:26 pm

I didn’t plan to talk about the Munda any time soon, in part because I recently wrote a post, The Munda as upland rice cultivators, which outlined my views. But there is a new preprint with new samples which attempts to estimate admixture times using genome-wide data. You can see the results above, and, also note that they found similar estimates using Y chromosome SNP variation around haplogroup O2a1.

The preprint is, The genetic legacy of continental scale admixture in Indian Austroasiatic speakers:

Surrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000 – 3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.78/0.22 are Lao people from Laos and Dravidian speakers from Kerala in India, while the South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data.

There is a weird pattern of the affinities in f3 statistics in the IBD in this preprint. I think the explanation that they give, that Vietnamese and Cambodians have been subject to later admixture, probably explains it. In the case of the Vietnamese, it’s southern Chinese ancestry. In the case of the Cambodians…it might be Indian ancestry! This might strike you as strange, but the Indian ancestry in the Cambodians may be more enriched for the West Asian component that’s not found in the Munda specifically: the element brought in by the Indo-Aryans.

The peninsular Malay groups are “proto-Malays,” and these groups tend to be somewhat higher in AASI-like ancestry as well as lower in Austronesian ancestry. High shared drift tendencies with Lao and groups in more isolated areas of Malaysia may be a function of the fact that these are less cosmopolitan populations, with less Indian and Chinese ancestry, than other mainland Southeast Asians and Malays proper.

Click to enlarge

These results are broadly in line with the Narasimhan et al. preprint, which is cited within it. In that preprint the Reich group outlines its general model, where modern South Asians can be thought of as a compound of several different ancestral populations of different affinities. The Munda in particular are enriched for “Ancient Ancestral South Asian” (AASI) vs. any other group, and the hypothesis is given is that the Southeasts Asian mixed first with with an AASI group which lacked the admixture with West Asians, and then mixed again with “Ancestral South Indians”, which had some West Asian (“Iranian Farmer”) ancestry.

Since ALDER based methods, last I checked, tended to pick up the last admixture event, the more recent time for northern Munda groups makes sense. Looking at the Y chromosomes it is pretty clear to me that some of the East Asian ancestry in Bengali-speaking agriculturalists in the lower Gangetic plain is from Munda groups. Conversely, some of the Munda probably admixed populations from in from the west practicing intensive rice agriculture, which apparently did not become a feature of the landscape until after 1000 BC.

One of my points in the post above I wrote on the Munda is that the common words for Austro-Asiatic languages indicates that they were upland rice farmers. This is exactly the modern distribution of the Munda. One hypothesis, which I now am skeptical of, is that the Munda once occupied the bottomlands and were driven into the hills by people from the west and south. I no longer believe this. Rather, the Munda may always have preferred the uplands, and so traversed the flat lands between the Khasi hills and the Chota Nagpur plateau. This preference for uplands may strike us as strange, but it’s not that rare. Yankee farmers in Ohio preferred upland zones, even though these were less agriculturally rich (farmers moving up from the South didn’t have this aversion).

A point observed and implied in the preprint is that the expansion of Indo-Aryans, Dravidians, and Munda, seems to have happened all rather close in time. Though the northwest region of the subcontinent seems to have developed a settled agricultural society by 3000 BC of long standing, its expansion was limited by climatic restrictions on its crop toolkit. But by 2500 BC it seems pastoralists were already pushing into the Deccan via the dry-zone on the eastern edge of the Thar down from the Punjab. The Toda people of the far south of India are probably representative of the lifestyle of these peoples, who were Dravidian-speaking.

A few centuries after this period is probably when the proto-Munda began pushing out of Southeast Asia. The DNA evidence is pretty strong this was a hugely male-skewed event once it got beyond the Khasi hills. Why? My hypothesis is that these were not quite small-scale peoples. Perhaps the male-mediation of a lot of gene flow in South Asia is due to the emergence of militarized confederacies where elite lineages engaged in conquest of territory from native groups. The Munda have very low frequencies of R1a, and very high frequencies of O2a. The admixture with Dravidian and Indo-Aryan speaking peoples that occurred between 2000 BC and 0 AD was probably overwhelmingly female-mediated.

The narrative above suggests that most of the genetic changes we see in South Asia to result in the landscape of the present occurred in the period between 2500 BC and 500 BC. About 2,000 years. And yet agriculture of some form arrived in Mehegarh in western Pakistan 9,000 to 7,500 years ago, depending on what dates you trust. What took so long? Similarly, millet and rice agriculture in China is 7,000 years old, but only around 4,000 years ago did rice farmers start pushing south (and probably west in the case of the Munda).

I’ll present the hypothesis here that this coincidence wasn’t a coincidence, and that certain things in relation to social complexity have a particular rate of change. In general I agree with economic historians who say that our need to posit an “Industrial Revolution,” or a “Neolithic Revolution,” is somewhat of an imposition because humans don’t want to think quantitatively. It probably takes small-scale societies moving from hunting and gathering to full-brown agriculture a certain amount of time, and then to proceed to greater social complexity that enables migration which is more than due to simple natural increase and Malthusian driven expansion. Mainland India beyond what is today Pakistan and much of Southeast Asia were “filled up” by agricultural peoples around the same time after a long incubation to the west and north because similar social forces were at play.

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