Week 6, Gene Expression Book Club – Not Born Yesterday

“Who To Trust?” That’s the title of chapter 6 of Not Born Yesterday, and this has a very Robert Triver’s vibe (e.g., his book The Folly of Fools: The Logic of Deceit and Self-Deception in Human Life). With the subtitle “The Science of Who We Trust and What We Believe,” I kind of wonder why this chapter exists, since much of the material is implicit across the earlier chapters.

Basically, we trust those who have an incentive to be truthful. We trust people with expertise. We trust people who are confident…but once someone is wrong, we trust those who were more provisional and less confident. Humans have a host of heuristics and cues to figure out who is less likely to lie.

Not surprisingly, the chapter throws cold water on the idea that scientists have a good analytic understanding of cues so that liars and cheats can be easily detected. None of the metrics and expressions seem to have passed peer review. Rather, the problem with lying is that it takes effort and deception is hard to maintain in terms of coherency and consistency. Liars trip up because it’s hard work, they don’t exhibit subtle physical clues (well, they might, but not well enough to turn it into a consistently applied system of detection).

A key concept in the book is vigilence. The gullible dodos are exceptions, not the rule. I do wonder about social differences due to cultural conditions, implied and hinted at in this chapter. People in WEIRD and high-trust societies are presumably less vigilant. A friend told me years ago Mormons made bad politicians in Congress because their peers always lied to their faces, and they simply never expected it. Mormon culture is high-trust, and lying in a brazen manner is not socially acceptable, so these individuals were not vigilant for it.

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Week 5, Gene Expression Book Club – Not Born Yesterday

James Surowiecki’s Wisdom of the Crowds came out in 2005. The basic insight is groups of people are often much more accurate than individuals. Not Born Yesterday accepts this finding, but chapter 5, “Who Knows Best,” punches back against overreading the result in all domains.

Wisdom of the Crowds came out in a decade when all sorts of cool psychology and neuroscience books were being published. Counterintuitive stuff that was entertaining sold (e.g., Jonah Lehrer’s How We Decide). That was before the replication crisis, and it turned out that a lot of the counterintuitive results were one-off’s and not general results. The 2010’s became the decade of boring psychology due to a correction against this pattern.

In this chapter, Hugo Mercier starts coming through on his claim that we’re not that gullible. People go along with the crowd, but not unreasonably so. The famous experiments that show conformity are actually not as illuminating as they’ve been made out to be. People know very well which line is longer, they just admit that they conform in public. And even then, most people refuse to conform. Preschoolers are aware of expertise. They know that doctors know more about plants, while mechanics know more about how to fix a toy. They trust adult judgment in things adults presumably can understand, but not where their opinions shouldn’t be weighted (e.g., children see that the adult has no more information than they do).

Humans are OK at weighing expertise, and gauging a sense when majority opinion can likely be right (e.g., situations when errors are independent and random). When you tell people that the majority went along with a particularly charismatic person, they discount the majority consensus.

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Moving up the “technology” category

Believe it or not, my Substack is now #8 for paid newsletters in the “Technology” category. Substack allows you to put in three categories. I selected Genetics, History, and Technology. Technology is the only tag that is being reported for the leader board, so there I am. I really wish there was a “Science” option, but there isn’t (I’ve complained to Substack about this).

I justify my inclusion there because I will be talking now and then about genomics and genetic engineering, and these are technologies. If I focused more on technology I could certainly charge more, since it would be industry relevant. But I really do enjoy writing about Zhou China and talking to scholars such as Armand Leroi, so I will continue to keep it a “dilettante’s corner.”

The leader right now is my friend Byrne Hobart’s The Diff. Some of the stuff he writes about is pretty incredible.

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2020 Holiday reading and beyond

Over at Substack someone asked if L. L. Cavalli-Sforza’s works from the 1990’s are worth reading. I had to say, sadly, that probably not. It’s 2020, and they’re just too out of date.

If you haven’t, you should read David Reich’s Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. It’s already a little out of date, partly due to work from his own lab, but it’s mostly on-point. If you haven’t read it, do so. I can’t see why anyone wouldn’t want to read this book, because you can “hum” through the statistical genetics parts if that’s not your cup of tea. If you aren’t into history, the statistical genetics is still interesting unless you are deeply involved in this field.

Adam Rutherford’s A Brief History of Everyone Who Ever Lived: The Human Story Retold Through Our Genes is also pretty good and relatively up-to-date.

In 2017 I posted about books you should read. I began to think about stuff I’ve read since then that has stuck with me. First and foremost, Imperial China, 900–1800. This is an excellent big-think book that will stay with you, and covers the period that really helps you understand modern China today.

An older book that I always recommend people, When Asia Was the World: Traveling Merchants, Scholars, Warriors, and Monks Who Created the “Riches of the East”. I think this book is relevant since we increasingly live in a multipolar world that’s recentering on Asia.

Another book that is essential reading is The Fate of Rome: Climate, Disease, and the End of an Empire. It’s an excellent environmental history that illuminates a topic most of us are interested in. Additionally, there are facts that are important to know. The author claims that pandemics are really a feature of the broad empires that arose around 0 A.D., while the Neolithic was characterized by endemic local outbreaks.

Outside of my usual domains, John Keay’s Midnight’s Descendents is a quick and readable history of India after 1947. Key is a writer who produces pretty good histories for laypeople, so I recommend most of his books

The First Farmers of Europe is a good academic book for non-academics. I found it via Peter Turchin. No fancy man, lots of facts. Just go slow is what I suggest.

Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not is another book I’d recommend to people despite it being academic. This work changed my priors a bit on the importance of ideology (perhaps more important than I’d thought).

I haven’t read many “dinosaur books” since I was a kid. But The Rise and Fall of the Dinosaurs: A New History of a Lost World is one of those I have. I highly recommend it despite its academic perspective.

Walter Scheidel is one of those scholars where I would recommend being a completist. He has a lot to say, and it’s novel. I can’t recommend Escape from Rome: The Failure of Empire and the Road to Prosperity enough.

I don’t plan on reading much about the Reformation in the future, as I’ve read a lot in the past. But Rebel in the Ranks: Martin Luther, the Reformation, and the Conflicts That Continue to Shape Our World was worth reading.

If you haven’t read Joe Henrich’s The WEIRDest People in the World: How the West Became Psychologically Peculiar and Particularly Prosperous, do so. It’s not necessarily going to convince you. But, it’s a place where you need to be to start a discussion about all things “Great Divergence.” Even if you think it’s full of crap, it’s something you’re going to have to engage. On the whole, I think your mileage will vary based on the portions of the book you agree or disagree with.

Of the fathers of population genetics, J. B. S. Haldane had the most interesting biography. So if that interests you, I would check out A Dominant Character: The Radical Science and Restless Politics of J. B. S. Haldane.

Stuart Ritchie is always worth reading. So check out Science Fictions: How Fraud, Bias, Negligence, and Hype Undermine the Search for Truth if you get a chance.

Richard Eaton’s India in the Persianate Age: 1000–1765 is important to read even if you aren’t interested in India. It illustrates global and cosmopolitan culture in a non-Western context. As the European West becomes less of the universal culture of the modern age, it will be useful to know about the past when it wasn’t as well.

Then, there is One Billion Americans: The Case for Thinking Bigger. Why am I recommending this? I think some of you should “hate-read” this. At some point, it is quite likely in the next decade that the “woke” wave will break, and we’ll be back to dealing with neoliberal shills like Matt Yglesias as the “Left” party. Instead of language games, there will be real policy direct from on high.

This is useful in the same way reading theology is useful. You may think it’s nonsense, but people take nonsense seriously. Honestly, I’m not sure if this is the best book to read if you already agree broadly with neoliberalism. But then again, I don’t read books for personal validation.

As a bonus, my favorite book from the 1980s. And from the 1990s. And 2000s. Not a surprise to long-time readers…perhaps.

And finally, I’m no longer the youngest obsessive reader in my line, so here are a few recommendations from the elementary-aged Khans for your own younger kids or grandkids.

My eldest raced through Sayantani DasGupta’s The Serpent’s Secret and Game of Stars when she found them (no ethnocentrism here… she picked them up based on the cover) and was proud to be the first on the waiting list at the library when the Chaos Curse released this spring.

She has also adored the Mysterious Benedict Society series.

Her highest recommendation though is for linguist and prolific author Donna Jo Napoli‘s mythology series. The National Geographic editions are oversized, beautifully produced and lushly illustrated by Christina Balit. Napoli comes at each project with a scholar’s delight in small details. There are frequent sidebars about the geographical settings depicted, historical and biological references and the linguistic considerations Napoli made in translating. So far, my restless child who won’t even so much as look at an ordinary book she’s already read has circled back and reread these editions cover-to-cover as many as five times each. Her favorites in order are Tales from the Arabian Nights, Treasury of Greek Mythology, Treasury of Egyptian Mythology, Treasury of Norse Mythology. The only one she has left is Treasury of Bible Stories.

One of her siblings meanwhile is dabbling in the deep-thinking currents of our time, with all the subtlety of early elementary school. His simplistic pronouncements, alas, are almost indistinguishable from what that great eminence of 2020 gifts us with here.

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Learning from variation in Northern Italy in response to COVID-19

One of the major issues when discussing pretty much anything is the tendency to aggregate nations into a single unit and then compare to other nations that are not comparable. For example, the United States is a federal republic of 330 million people. New York state is not Washington state. And neither is Texas.

The same applies to Italy, which is a diverse nation of 60 million. The normal way to understanding Italian variation is from north to south. But, during the recent COVID-19 outbreak one aspect that is important to note is that Lombardy and Veneto in the Po river valley have taken very different tracks. Lombardy is about twice as populous as Veneto but has five times as many confirmed cases of Covid-19. And 15 times the death toll (8905 vs. 631 dead as of April 5th).

A Italian-speaking friend, who has been tracking the Italian press notes that the big difference seems to be that Veneto is attempting to implement the test-and-trace philosophy that South Korea rolled out. And, in Veneto, they aggressively test people who are not symptomatic to catch silent spreaders who don’t exhibit Covid-19 (in contrast to Lombardy where they tend to test once symptoms present and not even always then).

Below is a recent interview with professor Andrea Crisanti, quickly translated from Italian, where he outlines his philosophy and the path he sees forward for getting COVID-19 under control.

Read More

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Why Vox/Recode was telling you COVID-19 was less dangerous than the flu (1 month ago): Explained

I recently took to Facebook to explain why my family and I are self-quarantining. It’s not just like the flu. But many people disagree. Many, though not all, are “MAGA-people.” Middle-American types who trust Donald Trump and Rush Limbaugh. Where are they getting their talking points? Some of it is from Limbaugh, Sean Hannity, etc. (the son of the President of the United States of America for example)

But today I realized that there was “mainstream media” validation out there. On February 13th Vox/Recode published “No handshakes, please”: The tech industry is terrified of the coronavirus. I didn’t read beyond the headline, because I didn’t take the piece seriously.

Here is what I assumed was going on: the editors at Recode were settling some scores with “tech-bros” with whom they had an adversarial relationship. The journalist who wrote the piece was almost certainly just a pawn in this game of middle-school level social competition and sniping. Underlings know what they editors want, and they’ll produce it. Trust me. I’ve been the target of this myself. Much of the media is dishonest manipulation and an expression of power. If you don’t know that, you’re an idiot (to be frank).

Ten years ago the tech-press was just a marketing and publicity arm of Silicon Valley. That changed with a substantial number of the tech-journalism elite becoming skeptical and antagonistic toward the megalomaniacal and somewhat crazy tendencies of the tech-elite (these tendencies are objectively true, though they are features, not bugs!). Much of the antagonism is now masked with social justice and Lefty politics, but ultimately a lot of this is personal. Journalists have power and influence, but not too much money and security.

They think they’re “punching-up” so it’s OK.

Today people are surfacing this Vox/Recode piece again to settle some scores. So I reread the whole thing to be fair. This part shocked me:

“That’s like saying you can’t come in if you visited Chicago because of the flu outbreak in New York City,” the employee told Recode [find someone to say what you want to say -Razib].

Some [“Some”, who? -Razib] have criticized comparing the coronavirus to the flu because it has a far higher fatality rate and that it distracts from the new virus’s severity. But the fact remains that, so far, the flu has impacted far more people [No shit. Exponents. It’s true. It’s disturbing -Razib]. The CDC estimates that 10,000 people have died from the flu this season, with some 19 million people in the US having experienced flu illness. Data from the CDC suggests that the flu is a greater threat to Americans than the coronavirus. Yet unlike the flu, the coronavirus is new and not well understood, which makes it especially scary to the public, including Silicon Valley’s elite.

What. The. Fuck.

This was, and is, technically true. But we all know this is misleading. In mid-February, there was some uncertainty and lack of clarity. Being cautiously skeptical would have been fine. But the tone of this piece is not sober. On Twitter, the tech-journalism elite made their views more nakedly clear. The “tech-bros” are weird and nutty. The coronavirus alarmism was an opportunity to get at them. This was middle school. Not objective analysis.

To be clear, I’m angrier at Rush Limbaugh, Donald Trump Jr., Donald Trump, and Sean Hannity. People need to be calm. They don’t need to go crazy. But it was clear a long time ago this was worse than the flu, with high downside risk. Now many MAGA-boomers are now digging into the idea that it’s not as bad as the flu (and making life decisions that are agonizing for their children, like going on vacation because it’s cheap and no lines in airports).

Vox has some great journalists. I probably read everything Julia Belluz writes. These are big organizations, and there isn’t always clear communication or accountability. People differ in their opinions. But let’s be obvious what was happening above: some people within the organization were using “objective journalism” to settle scores. That’s what some journalism is. Now they’re trying to pretend like it didn’t happen. It happened. We will remember.

Put that into a “card-stack” somewhere.

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New version of Reich lab dataset

David Reich’s lab has posted an update of their ancient and modern DNA dataset. It’s in their Eigenstrat format. I converted it to Plink format and made it so that the population groups are now in the family ID column.

It’s a big dataset. There are two of them, one with 1.2 million SNPs, and another with 600,000 SNPs. The former has 6,676 individuals, and the latter has 10,215 individuals.

Here are the files for the 1.2 million SNPs: .bed, .bim., and .fam.

And for 600,000 markers, .bed., .bim, and .fam.

Here are the files all zipped together.

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Open Thread, 11/17/2019

Just noticed that the Kindle version of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past is $4.99. If you haven’t read it, I suggest you do it sooner rather than later.

The Dark Psychology of Social Networks. Perhaps a little alarmist. One thing is clear is that now most people are on the internet, median conversation is probably not as elevated (people are stupid). But there are structural and cyclical aspects of this. Ecosystems eventually all collapse.

Population-specific and transethnic genome-wide analyses reveal distinct and shared genetic risks of coronary artery disease.

‘I Will Never Be German’: Immigrants and Mixed-Race Families in Germany on the Struggle to Belong. In college, I had a philo-German friend whose mother was a German immigrant. His father was a Japanese American. He learned German in college to supplement what he learned from his mother and maternal grandmother (his grandmother was, to be frank, an unrepentant fan of Adolf Hitler). In his junior year, he went to do study abroad in Germany.

When he came back I asked him what he thought, since he had loved the idea of Germany and German culture (he had been into techno). He got angry, and explained he dealt with a lot of casual racism, and people would complain about how many “Chinese people” there were now in Germany around him in German, assuming he didn’t know German (they were complaining about him, as he looked visibly Asian, albeit he did actually favor his mom’s side in appearance). I never asked him about Germany after that.

History as a giant data set: how analysing the past could help save the future. Glad to see Peter Turchin getting some love. Of his older books, I really recommend Historical Dynamics: Why States Rise and Fall. I’ll be honest and that I thought Peter was full of it when he made his pessimistic predictions in 2010. He could be wrong still, but he wasn’t offbase to be worried.

Human Origins in Southern African Palaeo-wetlands? Strong Claims from Weak Evidence. Measured response. This is how it should be done.

Elevated polygenic burden for ASD is associated with the broad autism phenotype.

Five Polling Results That May Change the Way You Think About Electability. The fact that socially moderate downscale young Democrats don’t get a lot of “woke” language dovetails with Rob Henderson’s piece, Thorstein Veblen’s Theory of the Leisure Class—A Status Update. Freddie DeBoer wrote something along the lines of language being a way to maintain class privilege many years ago. The eternal rectification of names is the game of gentleman.

Got a copy of The Han: China’s Diverse Majority. China’s important. Know more. Not less.

A/T/N polygenic risk score for cognitive decline in old age.

Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages.

At Tennessee Titans Games, the Fiercest Tailgaters Are Kurds.

Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx.

Sex-specific genetic effects across biomarkers.

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The native and the coconut civilization

Recently a discussion emerged on Twitter about the relative success of Indians in America and Indian Americans and the origins of that success. While Noah Smith pointed to their cultural and economic status to begin the conversation, W. Bradford Wilcox noted the stability of the marriages of Indian Americans. There are lots of directions one could go with this discussion, but one response to Wilcox’s Tweet captures I think a way of thinking that is important to engage because it is influential:

Guess which immigrant group was colonized by a Western hegemonic power that indoctrinated the culture into American ideals, literally preparing them for upward assimilation? Also, Indian marriages are functionalist in nature, and not subject to ephemeral underpinnings of “love”.

One could take this as an affront to cultural or individual pride. That is, the success of Indian Americans being reduced to simply Western culture and civilization diminishes what they have achieved on their own (I’ll get back to the issue of marriage specifically).

This is not the issue that I want to explore, though I will note it here. Rather, let’s entertain the ideas and presuppositions embedded in this sort of assertion, and its correspondence to reality.

You could say that this attitude, which reduces non-Western peoples and societies as outcomes of Western history, is marginal. But the person who expressed the opinions is a graduate student in sociology, and this viewpoint does suffuse the assumptions of many educated Americans “in the know”, albeit less nakedly and brusquely expressed. Less enlightened Americans probably believe that Indian immigrants are just smart and well-educated (this is true), and that is the reason for their success (again, true). But those who are “in the know” “understand” that these sorts of reductive characteristics are outcomes of a particular historical process, and it is that historical process to which Indian American success redounds (“Well actually, British colonialism imparted bourgeois values to native allies in western India, and that’s why they succeed in the United States”).

Though I am not Indian American, I am obviously Indian American adjacent. Arriving in the United States just before elementary school, and growing up with parents raised abroad, I have a visceral understanding of intercultural dynamics which is probably not available to professional anthropologists. I am aware of elements of South Asian culture which are very different from American culture, and so am always curious about the new pattern of some Westerners to reducing South Asian culture as simply a postcolonial reaction to Western hegemony.

Obviously, on some level, the impact of that hegemony is hard to deny. Though Macaulay’s aspiration of creating “a class of persons Indian in blood and colour, but English in tastes, in opinions, in morals and in intellect” did not occur to full completion, the British period had a strong impact on the outlook and viewpoint of South Asian elites. Even those who were anti-colonial and anti-Western in orientation often reacted to European influence and domination. Their own nativist response would be incomprehensible without the British Other.

There is also the reality that for some aspects of culture native peoples may assert a deep and indigenous origin for practices and values, even if it is hard to imagine a particular phenomenon without European influence. A simple illustration of this is the popularity of drinking tea across the subcontinent, which arose through British commercial propaganda. Modern South Asians may not be aware of the origin of this deeply embedded aspect of their lives and assume it’s indigenous in a very deep manner.

A more subtle and rich illustration of this tendency is the Buddhist revival of 19th-century Sri Lanka. The peoples of this island have been Buddhist for a very long time, and have interacted with the Theravada societies of Southeast Asia for a thousand years. But, in the 19th-century Buddhism reformed itself in the face of Christian proselytization. Some Westerners, sympathetic to Buddhism (e.g., Henry Steel Olcott), were critical in buttressing the intellectual armamentarium of the local population. In the process, they may have influenced the self-conception of elite Sri Lankan Buddhists to perceive their religion as rationalist in a manner that was shaped by the post-Protestant Enlightenment and its critiques of Christianity. In this framework, Sri Lankan Buddhism can be thought of as fundamentally indigenous, but the movements of the last few centuries are impossible to understand without awareness of European influence, even if native Sri Lankans themselves now perceive these elements as deeply primal (i.e., the rationalist and less supernatural Buddhism is the “true Buddhism”).

Moving to the mainland of the Indian subcontinent, again it is not deniable that European colonial hegemony had a strong impact on the society. Consider that defining element of Indian civilization, caste. Some scholars have made a strong case that British systematic rationalization of governance and taxonomic anthropology of native peoples was critical in the crystallization of the caste-jati system (in particular, the 1871 Census of India). Yet genetics casts strong doubt on this claim as being the only explanation, as many jatis and broader caste groups, exhibit patterns of endogamy and relatedness which indicate the genealogical depth that is 1,000 years or more. As it happens, al-Biruni’s observations of India 1,000 years ago outlines a social structure which is broadly consonant with what we perceive to be Indian today.

What does this have to do with Indian Americans? First, it is famously well known that Indian American migration to the United States has been highly selective, biased toward individuals with high levels of skill and education. Additionally, these people are not a representative cross-section of Indians themselves in regards to ethnicity and community. There are, for example, very few individuals of Dalit background in the United States. And, there is a preponderance of individuals of higher status communities. Using the framework above, one might say that communities that have internalized European mores, outlooks, and skills, have been advantaged and that this is why they have immigrated to the United States.

The problem is that this is clearly wrong. Some communities in South Asia have been literate for thousands of years. This is well known. The Muslims who arrived as an elite class after 1000 A.D. noted which communities were literate, and elevated them into service. Additionally, other Indian groups were inducted into military service. This is not to say that South Asian class, caste, and professional affiliations have been communally static for thousands of years, but neither was the portfolio of skills and preferences arbitrarily poured into the minds of some Indians as opposed to others. Some Indian groups were useful in particular places and times to various elite groups, whether Hindu, Muslim, or British, and that utility redounded to the long-term trajectory of that community (e.g., Parsis).

In the American context, there is an underrepresentation of people from groups which are the majority of Indians, the broad peasantry. Rather, various mercantile communities and service professional communities are overrepresented (though there are farmers from the Punjab who have moved to the Central Valley). Much of the accumulated human capital in many of these groups predates the arrival of Europeans.

How a group of people reacts to new stimuli varies. The Indian Diaspora is highly skewed toward people from Gujurat and Punjab. In contrast, there are far fewer people in the United States from the upper and middle Gangetic plains, the civilizational heart of India (a fair number of peasants from these localities did migrate to Trinidad, Mauritius, and Fiji). The literate elites and landowners the Gangetic plain have not reacted to the legacy of European colonialism and globalization in the same manner as the literate elites and landowners of Gujarat. Some of this is happenstance, but some of it is probably the reality that Gujarat has long been integrated into the Indian Ocean trade networks, which even predates Islam.

This sort of analysis need not be restricted to South Asia. When Europeans encountered the Japanese in the 16th-century they were struck by their industry and ability to imitate and perfect new technologies. The isolation imposed by the Tokugawa in the early 17th-century dampened this perception for centuries, but after the reopening of Japan in the 19th-century the same underlying parameters came to the fore. The Japanese remained distinct, but also assimilated many Western techniques and social structures.

In this globalized world roiled by economic change and characterized by migration, there is a temptation to fall into the trap of simplistic theorizing. We must avoid that temptation if we are to understand the true shape of a thing, rather than the fictions one could spin-out from our theories and preconceptions.

Going back to the starting point of his post: the strong economic performance and robust families of Indian Americans is not just a function of hegemonic Western values. These people are not simply persons Indian in blood and color, but white in tastes, in opinions, in morals, and in intellect, though there is something of that, especially by generation 1.5 and above. But the entrepreneurial aspect of some Guju communities, to give an example, illustrates that folkways derived from the South Asian context have been transmitted to the United States. The “joint-family” is quintessentially Indian, and though it is not common among Indian Americans, it likely casts a shadow on Indian American family life (additionally, divorce is very taboo for many Hindus). Most Indian Americans today are immigrants, raised abroad, and their orientation and mores are fundamentally distinct from the native-born and native-raised.

Of course, assimilation happens. But even that is contingent. The America that the children of Indian Americans are growing up in is highly polarized and post-Christian. This has some downstream consequences for how 21st-century immigrants and their children view themselves in the body politic.

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The Yamnaya origins of the Tocharians?

Eurogenes points me to a new paper in Current Biology, Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan. The conclusion:

Combining both the genetic and archaeological evidence, we here provide the first direct evidence of an early stage of population admixture around 2,100 BP in Xinjiang in Western China. Our study supports the “Steppe hypothesis” over the “Bactrian Oasis hypothesis” for the peopling of the Xinjiang region. The high amount of Yamnaya or Afanasievo-related ancestry in the Iron Age Xinjiang individuals indirectly supports the introduction of Indo-European languages into the region that survived in the form of Tocharian until the late first millennium CE. We note that we need more individuals from different sites and time periods to shed more light on the genetic history of the Tarim basin and the whole Xinjiang region.

The ethnolinguistic pattern of the Tarim Basin in early historic times was complicated. In addition to very distinct “Tocharian” languages, some of the cities were dominated by Iranian peoples. The modern-day Uyghurs are almost certainly descended from some of these populations. Uyghur men carry both R1b and R1a.

These results from ~2,000 years ago of ten individuals (five of them well dated) suggest that the northern Tianshan was populated by peoples that were direct descendants of the post-Yamnaya Afanasievo, who mixed to varying degrees with trans-Siberian populations (the mixture seems to have had a wide range of fractions). Two of the males carried R1b, the haplogroup dominant among the Yamnaya, but not latter cultures of the steppe (Andronovo). These individuals lacked European farmer ancestry, again indicative of their isolation from dynamics on the western forest-steppe that resulted in genetic differences between the successors of the Yamnaya and the Yamnaya proper.

The argument here is somewhat by elimination. Historical records indicate that some of the cities of the Tarim, particular those of the southern fringe of the basin, were Iranian speaking. Additionally, Iranian cultures are associated with haplogroup R1a, and the Sintashta-Andronovo cultures all had European farmer ancestry. In contrast, R1b is rare outside of Europe (though it is found in Kalash and Yaghnobi), but is found among Uyghurs and among these samples. Tocharians are the most likely descendants of these people, who arrived in the region almost 5,000 years ago.

This explains how the Tocharian languages were so distinct, and, their deep separation from other Indo-Europeans. The Tocharians were isolated and diverged very early. Later they were joined by Iranian groups. Eventually both these were absorbed by Turkic populations, first the Uyghurs, and later the Karluk Turks (the modern Uyghurs revived an ancient ethnonym).

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