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American Math Olympiad Team, 2015

For various ideological reasons there is an idea in some parts of the academy that Asian Americans are not a “model minority.” That that “model minority” designation is a myth. The mainstream media often repeats the idea that this is a myth which has been “debunked.”

Actually, it hasn’t been debunked. Rather, through a set of common talking points and empirical shell games Asian American achievement is masked, obfuscated, and explained away. This is not to say that Asian Americans have not, and do not, experience racism. But, it is to assert that the perceptions of Asian American success in particular domains is not an illusion. Your eyes and mind are perceiving real patterns (see here for a typical example of the “Asian American model minority myth”).

From PBS, These groups of Asian-Americans rarely attend college, but California is trying to change that:

Chang, a 22-year-old psychology student at California State University Fresno who grew up in this Central Valley city, chose to study close to home, and she’ll probably remain on campus for her master’s degree. But for someone from an ethnic group that contradicts the Asian-American “model minority” myth, even this is a rare achievement.

As one group of Asians who don’t go to college in large numbers, the Hmong help illustrate the complex changing demographics of students arriving at American universities and colleges: increasingly nonwhite, low-income, and first-generation.

Among the 281,000 Hmong in the United States, 38 percent have less than a high school degree, about 25 percentage points lower than both the Asian-American and U.S. averages, according to the Center for American Progress. Just 14 percent have at least a bachelor’s degree, less than half the national average.

Upending the stereotype that most Asian-American children go to college, the Hmong and other Southeast Asian immigrants including Cambodians, Laotians and Vietnamese have markedly low college-going rates — especially compared with Chinese, Japanese, and Korean Americans, who are actually more likely than other Americans to earn bachelor’s degrees.

This is the “Hmong gambit.” I’ve been hearing about this for 20 years from Asian American activist friends. The Hmong are genuinely marginalized. They were marginalized in Laos as well, where they were a hill tribe outside of the pale of Theravada Buddhist civilization. The fact that they have particular trouble integrating into the United States in comparison to other Asian Americans is not surprising. But the Hmong are not very representative of California Asian Americans.

UC Berkeley provides undergraduate (non-international) student data. And you can find various Asian American ethnic numbers from the Census and other sites.

Berkeley 2015 % California 2010 % Ratio
Chinese 20.5% 3.9% 5.26
Filipino 3.4% 3.9% 0.87
Japanese 2.1% 0.7% 2.82
Korean 5.3% 1.4% 3.94
South Asian 8.2% 1.8% 4.55
Vietnamese 3.6% 1.7% 2.1

One thing you can see immediately is that the reporting is sloppy and uninformed. Vietnamese shouldn’t be bracketed with other Southeast Asians. They are somewhat overrepresented at Berkeley. This is not surprising. Many of the Vietnamese are themselves Hoa, or from the Catholic middle class. The Filipinos are represented at about their proportion in the population. The Chinese, South Asians (mostly Indian), Koreans, and Japanese are all overrepresented.

At this point you might wonder about all the other groups such as Pacific Islanders, Cambodians, and Mongolians (?). But look up the numbers and you’ll see that the six groups above represent 80-90% of Asian Americans in California. These are representative communities, not the Hmong.

Note: One aspect of the “model minority myth” myth is that the 1965 immigration system, which was highly selective for the first post-65 wave of Asians, shaped modern conceptions. More or less this is a lie, as the “model minority” thesis was formulated in the 1960s against the backdrop of black urban unrest, and when “Asian American” mean Chinese and Japanese, who were by and large descendants of very modest people. In the case of the Japanese in particular it is well known that those who left the home islands were often the most socially and economically marginalized.

 
• Category: Race/Ethnicity • Tags: Model minority 
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Screenshot 2016-08-28 15.41.08
About thirteen years ago I expressed the opinion that an understanding of population structure will become a matter of intellectual curiosity once we have a better understanding of the genetic basis of characteristics. A friend, who was a statistical geneticist, told me that this was unlikely. We were unlikely to capture the ability to predict all outcomes well enough on even high heritable complex traits to simply discard population structure information. Some of this is not due to genetics; different populations may expose themselves to different environmental conditions. For example, it would be useful to know which individuals in the CEU white European American data set are practicing Mormons, and which are not, because Mormonism tends to result in a lot of behavior modification.

But some of the concern about population structure has to do with the fact that genetic background matters, and we are unlikely to ever have total omniscience as to the nature of genetic interactions and dependencies. By this, I mean that if we have a strong causal signal which associates disease risk with a genetic variant, that risk is still conditional on dependencies of other genetic variations across the genome. Those variations are the outcome of demographic histories, which one can “control” for to some extent by accounting for population structure. In more plain language, a signal that predicts an outcome in Norwegians may not predict the same outcome in Nigerians. The may be due to different frequencies of other variants which are not directly causal, but interact with the causal signals, which vary between populations.

Screenshot 2016-08-28 15.58.43 More recently I’ve been a bit sanguine. I don’t follow the literature closely, but papers like High Trans-ethnic Replicability of GWAS Results Implies Common Causal Variants, make me wonder if the genetic background concerns weren’t over-wrought.

A new preprint, Population genetic history and polygenic risk biases in 1000 Genomes populations, suggests we should be worried. Or, more precisely, we should be cognizant of the limitations genetic background imposes upon us for certain classes of variants and disease. In particular, rare variants are going to be less portable across populations because of shallower time depth of their emergence, after, populations have diverged. So, if you have a low frequency major effect causal variant in Europeans, there is a much lower likelihood that it is in other populations.

The histogram above illustrates an excellent case study from the preprint. The genetic architecture of height and its genomic basis has been most well elucidated for Europeans. We know, for example, many of the loci which distinguish Northern and Southern Europeans, and, we know that selection has resulted in divergence between the two populations over the past 5,000 years. But as you can see the predicted heights seem to simply follow genetic distance from Europeans. SAS = South Asians, while AMR = a mixed cohort of populations from the Americas. EAS and AFR are East Asians and Africans. In reality, Africans are nearly as tall as Europeans (taller or shorter depending upon the reference European population), and taller than East Asians. The predictions here are off because the causal variants inferred from the studies of European cohorts are portable in direction proportion to shared demographic history. South Asians share a relatively ancient demographic history with Europeans, while many mixed groups from the Americas have Europeans as one of their recent founding populations. But in both cases the causal variants were likely segregating in the ancestral populations before divergence, so there is no major difference in the consequence.

The preprint has a lot more than just a reanalysis of GWAS. Using local ancestry deconvolution methods they show how one can infer history from patterns of genetic variation (though as always, this should not be taken as gospel, as there are biases in the methods currently used). The major take home is simple: population structure is real, and, it has real consequences functionally.

 
• Category: Race/Ethnicity, Science • Tags: Genetics, Genomics 
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512QZUX2sSL._SX331_BO1,204,203,200_ Over at The Genetic Literacy Project Jon Entine has a post up, Usain Bolt’s Olympic gold proves again why no Asian, white–or East African–will ever be crowned world’s fastest human. Fifteen years ago Jon wrote Taboo: Why Black Athletes Dominate Sports And Why We’re Afraid To Talk About It, so he knows something about this topic.

Actually, I think Jon is wrong on this. Better drugs and biological engineering mean that I suspect at some point in the near future the fastest “human” alive is going to be non-African, and, if I had to bet, Chinese. But you know what Jon meant.

There is a lot of detail in Jon’s post because he knows a lot about this topic. But at the end of the day the specific details are less important than the general theoretical framework, which makes it unsurprising that a single group of humans who are genetically related dominate sprinting. Unlike figure skating, sprinting is entirely objective. All that matters are physical inputs. Second, unlike swimming, which is also objective, sprinting seems to have pushed very close to the boundaries of what non-modified or drug-enhanced individuals are capable of. To my knowledge there’s no expectation of a Fosbury Flop in sprinting.

Therefore, sprinting is selecting for raw ability. Training is not irrelevant, but the issue with training is that others can train too. What can’t be mimicked is raw ability due to one’s biological aptitudes and abilities (again, excepting bioengineering). Let’s assume that Olympic caliber sprinters are among the 10,000 fastest humans on the planet, because not all people with the aptitudes become sprinters. Assuming a normal distribution, that’s about five standard deviations above the human norm. I suspect I’m being conservative. Someone like Usain Bolt is probably a six standard deviation unit human. Google tells me that a fit human can run the 100 meter dash in 13.5 seconds. The world record is about 9.5 seconds. The absolute range here is not incredibly large. Small differences in the mean across populations suggest that when you select for extreme individuals those small differences will make all the difference.

If sprinting was less objective, then there would probably be more equality in outcome. I suspect judges would be biased for various reasons, and one set of nations or people of a particular ethnic background dominating a field can get quite embarrassing. But sprinting is rather objective, and the socioeconomic obstacles are low. Given basic nutrition, and the ability to huff it, you have a shot. What matters is the magnitude of your ability.

principlespopulationgenetics One peculiar thing population genetics teaches us that non-adaptive traits are more heritable. This is due to the fact that selection tends to remove variation, selecting for fitter individuals. Humans are good runners, there are entire evolutionary theories based around our biomechanical modifications and adaptations. But there’s really no benefit in running in bursts of 10.5 in the 100 meter dash vs. 9.5. We’re not that sort of ambush predator. There’s probably some heritable variation in burst ability, but it’s small, and not visible in any normal set of tasks among large groups of humans.

But modern competitive sports at the Olympic level is not selecting for normality, it’s selecting from outliers. It isn’t that West Africans were guaranteed to be the best sprinters, it’s just that a priori it shouldn’t be surprising that in such a non-adaptively beneficial trait as running a few seconds faster in the 100 meter dash some populations had the genetic die loaded in their direction.

Note that I’m not denying any sort of selective or adaptive argument. There’s a fair amount of evidence that there is some selection in favor of greater height in Northern Europeans vs. Southern Europeans, which probably explains why Lithuanians are more prominent in basketball in relation to their numbers than Italians. But the selection wasn’t for basketball, and the fact that there is heritable variation suggests that selection wasn’t that strong and unidirectional….

Humans vary. Populations vary too. When you select from the tails of the distribution, the differences between populations are going to be very noticeable. If a sport is objective, and pushing its limits, it will select from the tails of the distribution.

 
• Category: Race/Ethnicity, Science • Tags: Race, Sports 
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Screenshot 2016-07-25 21.52.42
Update: If Pontus Skoglund fails to replicate your results it is not an optimal outcome….

end update
A new paper on on archaic admixture in Andaman Islanders has come out. It’s in Nature Genetics, Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. If you don’t have access, just read the supplements, they have the good stuff as usual.

The results here range from intriguing to clarifying. But I want to engage in a little post-publication criticism: I think the fact that the authors highlighted model-based admixture results is a disservice to the rest of their results. Daniel Falush will be out with a paper on best practices (or not) in relation to the utilization of model-based admixture soon enough, but the plot that is part of figure 1 is really in my opinion misleading in the broader context of their results. The JAR and ONG are Andamanese samples, while ILA and BIR are isolated tribal group in south to central India. These four groups are not very numerous, and, they are characterized by very small effective populations. In other words, the model-based admixture framework immediately infers these to be extremely close to idealized reference populations because they are so drifted. One can call this the “Kalash effect”, as the original STRUCTURE based analyses of the middle 2000s would routinely yield a “Kalash cluster.”

One consequence of the mix of populations that they have in this reference panel is some of the results are difficult to interpret. The Andamanese and Irula (a South Indian tribe) become nearly fixed for a major cluster respectively, and in the text the authors are interested enough to observe that these Andaman samples don’t show admixture because of this result. This is not necessarily true though. If these are the ‘purest’ of the samples that remain, then they will serve as the ‘pure’ reference. That doesn’t mean there hasn’t been recent gene flow into them. The same with the Irula. Because these two are highly drifted populations they are quite often going to arrive at these very high fractions in some particular K cluster.

Because of the large sample these rather obscure tribal groups, you have the result that Rajputs seem to share more ancestry with Chinese than the Bengalis (RAJ and BEN). This is in contradiction to everything we know. In reality, the Rajput samples have very little recent East Asian admixture, while the Bengalis are about ~10% East Asian on the time scale of the past one to two thousand years. I can offer a hypothesis for why the clustering algorithm converged on this result, but I’ll just suggest you read Lucy van Dorp’s Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference.

But what of the results overall? The intriguing aspect is the evidence that there is archaic admixture into the Andamanese, Australian indigenous peoples, and to some extent Indians (via their “Ancestral South Indian”) form a mystery hominin. The time scale they infer is on the order of divergence at least several hundred thousand year ago in the past. Presumably these results became clear because they had good high quality whole genome sequences (~10x and more coverage) with millions of SNPs to work with (and well ascertained), as opposed to the few hundred thousand in earlier work.

212978 One of the models the authors were testing is the idea that there were two waves out of Africa, with South Asian and Oceanian peoples in particular exhibiting hallmarks of admixture from an earlier migration. There are smattering of population genomics papers which support this proposition, but I will tell you most researchers who work with these data are skeptical. There were some methodological issues with some earlier findings, and limitations on the sample sizes and quality (whole genome sequence), or marker set (the SNP studies).

By and large these results support the idea of one migration. If one assumes Africans are one branch of the modern human race, all non-Africans are approximately equally related to Africans, because there is one major bifurcation between Africans and non-Africans. In contrast, the two migration thesis often posits that there was an earlier migration, that was later overwhelmed by a later migration. In that case, you might have scenarios where the second population shared more genetic drift with modern Africans because of a later separation. Or, there could be a scenario where the South Eurasian substrate shared more drift with Africans, shifting the affinities of the Andaman Islanders in that direction.

In any case, they did not see evidence of any of this. Rather, Andamanese share no more ancestry with Africans than you’d expect of generic non-Africans…sort of. As it turns out when using an outgroup with only ancestral allelic states as inferred from using the chimpanzee reference Andamanese actually have fewer African alleles that Europeans and East Asians. The same is true of indigenous Australians, though the authors did not tackle this issue in detail. Of course this could be Neanderthal and Denisovan ancestry. But it isn’t. We have the ancient genomes of these populations, and the Andamanese seem typical for a East Eurasian population.

They make the inference of a few percent admixture from a population which diverged from modern humans on the order of ~300,000 years ago through a lot of testing of explicit models. Again, read the supplements. Unfortunately they don’t have the genome of the mysterious ghost population, so they can’t make definitive conclusions.

The fact that East Asians and Europeans both lack this ancestral element is peculiar, because all the evidence puts the Andamanese on the same branch as the East Asians. So you can have models whereby a composite East Asian/European population engages in back migration to Africa. Or, perhaps Ancient North Eurasians, who contributed to both Europeans and East Asians? In any case, of the models they tested it does seem that archaic admixture from a ghost population is the most likely, but that does not mean that that is the correct answer. Obviously they did not exhaust the possibilities of models and scenarios. For several years now people have been seeing strange things in the data from Australasian and isolated Southeast Eurasian groups. There’s a story here, we just don’t know much of the outlines, we’re just grasping. Both Mait Metspalu and Luca Pagani have papers in the works….

What about the clarifying? It strikes me that they used some stringent selection tests (e.g., focusing on hard sweeps?), and still hit pay-dirt on positive results for the Andamanese. Both selection tests, and polygenic scores, suggest there’s a bias toward being small in these two groups. I’m curious if the Sentinelese would be the same. The thesis here is that islands result in dwarfism. But I wonder if the selection here is very recent indeed. The authors note that some of the sweeps are not complete. In the last few hundred years there has been a massive demographic collapse of the Andaman Islanders, and only the Sentinelese preserve their lifestyle in a pristine fashion.

This relates to the question in regards to phylogenetics. The authors indicate the the phenotype of these Austro-Melanesian populations is not necessarily due to shared descent from Africans, but adaptation to local circumstances. I don’t think they’ve proven it as such, but they’ve definitely shown that there’s a lot of selection occur in their new habitats. Curiously they don’t detect that there’s been adaptive introgression from the archaic, but I’m not sure if they have the power to detect that sort of thing anyhow. But, it might indicate that the admixture occurred further north?

Finally, I should mention that the Andamanese genomes are now online.

 
• Category: Race/Ethnicity, Science • Tags: Genomics 
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Shu_Qi_Cannes_2015 Facts are important. But they can be inconvenient. Despite the stream of “think” pieces about “hookup culture” over the past decade there is no evidence that young people today are more promiscuous than in the past. In fact, on the contrary. Young people today are by most measures less promiscuous than past post-WW2 generations, in particular, Baby Boomers. Those articles ultimately are not about the behavior of young people, but the fears, dreams, and nightmares, of a declining Baby Boomer cohort which refuses to go into the sunset quietly. I’m not a Boomer, so I won’t psychoanalyze their motives, but like literature the facts proffered in these essays are a means toward probing deeper issues and questions about the human condition, their generation’s condition and preoccupations, as opposed to being literally true (some of the more recent articles will even admit that the statistical evidence falsifies their premise, but then proceed to suggest there are anecdotal data that lend credence to their premise!).

This applies to other things. Today Quartz put up a piece, If Asian Americans saw white Americans the way white Americans see black Americans, which is not really about Asian Americans at all, but simply uses them as a prop, often in a mendacious manner. First, it gives a nod to the Asian American “Model Minority Myth,” stating that there is “perception that they are high achievers relative to other American ethnic groups.” Get it? There’s a perception. There’s a myth in some scholarly and political quarters that the model minority idea is a myth, founded mostly on assertion (e.g., just stating that it’s a false myth) and slicing and dicing the statistics to emphasize ways in which Asian Americans are disadvantaged in relation to non-Hispanic whites. For example, there is often a focus on the diversity among Asian Americans, ranging from affluent Indian Americans, to groups with more conventional socioeconomic profiles like Filipinos, and finally, those which are somewhat disadvantaged such the Hmong. This is to show that Asian Americans are not a model minority…some of them are struggling. But the logic is not applied to whites! Those who purport to debunk the myth of the model minority would not accede to debunking the idea of white privilege by pointing to the state of Appalachia, and rural white America more generally. Group averages for we, but not thee?

51fMlNGN4lL._SY344_BO1,204,203,200_ And yet the Quartz piece engages in some interesting jujitsu by actually reporting the statistics of Asian American advantage vis-a-vis white Americans in the service of a broader agenda of putting whites in their place in relation to their critiques of black Americans. In particular it quotes Anil Dash as saying “If Asian Americans talked about white Americans the way whites talk about black folks, they’d bring back the Exclusion Act.”

This to me is really bizarre, and why I term the piece mendacious: Asian Americans do talk about white Americans the way whites talk about black folks. This sort of thing was a clear subtext of Amy Chua’s Battle Hymn of the Tiger Mother. Many (most?) Asian American kids who grew up with immigrant parents were barraged with assertions about the disreputable character of their “American” (white) friends, and how it was important to keep on the straight & narrow. Immigrants from Asia often perceive white Americans to be sexually obsessed, lazy, and prone to a general amorality and fixation on short term hedonic interests. These are polite ways to condense the sort of attitude many Asian immigrants have toward the white American mainstream, which they worry will absorb and corrupt their children. Dash must know this, as he probably had immigrant parents, or was friends with people from immigrant backgrounds. Most white Americans don’t know this, partly because most white Americans don’t have non-white friends. But anyone from an Asian American background would be aware of the stereotypes and perceptions.

The tacit misrepresentation of Asian Americans here, not acknowledging that they do engage in the exact sort of behavior you are hypothetically positing they might engage in and so alienate white people, is not surprising. Asian Americans are often simply bit characters in a drama involving broader social and political streams which dominate the political landscape. For many decades conservatives asserted that Asian Americans were “natural Republicans,” and expressed confusion as to why more were not voting for their party. But this was an empty talking point; over the past generation the Republican party has become the de facto white Christian party, and many Asian Americans are not Christian, and all are not white. Some conservative Christian Asian Americans can identify with Republicans because of their religious ties, but socially conservative Indian Americans, to give one example, naturally have a difficult time identifying with a party which wears evangelical Protestantism on its sleeve as modern Republicans often do. This isn’t rocket science.

Screenshot 2016-05-12 21.34.16 On the flip side of this, many liberals erase Asian Americans from the landscape of our culture if it does not serve their framework of white privilege uber alles. When it came out many people pointed me to The New York Times infographic, Money, Race and Success: How Your School District Compares. The only mention of Asians is this: “Reliable estimates were not available for Asian-Americans.” But my wife pointed out to me that within the chart itself you still had Asian Americans tabulated! If you check the bubble plots at the top right , you see schools like Cupertino Union. It’s 73% Asian American. If you read this blog you know that it irritates me that Asian Americans are routinely elided out of these stories. It’s too regular to be due to a lack of data. It’s because it doesn’t fit the narrative of white privilege and domination. So Asian Americans are skipped over to make the picture neat and tidy.

Instead of taking reality as it is, in all its complexity and nuance, people attempt to fit the data into a narrative straightjacket. Complexity is a talking point only when confronted with a hypothesis you disagree with. When the data does not cooperate in a simple fashion with your own model, the data conveniently goes unmentioned. In a putatively multicultural America the dominant narrative on the Left side of the cultural and political spectrum is that of a dichotomy between whites, who have privilege, and non-whites, who are oppressed.

The black American template, unique, and rooted deeply in the soil of this country, is injected into strange and inappropriate contexts when it comes to people whose ancestors are from Latin America and Asia. White liberals and minorities are assumed to naturally form an alliance against the majority white rump; white liberals because of their moral virtue, and minorities because of their interests. The injustices experienced by someone with a name like Raheem Washington, who grew up in the inner city, are rather easy to enumerate. Raheem Washington begins life with some disadvantages. But there is a particular mainstream narrative where someone with a name like Deepa Iyer (Update: When I wrote this post I actually didn’t know who “Deepa Iyer” was, I just thought up a plausible name! Turns out there really is a Deepa Iyer of some prominence!!!), who might have elite educations, affluent parents, and a good secure career, has more common with Raheem Washington than their white colleagues at the university that they might work at. And of course, there is the further aspect that often goes unmentioned that someone with the name Iyer is from the top echelons of South Asia’s caste system, and so benefits from thousands of years of privilege! And yet it is common among Indian Americans for literal Brahmins to style themselves PoC tribunes of the plebs, oppressed by white America.

A genuine multiculturalism would actually acknowledge the real empirical texture of this nation’s changing demographics. And, a genuine multiculturalism rooted in fact, rather than vacuous critical theory, would dig deep into the richness of human history, rather than outlining broad sketches where white privilege reigns supreme from Sumer to America. As it is, often liberal multiculturalism is simply an inversion of white supremacist theory. That’s unfortunate, because there are real political debates and values divergences which we can grapple with and debate as a society, but the water is immediately muddied and when the facts are subordinate to an ideological narrative. No side really wishes to live in the reality we are given, instead of their imagining.

* Many of the things I said above can be generalized to the American Right as well, though the particularities will differ.

** I shouldn’t have to say this, but any racist comment isn’t going to be published. That’s not going to stop some of you, but I thought I’d give you fair warning.

 
• Category: Ideology, Race/Ethnicity • Tags: Asian Americans 
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Sardinian actress

Sardinian actress

Several years ago a paper was published, The History of African Gene Flow into Southern Europeans, Levantines, and Jews:

Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45,000 years ago. However, there has been no accurate characterization of the proportion of mixture, or of its date. We analyze genome-wide polymorphism data from about 40 West Eurasian groups to show that almost all Southern Europeans have inherited 1%–3% African ancestry with an average mixture date of around 55 generations ago, consistent with North African gene flow at the end of the Roman Empire and subsequent Arab migrations. Levantine groups harbor 4%–15% African ancestry with an average mixture date of about 32 generations ago, consistent with close political, economic, and cultural links with Egypt in the late middle ages. We also detect 3%–5% sub-Saharan African ancestry in all eight of the diverse Jewish populations that we analyzed. For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas.

At the time Dienekes had a pretty strong critique of the paper: the authors assumed that Northern Europeans were an unadmixed reference population, when in fact these populations may have had mixture from East Asians. He presented PCA plots which illustrated the fact that CEU (whites from Utah with British and German ancestry) sample were shifted toward Chinese in comparison to Sardinians. All these years later I think that in fact there is another explanation besides East Asian admixture to explain this: the Chinese themselves have some admixture from West Eurasians. The Sardinians are notably lacking in some admixture components common among mainland Europeans, so the West Eurasian admixture into Chinese probably is closer to mainland Europeans than it would be to Sardinians.

So what about the Sardinian admixture from Africans? The same dynamic might be at play here: old admixture from “Early European Farmers” into Africans might explain why they’re closer to Africans.

But let’s assume that the Sardinian admixture from Africans is legitimate. What does that mean for estimates of ancestral derivation from continental populations than you see in the DTC personal genomics firms that report ancestry results? It can only mean that among people of Southern European ancestry a few percent of African ancestry is being “masked” because it is part of the reference population set. This came to my mind because a half Cuban friend of mine had ~2% African ancestry. Reasonable. When I checked by running unsupervised ADMIXTURE he had ~4%. Then I noticed that the Sardinian reference set was often in the 1-2% range. One explanation for the discrepancy then would be that a few percent of African ancestry in his genome was simply swallowed up by the reference population in the supervised learning framework.

 
• Category: Race/Ethnicity, Science • Tags: Admixture 
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Great_Andamanese_women_-_1876

51dqYKA64vL._AC_UL320_SR200,320_ The Andamanese are unique in the world in that they are a South Asian people who are known to have maintained a hunter-gatherer lifestyle down to the present day uninterrupted. Literally every other South Asian population has evidence of mixture with West Eurasian groups in the last 10,000 years, with the typical South Asian being about an even mix of West Eurasian, and an indigenous population with roots in the subcontinent that go back to the Pleistocene. It would be false to say that the Andamanese are ancestors of modern Indians. First, they’re not an ancient people, but a modern population. Second, the last common ancestors between mainland Indians and Andamanese probably date to the Pleistocene, on the order of ~20,000 years ago or so. They are genetically important because they allow researchers to make inferences about Indian populations which no longer exist without mixture with West Eurasians. But, they are no more ancient or pure than any other group of people in the world.

With that, this article in The New York Times strikes me as tragic, and exposes a lacunae in the ideals of universal morality that most moderns espouse, A Killing Tests India’s Protection of an Aboriginal Culture. The gist is that the Jarawa people, who are to some extent presumed an uncontacted tribe which is left to its own devices, have a tradition of killing infants born to widows and those of mixed-race (presumably fathered by non-Jarawa men). The authorities on the island have generally looked the other way when these babies were were killed, but recently the death of a 5 month old by drowning has prompted authorities to begin an investigation into the murder.

Here’s an important section:

Even before the police heard of the baby’s killing, the authorities on South Andaman Island were struggling with the question of whether to allow the Jarawas, who are classified as a “particularly vulnerable tribal group,” more access to the world outside their reserve.

The top official on the Andaman Islands, Lt. Gov. A. K. Singh, said that upon taking up his post in 2013, he had encountered two schools of thought. One, held by officials and academics on the left, he said, was that “any contact of the primitive tribe with modern civilization has been detrimental.”

The other school questioned how the government could deny the tribe the benefits of modern life. “Mankind has progressed by leaps and bounds,” Mr. Singh said. “Are they to remain in that state? Have we given them the choice?”

Zubair Ahmed, a journalist, said the policy of minimizing interaction with the Jarawas had run into a problem: Members of the tribe are curious about what surrounds them.

“We have seen them coming out, coming out on their own,” Mr. Ahmed said. “You cannot push them back inside the forest. They want to have a phone. They want to ride in a vehicle.”

nihms137159f4 First, the Jarawa uniqueness is not in their genetics, but in their culture. The reality is that these children don’t need to be killed to maintain cultural integrity, since they are going to be raised in their mother’s culture in any case. Nepal is 80% Hindu, but far less than 80% of its genetic character is typically South Asian (specifically, there’s a lot of Tibetan/Himalayan ancestry in many Hindu groups, including among Nepalese Brahmins). The Jarawa are not that genetically unique; they are descended from an African population that left ~50,000 years ago, just like all non-Africans are. They’re not really pure, as such, but simply isolated and moderately unique. If genetics was so important they should all get genotyped or sequenced before they are assimilated, which seems inevitable.

Second, if you really care about maintaining a reserve of Andamanese uniqueness the Jarawa are not what you want. As is noted above, and highlighted in The Land of the Naked People, the indigenous people of the Andamans are attracted to modern ways just like every other group in the world. When they encounter sugar and alcohol, they’re drawn to them, though as hunter-gatherers their morbidity is often very high. And in any case, the Sentinelese are a truly isolated people, not cohabitating in the same land as settlers from the mainland. The absorption of the Jarawa would not be that consequential with that taken into consideration.

Finally, passages like this illustrate why liberal universalism (and institutional ethical religions) became ‘a thing’, so to speak:

Others go further, saying the state has no business interfering in the tribe’s tradition of killing children of mixed blood.

“Such things were usually ignored,” said Samir Acharya, an activist with the Society for Andaman and Nicobar Ecology. “I think they have the right to maintain the purity of their race. If they decide such a child should be wasted, let them do it.”

The Jarawa are humans, and as humans they should be subject to laws. They are not a nation-state, and live within India. Because of their vulnerability to diseases, as well as their hunter-gatherer lifestyle, there is great danger in integrating them into the modern world. But it is their right as humans if they so choose. And, as humans they are also subject to the same bans on activities such as infanticide.

 
• Category: Race/Ethnicity, Science • Tags: Andaman Islanders 
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舒淇“Seek knowledge even in China”

- Muhammad

One out of five people in the world today are of the Han ethnicity. Colloquially known as Chinese. Like the West China has a long history, and its development can be traced, more or less, over the past 3,000 years. Because of the history of a system of taxation coordinated from the center we also know about aspects of its demographic expansion as a social, cultural, and biological entity from the North China plain south toward the edges of Southeast Asia (e.g., between the Tang and Song there was a shift in taxation from the northern provinces to the southern ones because of demographics). The Retreat of the Elephants: An Environmental History of China documents the movement out of the north, and eventually the shift of the center of Chinese civilization at an equipoise between the subtropical rice consuming south threading arable sections around rugged panoramas, and the old north, where a continental temperate climate characterized fields of millet and wheat and an open landscape. These environmentally contingent models of economic and agricultural production have even been used to infer broader social-cultural patterns which characterize Chinese civilization, such a recent paper in Science, Large-Scale Psychological Differences Within China Explained by Rice Versus Wheat Agriculture.

history-of-china But when you are focused on the genetic origins and distribution of Chinese populations, the answers are a bit different from the cultural history. In History and Geography of Human Genes L. L. Cavalli-Sforza reported that North and South Chinese were genetically very distinct; with the northern populations being closer to northern Northeast Asians and the southern ones closer to Southeast Asians than either were to each other. He was wrong. Genome-wide analyses make it clear that Chinese populations exhibit relatively little intra-ethnic variation, though the southern groups are closer to Southeast Asians, in particular Tai and Vietnamese, and the northern Chinese are similar to Koreans and other Northeast Asians.

To get a sense of this, I plotted some East Asian HGDP groups with 1000 Genome Chinese on Pcaso. You can manipulate and examine the PCs yourself. What you see is that Southern Chinese are very distinct from the HGDP samples from northern China. The individuals from Beijing span the whole range of Han variation, probably because Beijing is a cosmopolitan city. Across PC 1 the South Chinese are clearly positioned between the North Chinese and Tai and Vietnamese. Fromm this can we conclude that the South Chinese emerge from an admixture event between migrants from the north and indigenous peoples? Not necessarily. Or at least there may be more to the story than a PCA can tell us.

china I ran TreeMix 10 times, and the graph to the left is pretty representative (I rooted with Cambodia and removed some of the groups you can see in the PC). You can view all the other plots in Dropbox. These graphs do seem to suggest that the South Chinese population has received substantial admixture from an indigenous Southeast Asian population. What I’m curious about though is the relationship of central Chinese ethnic minorities like the She people to the Han majority. On the PC plots the She and Southern Chinese are basically in the same position. But not so in TreeMix, where the long branch out toward the She tip indicates some sort of bottleneck or lower effective population. In addition, the Southern Chinese are near the She, but the gene flow is moving from a Tai or Vietnamese group on TreeMix. Why?

One model which we can’t necessarily reject at this point without further investigation is that like the Hui the ethnic minorities across China resemble nearby Han because of gene flow form the Han. Another model is that the Han absorbed in totality indigenous groups very different from the ones which were, and are, resident in the rugged hinterlands, and are today national minorities. Finally, there is the possibility that the North Chinese themselves are complex mixes due to intrusion of Turkic groups between the Han and Sui-Tang, and later back-migration from Central China as the empire expanded in comparison to barbarian groups.

Finally, the genetic homogeneity of Han and many of their national minorities (the Fst values are invariably small) suggests to me that all underwent agricultural expansion during the Holocene, but there was a second stage where the proto-Han marginalized the other groups to become so numerically preponderant. This explains the recent coalescence of ancestries across many of these populations, and the weak genetic differentiation between the Han and minorities.

 
• Category: Race/Ethnicity, Science • Tags: China, Genetics 
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twitterethnicitychart

Twitter workforce breakdown

diversity_brief_fig2 The above statistics on the labor force at Twitter compared to the overall labor force indicate that non-Hispanic whites are underrepresented in tech firms in Silicon Valley. This is true overall in prominent tech firms. 51% of Facebook’s employees are non-Hispanic whites.

So how to make sense of these sorts of articles:  Twitter’s White-People Problem? And what about passages such as this which seem to totally defy statistical/demographic reality:

 But while Twitter the platform is bustling with all types of racial diversity, Twitter the company is alarmingly white.

Twitter isn’t alone. Most of the biggest tech companies in Silicon Valley are overwhelmingly white and male. While blacks and Latinos comprise 28 percent of the US workforce, they make up just 6 percent of Twitter’s total US workforce and six percent of Facebook employees.

Of course this is just a lie. Very few people would say a workforce that is 50 to 60 percent white, true of both Google and Microsoft, is “overwhelmingly white.” In fact, it’s less non-Hispanic white than the US labor force as a whole. I’ve linked to statistics in this very piece. They take about 10 seconds of browsing search queries to understand this.

But you don’t need to know statistics. Eat at a Google cafeteria. Or walk around the streets of Cupertino. There is no way that one can characterize Silicon Valley as overwhelmingly white with a straight face. Silicon Valley is quite diverse. The diversity just happens to represent the half of the human race with origins in the swath of territory between India and then east and north up to Korea.

The diversity problem isn’t about lack of diversity. It is about the right kind of diversity for a particular socio-political narrative. That’s fine, but I really wish there wasn’t this tendency to lie about the major obstacle here: people of Asian origin are 5% of the American work force, but north of 30% in much of the Valley. If you want more underrepresented minorities hiring fewer of these people would certainly help. In particular the inflow of numerous international talent coming from India and China could be staunched by changes to immigration law.

But these are international companies. Though they genuflect to diversity in the American sense (blacks and Latinos), ultimately they’ll engage in nominal symbolic tokenism while they continue on with business, with an increasingly ethnically Asian workforce and and increasingly Asian economic focus. Meanwhile, the press will continue to present a false caricature of a white workforce because that’s a lot more of a palatable bogeyman than Asian Americans and international tech migrants, and the liberal reading public seems to prefer the false narrative to engaging with reality.

Addendum: The first article was in The Nation. Take a look at their masthead. Most of the names I recognize are mighty, perhaps even alarmingly, white….

 
• Category: Race/Ethnicity • Tags: Race 
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Youngronaldfisher2In New Creationists a philosopher at Duke recounts his experience when he attempted to explore the implications of group differences in ethics. He stated:

After reading some recent work on the biology of group differences last summer, it occurred to me that as an ethics professor, I should write something about the moral upshot: if there are such differences, what are the consequences for how we should treat one another? Should we support policies that attempt to equalize opportunities only if they produce equal outcomes?

My conclusion was modest: if there are biological differences between groups, and if, as Lee Jussim has argued, some stereotypes turn out to be accurate in part because of correct generalizations about biological differences, these facts should not undermine our commitment to treating one another as moral equals, or to increasing opportunity for all, regardless of group membership.

But I had committed a sin in the eyes of the two referees who read and commented on my paper. I simply acknowledged the possibility of group differences while arguing that whether or not they exist, they should not matter. For having done that, the two journal referees used expletives and exclamation points to give the most venomous and dismissive feedback I have ever encountered. (Needless to say, the paper was not accepted for publication after such hostile comments.)

 

This is obviously a touchy subject to many reasons. But, the extremely vehement reactions on this topic reveal an aspect of how ideas are policed in our society. Because I have a particular reputation I am privy to viewpoints from many people that they would be terrified to share with others. For example, many young geneticists seem to view the idea that “race is a myth” to be a noble lie.

There are legitimate issues in regards to phylogenetic classification systems. But, the key that many geneticists have noticed is that the lay public makes incorrect inferences from the assertion that “race is a myth.” For example, many people are confused as to why human populations exhibit structure, and one can generate phylogenetic trees. That’s because people translate the idea that race does not exist to one where human population structure is arbitrary and trivial. The conclusion obviously does not follow, depending on your definition of race. But I think one can see how the educated public is coming to these conclusions.

Here’s an article from the year 2000 in Do Races Differ? Not Really, Genes Show:

Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level. But the more closely that researchers examine the human genome — the complement of genetic material encased in the heart of almost every cell of the body — the more most of them are convinced that the standard labels used to distinguish people by “race” have little or no biological meaning.

They say that while it may seem easy to tell at a glance whether a person is Caucasian, African or Asian, the ease dissolves when one probes beneath surface characteristics and scans the genome for DNA hallmarks of “race.”

On the one hand there is an aspect of this article which is almost quaint. Note the references to 80,000 genes and such. But the general spirit captures the modern Zeitgeist well, and it is not dated at all. The idea of race implicit in this piece, and commonly held by the general public, is typological. That is, races are like Platonic ideal forms, and genes and traits are used to explore these ideal forms.

This is false. Races are not like ideal forms. That’s in part because modern human populations are by and large the consequence of massive admixture events between deeply diverged lineages. But, that does not negate the reality that population structure is a robust phenomenon, and, that its consequences are not trivial. My hunch is that some of the eye rolling that I’ve seen when younger geneticists refer to the idea that race is a myth has to do with the fact that population structure is such a big deal for genome-wide associations.

One of the implications of the above passage is that visual inspection allows for a clearer differentiation between individuals from different populations than genetics. This is false. As it happens the groups referred to above are among the most differentiated, as they don’t share common ancestors for ~40,000 years (South Asians on the other hand share ancestry with both “Caucasians” and “Asians” over the last 40,000 years), and are positioned at the extremities of the Afro-Eurasian world island. Genomics actually gives a clearer and more precise picture of population genetic differences.

The problem, if there is one, is that these population genetic differences are not necessarily good fits if one assumes a Platonic model of racial categorization. I think this explains the irritation and frustration with people who are confused as to the ancestral quantification results from firms like 23andMe. The results are true, and robust, reflections of genetic variation. But population groups are reifications, attempting to squeeze human digestible insight from systematic variation at hundreds of thousands of markers whose pattern of differences are a consequence of tens of thousands of years of population history.

Which brings me to the UNESCO statement on the Race Concept. Published around 1950 in a few versions these statements were signals that there was a change in the winds after World War II. Much of today’s conventional wisdom is prefigured in these statements. But if you read the 1952 version much of it is pretty moderate and I think it would be seen as “problematic” by many thinkers today. There are many familiar names (and some not familiar to me) in terms of scientists consulted. E.g., H. J. Muller, Theodosius Dobzhanksy and Ernst Mayr. But for me R. A. Fisher’s comments stood out. I knew he was a dissenter from the statement, but I’m going to cut and paste the whole section from him because I think it’s pretty interesting (and many might agree with him):

In so far as the Statement condemns any defamation of races and emphasizes the appalling nature of the recent abuse of racial theory, it has my full and unqualified approval. I wholeheartedly agree, also, with its explicit and implicit finding that anthropology and racial studies afford no justification for the assumption that members of any particular race are not entitled the enjoyment of all fundamental rights, or for any form of racial discrimination. And I am very glad that, after all the horrors that have been perpetrated, these principles should have been enunciated clearly and publicized widely by an organization of such standing and by distinguished men as the authors of this Statement.

But the Statement also purports to be an authoritative body of scientific doctrines, and this is quite a different matter. Without touching upon the content of these doctrines, and quite apart from whether or not they meet with my approval, I must register my fundamental opposition to the advancing of scientific theses as such, and protest against it.

I recall the National Socialists’ notorious attempts to establish certain doctrines as the only correct conclusions to be drawn from research on race, and their suppression of any contrary opinion; as well as the Soviet Government’s similar claim on behalf of Lysenko’s theory of heredity, and its condemnation of Mendel’s teaching. The present Statement likewise puts forward certain scientific doctrines as the only correct ones, and quite obviously expects them to receive general endorsement as such. I repeat that, without assuming any attitude towards the substance of the doctrines in the Statement, I am opposed to the principle of advancing them as doctrines. The experience of the past have strengthened my conviction that freedom of scientific enquiry is imperiled when any scientific findings or opinions are elevated, by an authoritative body, into the position of doctrines.

A different section of statement relays Fisher’s view of the empirical realities, which would make him extremely unpopular today:

Sir Ronald Fisher has one fundamental objection to the Statement, which, as he himself says, destroys the very spirit of the whole document. He believes that human groups differ profoundly “in their innate capacity for intellectual and emotional development” and concludes from this that the “practical international problem is that of learning to share the resources of this planet amicably with persons of materially different nature, and that this problem is being obscured by entirely well intentioned efforts to minimize the real differences that exist”.

This sort of comment from Fisher makes sense in light of his personality. I’m tempted to think that today he would be diagnosed as being “on the spectrum.” Arguably the most eminent evolutionary geneticist of the 20th century, he also made many original contributions to statistics. But as documented in his daughter’s biography of her father, he was a monomaniacal and selfish person, who lacked many social graces. There is a section in R.A. Fisher: The Life of a Scientist which documents his tendency to engage in arguments with people who shared his general conclusions on a given topic, but where he believed they engaged in fallacious reasoning (in this he seems to resemble Karl Popper). This tendency is clear above. Though he agrees with a broad liberal humanitarianism which looks darkly upon considerations of race, he disagrees with the presumption that these values are rooted in empirical facts.

Finally, I want to quote page 238 of my edition of The Genetical Theory of Natural Selection:

The general consequences of race mixture can be predicted with confidence…Their general character will therefore be intermediate, but their variability will be greater than that of the original races. Morever, new combinations of virtue and ability, and of their opposites, will appear in the mixed race, combinations which are not necessarily heterozygous, but may be fixed as permanent racial characters. There are thus in the mixed race great possibilities for the action of selection. If selection is beneficient, and the better types leave the greater number of descendants, the ultimate effect of mixture will be the production of a race, not inferior to either those from which it sprang, but rather superior to both, in so far as the advantages of both can be combined. Unfavorable selection, on the other hand, will be more rapidly disastrous to a mixed race than to its progenitors. It should of course be remembered that all existing races show very great variability in respect of hereditary factors, so that selections of the intensity to which mankind is exposed would be capable of producing rapid changes, even in the purest existing race.

41PHSZN6AEL Fisher was writing this in the 1920s. This was near the tail end of the peak of white supremacy across the world. Charles Davenport, the director of Cold Spring Harbor Laboratory, published Race Crossing in Jamaica in 1929. It presented a view where mixed-race children suffered due to crossing between diverged lineages. This was not an atypical view at the time. The man whom Fisher succeeded to a great extent as Britain’s most eminent statistician, Karl Pearson, was a socialist and feminist (Fisher was a political conservative whose views on women were more regressive than Pearson) who also believed that inter-group competition with “inferior races” was a major driver of the evolutionary progress of Europeans. The above passage shows that Fisher’s logical mind internalized Mendelianism and its necessary implications to such a great extent that as early as the 1920s he was already dismissive of the racialism ascendant at the time. But by the 1950s the dominant viewpoint differed, and here Fisher again stood his ground, not changing the things he had written in the later eugenic sections of tGToNS.

Note: R. A. Fisher had some unfortunate views on smoking. See When Genius Errs: R. A. Fisher and the Lung Cancer Controversy.

 
• Category: Race/Ethnicity, Science • Tags: R. A. Fisher, Race 
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ncomms10326-f351IQSePVDRL._SY344_BO1,204,203,200_ It has been an open question for historians of the fall of the Roman Empire the extent to which ethno-tribal migrant caused the transformation toward the post-Roman order. In Britain, for example, there has long been debate as to whether the shift from a predominantly Celtic population with a cosmopolitan Latin-speaking patina (at least demographically in terms of origins; I understand there are those who argue that late-Roman Britain was predominantly Latin-speaking), was due to a mass migration of Germans, or more a matter of institutional and cultural defection and conversion. In the early 20th century the model in vogue was predicated on migration. The Welsh and English were perceived by many to be distinct races, with the latter having affinities with the Germanic peoples in blood as well as speech. In the late 20th century the pendulum swung in the other direction. I recall reading Norman Davies’ The Isles in 2000, and he relayed the conventional view of historians of the period that the post-Roman world of Britain saw the conversion through elite emulation of Britons into Saxons (and Angles and Jutes) based on documentary evidence of co-existence and subordination of a Celtic population in early Anglo-Saxon England.

Ten years later Peter Heather wrote Empires and Barbarians to resurrect a moderate migrationism for the post-Roman world. What he was rebutting was the perception that the idea of German folk migrations, which included the movement of women and children along with men, was a post hoc myth. Though even the most extreme cultural constructionist would assent to the proposition that some Germans did migrate into the late Roman world and capture the post-Roman successor states, they usually emphasized that tribal identities were ad hoc, novel and newly constructed, and German identity was highly malleable easily co-opted by aspirant non-Germans. In other words, the Goths, Vandals, and Anglo-Saxons were motley coalitions of opportunists, whose ethnic self-identity was a matter of recent myth.

Some of this is certainly true. Going back to Anglo-Saxon England, Alfred the Great’s early genealogy is littered with names that seem to exhibit a British, not German, provenance. It is not unreasonable that British warlords would on occasion switch sides to maintain their position at the top of the status hierarchy, just as some Visigothic nobles in Spain after the Muslim conquest converted to the new religion and became progenitors of the local Islamic aristocracy.

But we shouldn’t go too far. Last year PoBI finally published their paper, The fine-scale genetic structure of the British population, and confirmed the suggestions of earlier genetic work that a substantial proportion of the ancestry of the contemporary English population derives from Germans. Not the majority, but a substantial minority. In other words, Peter Heather was correct in England. Cultural change was catalyzed by substantial demographic change. There is more and more evidence that in two areas of the post-Roman world where Romanitas faded, with the local decline or extinction of Christianity and Roman speech (whether Latin or Greek), Britain and the Balkans, there was substantial demographic change induced by a migration into Roman territory of Germans and Slavs respectively.

51sdHZvYfTL._SX334_BO1,204,203,200_ With that, I submit two open access papers on ancient genomes from Britain: Genomic signals of migration and continuity in Britain before the Anglo-Saxons and Iron Age and Anglo-Saxon genomes from East England reveal British migration history. The plot at the top of this posts shows a striking result: most of the Roman era individuals are genetically least differentiated from the Welsh, and modern East Anglians are the most shifted toward the Dutch. This is exactly the pattern we would expect from archaeology, as the pale of German settlement was along the Saxon Shore.

So genetics tells us that extreme positions of total replacement or (near) total continuity are both false. Rather, the genetic landscape of modern England is a synthesis, with structure contingent upon geography. But, it also shows us that substantial demographic change which produces a genetic synthesis can result in a total cultural shift. Though we may think of elements of culture as entirely modular, with human ability to mix and match components as one might see fit, the reality is that often cultural identities and markers are given and taken as package deals. But, it probably took the transplantation of a total German culture through a mass folk movement to give the Saxons enough insulation from the local British substrate to allow them to expand so aggressively and become genetically assimilative and culturally transformative.

 
• Category: History, Race/Ethnicity • Tags: Anglo-Saxons, Genetics 
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Sharia should be law of land Muslims who believe sharia should be law who accept death penalty for apostasy % of Muslims who accept death penalty for apostasy
Afghanistan 99% 79% 78%
Pakistan 84% 76% 64%
Egypt 74% 86% 64%
Palestinian territories 89% 66% “59%
Jordan 71% 82% 58%
Malaysia 86% 62% 53%
Iraq 91% 42% 38%
Bangladesh 82% 44% 36%
Tunisia 56% 29% 16%
Lebanon 29% 46% 13%
Indonesia 72% 18% 13%
Tajikstan 27% 22% 6%
Kyrgyzstan 35% 14% 5%
Bosnia 15% 15% 2%
Kosovo 20% 11% 2%
Turkey 12% 17% 2%
Albania 12% 8% 1%
Kazakhstan 10% 4% 0%

41nsHqj5QIL._SY344_BO1,204,203,200_ The above data is from Pew. Questions were asked only of Muslims. In some nations, such as Turkey, “Muslims” include basically the whole population, at least nominally. In others, such as Malaysia it is somewhat over half the population. The first response column is the proportion of Muslims who wish to enact sharia as the law of the land in a given nation. The second set of responses are those Muslims who agree with the first question, and also agree with the traditional death penalty for apostates in Islam. Multiplying the two out, and you get the total proportion of Muslims in a given country who assent to the traditional death penalty for apostates in Islam. This is probably a floor, in that a minority of those Muslims who don’t want sharia enacted may agree with the death penalty for leaving Islam for a variety of reasons (Muhammad Ali Jinnah, who was neither personally religious or observant, nevertheless defended the killer of a “blasphemer” during the British period on the grounds of communal honor).

What you see above are a range of attitudes, and interesting conflicts with public practice. In Indonesia it is not illegal to convert from Islam to another religion, and this is done. But about ten percent of the population still accepts the death penalty for apostasy, at least nominally. In Malaysia it is very difficult for an ethnic Malay to convert to another religion, as the connection between that identity and Islam is quite close, though there is often more latitude for non-Malays. About half of Muslims accept the death penalty for leaving Islam. The difference between Indonesia and Malaysia probably is a reflection of divergent social norms which arose in different historical contexts (in Indonesia, the conflicts were as much between Muslim groups of various sects and ethnicities, while in Malaysia the cleavage was more between the non-Muslim Chinese and the Muslim Malay). Just because a given percentage agree with the death penalty for apostasy does not entail that they’d automatically kill an apostate personally, but it probably indicates a level of tolerance and acceptance of intimidation and violence directed toward the act of apostasy.

51+cUvOGl1L._SY344_BO1,204,203,200_ It is instructive to compare Bangladesh and Pakistan. About ~1/3 of Bangladesh’s Muslims (~90% of the population) agree with the death penalty for apostasy, while ~2/3 of Pakistan’s Muslims (>90% of the population) do so. The reason that there is no campaign against secular bloggers in Pakistan is that secular bloggers in Pakistan would be insane to be as public and vocal as their equivalents in Bangladesh. With the majority of the population accepting the legitimacy of capital violence against those who are more extreme in their defiance of religious orthodoxy, the equilibrium state is for that dissent to exist in an underground fashion. Bangladesh is somewhat different because of its peculiar history. As a multi-ethnic nation which was to serve as the state for the Muslims of the Indian subcontinent Pakistan’s attachment to religious identity is nearly necessary. In contrast, Bangladesh’s origins occurred through a rebellion by a left-wing nationalist movement grounded in the ethnic rights of Bengalis within the then Pakistan (and an Indian intervention!), and predicated on a common linguistic heritage. The national anthem of Bangladesh was written by the Hindu Bengali Tagore (compare the lyrics of the Bangladesh anthem with Pakistan’s).

There is a culture-war within Bangladesh, and it is conditioned on an understanding of the nation’s identity in religious terms. This is clear when you notice the official name of the nation: the People’s Republic of Bangladesh, a nod to the dominant party’s affinity with 20th century socialism. But, in 1988 Islam was also added as the “state religion,” a move that was rumored at the time to be motivated by potential aid largesse from Middle Eastern petrostates. In contrast, Pakistan is the Islamic Republic of Pakistan.

This is the context of the literal war within Bangladesh between those aligned with Islamism of various sorts and their critics, who range from non-Islamist Muslims to intellectuals from a Hindu background and outright atheists. Over the weekend there was another attack, prompting protests. Here are some relevant aspects:

Hundreds of people, including writers, publishers and bookshop owners, took to the streets of the capital, Dhaka, on Monday to protest against what they said was government inaction over a string of attacks, including the murder on Saturday of a publisher of secular books.

Rallies were also held in other cities and towns to demand more protection for publishers, bloggers and writers, some of whom have fled the country or gone into hiding.

The people who have so far fallen victim to the attacks are thinking people, those who believe in freedom of expression, and those who believe in secular values. A series of killings have taken place but now the focus is on publishers … I feel absolutely traumatised,” said Mohiuddin Ahmed, a publisher in Dhaka.

Fears of Islamic extremist violence have been rising in mainly moderate Muslim-majority Bangladesh after four atheist bloggers were murdered by machete-wielding attackers this year.

Two foreigners – an Italian aid worker and a Japanese farmer – have also been killed, while Dhaka’s main shrine for the small local Shia Muslim minority was bombed last month, killing two people and wounding dozens.

While it was believed to be the first attack on Shia Muslims in Bangladesh, in the past two years banned Islamic militant groups have killed more than a dozen Sufi Muslims and attacked Hindus and Christians.

The killing of foreigners has worried the country’s expatriate community and threatened its fragile economy, which is heavily reliant on foreign aid and a $25bn (£16bn) garment industry making clothing for international brands.

Points I want to note:

* Dhaka is a city of ~15 million, but “hundreds” of people show up at a protest. Lots of people are sitting this out, because they are scared. But, the terror is not such that some people won’t bravely stand up for freedom of expression, even for a group which is uniformly reviled within Muslim societies as traitors.

* Rallies outside of Dhaka suggest that the cultural division here is national, and not a function of metropolitan cosmopolitanism (it plays out a bit in my family, which divided down the middle between more religious and less religious).

* The attacks on intellectuals have a dark resonance for many Bangladeshis. During the war against Pakistan many creative intellectuals were killed in a targeted manner by the army because of their utility to the independence movement. And, it is known that some of the Islamist groups have roots which go back to pro-Pakistan elements during the 1971 war.

* The attacks on Shias indicates that these activists are adopting the norms of international Sunni Islamists, who target Shia. The attacks on foreigners also suggests that they want to move the needle on the climate in Bangladesh in terms of openness, trade, and general tolerance.

* Over the years Bangladesh, despite its corruption and political paralysis, has kept its head down in terms of international entanglements and domestic Islamic violence. This has allowed for the development of a non-aid based economy, and a flourishing NGO sector. The sort of institutional stability needed for this sort of development to proceed could easily be suborned by sectarian violence.

It strikes me that we’re at a precipice. The last time I went to Bangladesh was in 2004. If these killings continue, then I may not go back for decades. The government has a problem, in that it’s not very effective, and, there is probably some popular sympathy for this sort of violence, which the rival center-right Bangladesh National Party will want to tap into.

There are many people whose feelings on this issue are rather confused and inchoate. Here’s something from reddit (in response to someone posting one of my posts):

I feel like its one of those new ‘modern’ trends to declare oneself atheist in Bangladesh. Atheist muslims have always existed and will always continue to exist, its nothing new. As long as you arent shoving your views down other people’s throats or hating on other people’s beliefs (or lack of beliefs), there’s nothing wrong with it at all. Even in Islam, the only time capital punishment is applied to an atheist is when the atheist is going around giving hate speeches against the religion. Religious hate speech is punishable by law under Islam. But as far as your belief goes, how would anyone even know what’s in your heart?? Belief is a very personal thing, and no one can be certain of what’s in someone’s heart but the person and God himself.

I am very religious and very spiritual, but I was born and raised in Canada so I have friends of various faiths. We all share our beliefs and try to see things from each others’ points of views, but we never disrespect each other or put down each others’ beliefs even if something doesn’t make sense to us. The problem with these “modern” attention-seeking atheists is that they try to declare their views (atheism) by insulting the views of others (theism). Just because you have a difficult time comprehending the possibility of a universe outside our material universe, it doesn’t mean that other people can’t grasp this concept. Personally, I really dislike closed-minded, one-sided, ignorant people. Whether that’s an atheist or a theist is irrelevant. The ‘modern’ atheists in BD are all just closed-minded, arrogant, one-sided, ignorant attention-seekers. There’s nothing ‘educated’ or ‘enlightened’ about them at all.

To which one commenter responded: “Sure, but should they be chopped up with machetes in public?”

I can agree that many atheists are obnoxious, including myself on occasion. I find many religious people obnoxious too, but they should be free to practice and preach. Growing up in a Muslim milieu I can tell you that many Muslims were offensive and obnoxious when it came to generalizations about other religions, in particular Hindus. That’s their liberty in the United States of America, we don’t live in India where “hurt feelings” rule the day with an iron grip.

To me it is interesting that many liberals I see on the internet with whom I am on good terms otherwise with seem more focused on policing “Islamophobia” than in the genuine illiberalism which is so common among today’s 1.5 billion Muslims. So in response to the killings I put up a tweet which was self-consciously inflammatory:

The_God_Delusion_UK But, this is the United States, and you can say harsh things about religion. In particular, this religion has been sanctioning death to those who criticize it for a while now, so I take my American liberty to criticize when I can. Nevertheless, some were more curious about the jibe against Islam than the fact that people in Bangladesh are getting killed for criticizing Islam.

The data are what they are. I’ve pasted some of this at the top of the post to show how deep the animus goes against dissenters in Islam. And by Islam, I mean Muslims. Yes, Kosovo is tolerant. But there are fewer than 2 million people who live there. In contrast, Pakistan has nearly 180 million Muslims!

Several years ago the financial journalist Heidi Moore decided to “whitesplain” Islam to me. Her contention was that Richard Dawkins was racist and should not generalize about Islam. Similar barbs have been thrown at Sam Harris. As a point of fact I believe many of the things that Dawkins and Harris have said are not grounded in an empirical basis, nor are their analytic frameworks to my liking. But, I also think it is ludicrous to assume that their attitude toward Islam is rooted in racism, as opposed to a generalized distaste for monotheism, as well as a concern for the intolerance against atheists which is so common within the world of Islam and among Muslims.

The reality is that many liberals who are deeply worried about Islamophobia know as much about Islam as Ben Carson does. That’s a fact. I say this as someone who knows a fair amount about the religion, despite my obvious distaste for it. The arguments that American liberals and conservatives have about Islam are not about Islam, but about each other’s self-perceptions, and their cartoon of what Islam is.

That’s “problematic”, as they would say. There are 1.5 billion Muslims, and many of them are on the move. They’re going to be in your neighborhoods, assuming you aren’t part of the socioeconomic elite, which will no doubt insulate itself from the diversity that it welcomes rhetorically. We had better actually deal with reality of the world out there, rather than our own imaginings.

 
• Category: Foreign Policy, Race/Ethnicity • Tags: Islam 
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He under whose supreme control are horses, all chariots, and the villages, and cattle; he who gave being to the Sun and Morning, who leads the waters: He, O men, is Indra.

To whom two armies cry in close encounter, both enemies, the stronger and the weaker; whom two invoke upon one chariot mounted, each for himself: He, O ye men, is Indra.

- Rig Veda

Sons of Indra

Sons of Indra

Five years ago I found out that my friend Daniel MacArthur and I are members of the same Y chromosomal haplogroup, R1a. Both of us thought it was rather cool, that ~5,000 years ago there lived a man who was ancestral to us both on the direct paternal line. Five years on, and both Dan and I have sons who continue this lineage. True, surely Dan and I share more than one lineage of connection over the past ~5,000 years, the Y chromosomal one is simply the one that is genetically irrefutable since recombination does not break apart the sequence of variants, the haplotype, allowing the inference to be as simple as taking candy from a baby. The common ancestral information is transmitted as a whole block, excepting the mutations which separate us from our common forefather. Additionally, since he has attested South Asian ancestry (< 200 years), we probably share many lines of descent over the past ~3,000 years (one of Dan’s ancestors was stationed in Bengal in the 19th century, so I think our genealogies intersect a decent amount for non-related individuals).

Screenshot - 10272015 - 03:41:22 PM But there’s something special about R1a beyond the fact that it binds me paternally with a host of people who I know from all around the world. The figure to the right is from the supplements of a Genome Research paper, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. You see that R1a1 diverges by very few mutational steps, and a rake-like pattern defines the phylogeny. That is in keeping with a history of relatively recent diversification, and rapid population expansion. The Genome Research paper found that R1a, along with a host of other Y chromosomal lineages, have undergone very rapid demographic expansion over the past when put through the sieve of phylogenomic inference. This is similar to what you see with the Genghis Khan haplotype. Remember, this is a very specific signature of direct male descent. It does not necessarily extrapolate well to the rest of the human genome. So, though Daniel MacArthur and I share a common Y chromosomal lineage, he is Northern European and I am South Asian, with all that implies for the set of genealogies which come together to contribute to the patterns of variation we see in our whole genomes.

Screenshot - 11012015 - 11:20:26 AM But recently we’ve been gaining even more understanding at the phylogeography of R1a, and its likely history. To the left is a figure from the supplements of Reconstructing Genetic History of Siberian and Northeastern European Populations. You see in this chart a few important things. First, the sister to the haplogroup R, which includes R1b and R1a, and therefore huge numbers of European, West, and South Asian men, is Q, an Amerindian one. The Mal’ta boy, who lived ~24,000 years ago, seems likely to have carried a basal R1 lineage. This is reasonable because most people peg the divergence of R1a and R1b ~20,000 years ago (or somewhat more recently). A major takeaway here is that the dominant lineages across much of western Eurasia today on the male side seem to derive from a group with central Eurasian affinities. The two R1 lineages are very rare in Europe before ~4,000 years ago, according to ancient DNA. This is also concomitant with the arrival of “Ancient North Eurasian” (ANE) ancestry, which is closer to that of Mesolithic European hunter-gatherers than East Eurasians, but still rather anciently diverged, on the order of ~30-40,000 years before the present. Amerindians also have substantial admixture from this group, as do many groups in the Caucasus, and South Asia.

 

The second major issue that is evident from this figure is that Western and most Eastern European R1a diverge from South Asian and Central Asian R1a. The Altay population in this paper are Turkic, but “trace approximately 37%…of their ancestry to another unknown population, which the model predicted to be related to modern Europeans.” And, its R1a looks basal to the South Indian sample, which because it is from Singapore, is likely to be Tamil. Nearly 15 years ago in The Eurasian Heartland: A continental perspective on Y-chromosome diversity, Spencer Wells reported R1a at reasonable frequencies even among non-Brahmin South Indians. More recent work using more markers suggests that R1a has two very common major lineages in Eurasia, with one very common in Eastern Europe, and decreasing in frequency west, and another common in South Asia, with appreciable fractions in regions of Central Asia such as the Altai mountains. Going back to the earlier work, and connecting the dots, it looks like these two “brotherhoods” of R1a diverged on the order of ~4,000 years ago, both undergoing rapid expansion in different regions of Eurasia.

Oh, but there’s more! Eight thousand years of natural selection in Europe has been updated with new ancient DNA results form Iosif Lazaridis’ work. As you might know by now it seems likely that the Indo-European languages were brought into Europe by peoples related to (descended from?) the Yamna culture of the trans-Caspian steppe. The Yamna were genetically a compound population, with about half their ancestry being derived form “eastern hunter-gatherers” (EHG), who themselves were a equal compound between “western hunter-gatherhers” (WHG), the latter presumably descendants of the Pleistocene populations which had retreated to the habitable fringes of the continent, and the previously mentioned ANE group, with Siberian affinities. The other half of the Yamna peoples’ ancestry derives from something similar to that of the early European farmers (EEF), but somewhat different. In particular, rather than western Anatolian affinities, this ancestry seems more trans-Caucasian or eastern Anatolian, with Armenians and Kartvelian groups either being source population, or related to the source populations.

Intriguingly, the Yamna carry the R1b haplogroup, today rather rare in Eastern Europe, but common, and modal, in Western Europe, with extremely high frequencies along the Atlantic fringe. The new version of the preprint now reports some ancient DNA results form the successor culture to the Yamna, the Srubna. There are two intriguing aspects to the new results. First, the Srubna have nearly ~20% ancestry from a population related to the EEF. There are two possible options here. One, that there was back-migration from Europe after the initial migration west. Second, that an EEF-like migration occurred directly from the Middle East to the steppe. But now, from the preprint:

Srubnaya possess exclusively (n=6) R1a Y-95 chromosomes (Extended Data Table 1), and four of them (and one Poltavka male) belonged to haplogroup R1a-Z93 which is common in central/south Asians…very rare in present-day Europeans…and absent in all ancient central Europeans studied to date.

First things first. There are some “Out of India” theorists who posit that R1a derives from South Asia. If you take a very deep time perspective this may be true; recall that much of Eurasia was not habitable during the Last Glacial Maximum (LGM), so the distribution of populations was very different from what we see today. But, on the scale of ~4,000 years ago it seems that one can say that the very common variant of R1a found in the eastern Iranian world and South Asia likely derives from the steppe. The reasoning here is that while peoples in South Asia have elements of ancestry across their genome with affinities to the steppe people (e.g., ANE), there is little evidence for South Asian distinctive ancestry (e.g., ASI) in the steppe people. Additionally, the majority of South Asia mtDNA does not have a West Eurasian profile, but is closer to the lineages of eastern Eurasia. This is strongly suggestive of mostly male migrants. What we can say definitively is that it looks as if male lineages overturned each other multiple times on the steppe. First, R1b was dominant. Then in the same region one lineage of R1a came to the fore, only to later be marginalized by another lineage of the same haplogroup. Finally, in Central Asia more generally the Turkic migrations reshaped the whole ethnographic landscape within historical memory.

F5.mediumThough I begin this post with Y chromosomes, I will not end with them. My belief though is that the Y chromosomal story gives us a deep insight into the nature of social relations over the past ~5,000 years. More on this later. But, the constant turnover of the Y chromosomal record should clue us in to the fact that human demographic history exhibits punctuated turnover events, which reshape the genetic landscape radically over a few centuries. This is a far cry from a model of a set of serial founder events from Africa, dispersing outward as a phylogenetic tree overlain upon a spatial map over a time-scale of tens of thousands of years in Fisher waves.

Specifically, I’m referring here to the 2005 paper, Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Currently, the best rejoinder to this model is probably Towards a new history and geography of human genes informed by ancient DNA, by Joe Pickrell and David Reich. In this review the authors show that though the serial founder bottleneck framework is consistent with the data at a certain level of granularity, it is not the only possibility. What ancient DNA in particular is telling is that local geographic continuity of lineage is often very rare. This result then should make us skeptical of taking contemporary genetic variation, inferring phylogenies, and then overlaying those phylogenies upon the spatial distribution of particular ethno-linguistic groups. Of course, on a coarser scale of granularity the “Out of Africa” model inferred from older genetic work from the pre-ancient DNA era is probably correct. That is, African populations tend to harbor lots of genetic variation, and are basal in relation to non-African lineages. Or, put another way, non-Africans are a derived lineage of Africans. ~100,000 years ago almost all of the ancestors of non-Africans would have been in Africa (or perhaps the biogeographic extension of Africa in the Middle East).

But the story beyond that scale is more complex. At least some of the first settlers of Europe have no modern descendants in Europe. In fact, these populations are nearly as close to East Asians as they are to modern Europeans, suggesting that the modern east-west and north-south axes in Eurasia are products of events of the last few tens of thousands of years at most. In fact, the synthetic origins of Europeans and South Asians is strongly suggestive of the likelihood that inferences from modern genetic variation only have time depths back ~4-5,000 years or so in much of Eurasia. A recent paper in Science, Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, suggests widespread back-migration to Africa itself from Eurasia! Though I disagree with the interpretation in some details (I don’t believe that this occurred ~3,000 years ago), the circumstantial evidence from this and other studies is strong that there has been several waves of migration of Eurasian groups back to Africa. Excepting the northern fringe of the continent in no region is this preponderant, so that the status of Africa as the home of the original population of modern humans from which others derives, remains unshaken. For now.

Nevertheless, both ancient DNA and whole genome sequencing are fleshing out surprising and enigmatic details in relation to how human genetic variation came to distribute itself around the the world today. Here we can come back to Europe. Mostly because there has been a lot of genetic work on this continent, and the ancient DNA is probably thick enough that we won’t find any major new surprises. In short, the phylogenomic history of the continent over the past ~10,000 years has been “solved” more or less. What did we find out? What can it tell us about the more general human story?

nature14317-f3 We can start with the present. As noted in The History and Geography of Human Genes Europe is a very genetically homogeneous continent. The distances as inferred from allele frequency differences between two given populations is very low, and Northern Europe between the Atlantic fringe and the great Eurasian plain in particular is very uniform in terms of the total genome. Today, we know why. As outlined in Massive migration from the steppe was a source for Indo-European languages in Europe, Northern Europe was demographically shaken ~4,000-5,000 years ago by population movements triggered by peoples which left the steppe. It was not a total replacement. But the world of the first farmers, who had issued out of the Middle East ~8,000 years ago, was rocked in the north. The male Y haplogroups associated with these old farming groups, such as G2a, are found at low, though relatively even, proportions all across Northern Europe today.

One interesting aspect of the story is the huge genetic distance between some of these ancient groups. For example, that between the first farmers from the Middle East and their nearby hunter-gatherer neighbors ~8,000 years ago was of the same order as between Europeans and East Asians! This is more than ten times the larger genetic distances you can find in Europe today, but this persisted for thousands of years, though it seems that hunter-gatherer ancestry increased over time among the farming populations, likely through admixture with the local substrate. The reason for this high genetic distance is because the early European farmers carried ancestry which has been termed “Basal Eurasian” (BEu). This points to the fact that these people seem to have diverged first away from all other non-Africans when it comes to Out-of-Africa populations. In other words, ~40% of the ancestry of early European farmers is from a population which is more genetically distant from European hunter-gatherers than Andaman Islanders are. It was the arrival of the steppe people which resulted in the leveling of the genetic distances across much of Europe, overwhelmingly so in the north, and to a non-trivial extent in the south.

nihms132060f1 So if Europe went through a great homogenization and leveling ~4,000 years ago, why does the “genetic map of Europe” exist? That is, why does geography predict variation in genes so well? There are three things one might say about this. First, PC 1, the larger dimension of variation is north-south. This comports with the idea that the heritage of the early farmers persisted in the south to a far greater extent, and the Indo-European demographic impact was more modest, if not trivial. An earlier explanation I had seen floated around was that there was a north-south gradient due to expansion from the post-Pleistocene refugia, via the serial bottleneck effect. The real explanation for the north-south difference though seems more likely to be the differing proportions of Indo-European ancestry, overlain upon the early farmer and hunter-gatherer ancestry.

The second issue to consider is that the underlying genetic variation in Europe was absorbed into the expanding population. Even if the steppe invaders differed little from east to west, there were differing levels of absorption of the substrate, and after several thousand years there had likely been some divergence between the different early farmer groups, perhaps due to differing levels of admixture with hunter-gatherers. Basically, PC analysis could still pick up the signal of underlying variation even if that component was minor if the dominant element was not particularly structured (you can pick up indigenous structure in Mestizo populations in Mexico for this reason).

Finally, after the initial punctuated change, there was an equilibration as isolation by distance dynamics resulted in divergence across the North European plain. We have enough historical records to know that aside from the Slavic migrations there seems to have been little change in the population structure of Europe since the Roman period (the Saxon migrations were not trivial, but they were neither preponderant nor continent-wide in impact).

What general inferences can we glean from this specific European case? As Graham Coop’s group has noted, one must account both for continuous gene flow via isolation by distance dynamics, and pulse admixture events between very distant populations. Consider the metaphor of a forest expanding over the landscape. There will be local structure, accrued over generations, hundreds and thousands of years. But perhaps periodically a fire will sweep through the landscape and clear huge swaths of territory. Into this virgin landscape may expand forests which derive from isolated reservoirs which escape the flames. Over time geographic structuring will be evident again, and depending on the number of refuges the jigsaw puzzle of genetic islands expanding into the gaps will fade somewhat as migration smooths the edges.

The reference to fire here is conscious, insofar as fire can immolate structure which has taken generations to develop. Before the steppe people arrived in Northern Europe the first farmers had established a long-standing cultural commonwealth of sorts. Their legacy had persisted for thousands of years. Then, in a period of centuries, it all changed. Why? Culture.

Outright genocide with weapons is a dangerous business. Societies which engage in endemic long-term warfare as a primary male vocation, such as highland New Guinea, have high mortality rates. But in the context of the Malthusian world, where villages persist on the knife’s edge of subsistence, marginalization and disturbance of long-held patterns is all that might be needed for cultures to descend into famine and starvation. In 1493 Charles C. Mann notes that the mass death triggered by the arrival of Europeans and Africans to the New World had as much to do with the destabilization of society by illness as much as the illness itself. In a world where all hands were on deck to bring in the harvest, the loss of critical labor during those periods could result in starvation, and high death rates led to the rapid collapse of the institutions which served as scaffolds for the maintenance of everyday life.

The scenario then might be one where populations on the Eurasian steppe develop some of the basic elements which would lead to agro-pastoralism, and undergo population expansion. With numbers, and well fed on the agro-pastoralist diet, these tribes might have poured into the lands of the farmers as rapid mobile groups in their wagons. The pattern in antiquity down to the early modern period, from the Goths to the Mongols, was to extract rents and treat the farmers as cattle. There was no incentive for one to starve cattle, and so the demographic impact of conquests was relatively modest.

But what about a world with less institutional complexity? In a world where the basic levers of rent to extract from the conquered did not exist, the natural path would be to replace them. The story goes that Genghis Khan had hoped to turn North China into a vast pastureland by driving out the peasantry (and almost certainly killing most of them through starvation), but his sage Khitai adviser explained the wealth that could be gained by taxing humans rather than raising stock on land. But the Khitai themselves were a semi-civilized people with centuries of experience milking the Han peasantry, and were heirs to a tradition of pastoralist predation that went back to the Hsiung-Nu. And yet no doubt there was a time when the idea of collecting rents from a conquered people was an innovation in and itself. The genocidal antics of the Israelites in the Hebrew Bible strike us as dark and atavistic, but they reflect a cultural mindset which is nearly contemporaneous* with the arrival of Indo-Europeans to Europe.

This plausible sketch puts into better perspective Steven Pinker’s thesis in Better Angels of Our Nature as well as Peter Turchin’s War and Peace and War. The emergence of state institutions and pacific ideologies in the past ~3,000 years may be a sort of response to the high-stakes inter-group competitions which would level societies and turnover populations on a regular basis in the human past.

And yet not all was as sweetness and light. In terms of their total genome the differences between the Srubna and their predecessors were not very great. Conversely, the differences in the total genome between Slavic people and South Asians are legion. But interlaced more recently across the landscape of a more stable structuring of genetic variation, a great regrowth of the forest through isolation by distance equilibration if you will, has been the explosion of powerful patrilineages which trace out an intriguing skein across the landscape. The total genome signal of these men may quickly decay over the generations, as their female-line descendants lose the golden allure of their status, but their male-line descendants continue to accrue mating prowess by dint of their association with great kinship units which succeeded in a winner-take-all game with other such groups of men. On top of the story of migrations of whole peoples, and the extinction and absorption of others, is the story of bands of men operating as units, related either in truth or fictively, which extract rents across a thickly populated landscape of human cattle. Another way to state this is that the thuggish state which imposed a monopoly of violence on a chaotic world where small-scale conflict was becoming too expensive allowed for the emergence of patriarchy as we understand in its customary form. Like so many hirelings, the men charged with protecting the people, made the whole world their possession and left dreams of their people behind.

John Ross, Cherokee Chief

John Ross, Cherokee Chief

While the cultural and genetic affinities of folk wanderings were tightly coupled, I am not sure that the Y chromosomal lineages are so neat. The Hazara people of Afghanistan exhibit an Asiatic appearance in comparison to other Afghans, and their Y chromosomes suggest a close connection to the Khalkha Mongols, but they are Shia Muslims who speak Persian. It does seem that the R1 lineages ascendant in Europe and South Asia owe their success to the Indo-Europeans, but both R1b and R1a transcend a connection to Indo-European ethno-linguistic groups. In some cases, as in that of R1a in the Levant, one might see in that a submerged Indo-European element, from the Mitanni down to the later Persian and Kurdish peoples. But in other cases, such as R1b among the Basque and R1a among Dravidian-speaking tribal people in South India, what we are seeing is the long arm of the patriarchy reaching beyond bounds of cultural and genetic affinity. The great Cherokee chief John Ross was famously 7/8th Scottish in ancestry. But he was a voice for the Cherokee people nevertheless. In most places where the Mongol hordes washed over they assimilated to the cultural folkways of the people whom they conquered. Like modern corporations the patriarchies were only loosely associated with other units of human organization, even if they used them as their vehicles of choice.

And so the story ties back to the beginning. Many of us are the sons of Indra, Zeus, and Thor. The descendants of Herakles, and of Abraham who haggled with God himself. Of Ishmael, whose hand will be against everyone and everyone’s hand against him. Of Niall of the Nine Hostages, and Temujin. The interests of men like this know no nation, nations are but ends to their will. The tension we see in our modern world, between egocentric plutocratic elites jostling nation-states like playthings, might be simply the repetition of an old pattern. In the Bible Saul was rebuked for not destroying all the capital of the Amalekites, perhaps reflecting the tensions of interests which reflect the leader of a people who must act in the collective good, but have their own selfish needs and dreams of self aggrandizement for their own very particular posterity.

Addendum: Ancient DNA will expand in its ability to discern various patterns in the past. But the general disturbances will fall in line with what I have outlined above, I believe. Rather, the move will be from phylogenomics, to population genomics. Phylogenomics leverages genomic methods to attempt to infer phylogenetic patterns. Population genomics explores the classical parameters which shape the change in allele frequencies in lineages, and ultimately, deep evolutionary questions. We now know from ancient DNA that in all likelihood the phenotype which we associate with modern Europeans is a novel configuration. To some extent this is to be expected, as the basic elements which combine to form the European genome, fusing together lineages which diverged at least ~50,000 years before the present (BEu vs. everyone else outside of Africa) and ~35,000 years before the present (ANE vs. WHG), only came together around ~4,000 years ago. But there is more, as natural selection seems to have changed allele frequencies after these elements came together. That is, selection may have been operating across the European landscape when Hannibal was skirting the Alps!

And again, this is likely a general story. Physical anthropologists have long wondered why classical East Asian skeletal morphology seems to be scarce in the prehistoric past. But what if the classical East Asian appearance is relatively new? The Ainu, who have long been considered at “Lost White Race” turn out to be a basal Northeast Asian group. It may be that they retain more of the “ancestral” features of East Eurasians.

The first age of selection studies in the 2000s was fraught with confusion and false positives. To a great extent we still don’t know what to make many of the signals, which are deposited in the middle of obscure open reading frames. But the real golden age of selection will probably begin when we have more temporal transects with whole genome sequencing of ancient DNA, and with the phylogenomic context relatively robust as an interpretative framework.

* I am aware that the Hebrew Bible coalesced between thousands of the years after the arrival of Indo-Europeans to Europe, but it no doubt distills very ancient folkways. This seems obvious for example in the recollection of the Sumerian flood story.

 
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Rosenberg2007

The bar plot above shows the Kalash people in yellow as very distinctive group among a panoply of Eurasian populations. The figure is from a Rosenberg lab paper. There’s nothing aberrant about this result, you can generate this plot pretty easily by using any motley set of markers. The Kalash are distinctive. But it is important to keep the distinction in perspective. They’re not a relic population, remnants of an ancient race lost to time and memory. Rather, they happen to be a highly diverged northwest South Asian group. Their divergence is due to a small isolated breeding population which has been highly endogamous.

What this means is that the Kalash have a low long term effective population and have been more strongly impacted by drift in their allele frequency spectra. Small populations are subject to great allele frequency volatility generation to generation, and tend to lose a lot of their genetic diversity, and also fix many alleles. One consequence of this is genetic inbreeding and a higher recessive disease load. These populations with a lot of drift will have less efficacy of selection in removing deleterious alleles, and if a recessive expressing variant is fixed, then that’s that.

But another major consequence of strong drift on a population so that everyone is quasi-related for all practical purposes is that when you attempt some sort of clustering they naturally fall out as a very natural grouping. They’re low hanging fruit. When you plot populations on on a PCA you normally remove closely related individuals, because they will naturally form a tight cluster, and overwhelm the between population variation you’re looking for, hogging up all the highest dimensions making them distinct from non-relatives. Inbred groups like the Kalash do the same thing, if less boldly so. If you can keep this in mind it will allow for proper inferences about the natural history of a population. If you can’t, then you will be confused.

This is preface to a nice paper in PLOS GENETICS, Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference, which reports that an earlier publication, Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool, did not control for the effect of drift due to endogamy and so came to the wrong conclusion.* I won’t repeat the methods they used, as the paper is open access. But, they account for drift much better, and show that the divergence of a presumably genetically distinct caste had much more to do with increased drift due to endogamy than it did with the separation of the two lineages at some time in the distance past. Remember, drift builds up over any two pair of lineages which separate. But if the population size in one of the daughter lineages is very low, then drift will shift it away from the ancestral frequency spectra much faster, producing an artificially “long branch.”

The Kalash and the Ari are extreme cases of this. But they illustrate the general principle that we should be cautious about making inferences when we don’t control for the vicissitudes of demographic history, which may skew the power of our methods to see in a fair and balanced manner.

* There’s an overlap of authors across the two publications, showing that scientists do and can overturn their own conclusions if new data or analysis can persuade them.

 
• Category: Race/Ethnicity, Science • Tags: Genetics 
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Rplot26

553x457xchina-labeled.gif.pagespeed.ic.FPOfoCReDL I was having a discussion on Twitter with Jessica Chong about the nature of Chinese genetic variation. There’s been a fair amount of work on it. But, I have the 1000 Genomes data, in addition to others, and wanted to place them in their proper context myself. First, I did a preliminary PCA, and it was clear that the 1000 Genomes Northern Chinese (CHB) had a lot of Southern Chinese, and the Southern Chinese (CHS) were two distinct clusters (CHB was collected at a university). Looking up the provenance of these samples, it turns out that CHS were collected in Hunan and Fujian. So from these probably corresponded to two clusters I found in the data.

In History and Geography of Human Genes L. L. Cavalli-Sforza reported that Southern Chinese formed a clade with Southeast Asians, while Northern Chinese formed one with Northeast Chinese. Genome-wide results don’t seem to support this inference. The Han do exhibit north-south structure. But, they’re not that diverse for more than one billion individuals (Fst lower than Intra-European). As observed in whole genome sequence analyses the Han Chinese have undergone massive demographic expansion over the past 5,000 years.

I decided to run TreeMix to explore this issue further. I was prompted by the observation that North and South Chinese often show gene flow from northern and southern East Asian ethnic groups. I pushed the data set’s number of migrations to 10. This is high, I wouldn’t normally do this, but I wanted to see if there was any consistent gene flow to Han Chinese, even if it wasn’t one of the marrow edges. The results are below in the plots.

This what I can say:

1) The North Chinese have a faint migration edge from nonspecific northern Asians. Probably this is a composite signal of the past few thousand years. Or, they’re an old signal of the absorption of groups from antiquity such as the Rong and Di.

2) The Southern Chinese do have closer affinities to southeast Asian groups and ethnic minorities in the south. The group I labeled “South_China2″ is more Southeast Asian in affinity than “South_China.” These are probably Hunanesse and Fuijianese respectively. I drew these conclusions from the fact that the “South_China” group is often near a node close to the She minority, which is present in Fuijian. In contrast, the “South_China2″ cluster is often near the Tuija group, which is present in Hunan.

3) Though the North and South Chinese groups are placed on different branches of the graph in these trees note the strong migration edge, especially into the Fuijian cluster. They’re genetically not that far apart. Observe that on the PCA the southern groups seem between Southeast Asians proper, and Northern Chinese.

4) The Yakut are donors to lots of groups in North China. I’m pretty sure that this is a signal of the Turkic expansions, which the Yakut have affinities too because they’re Turkic.

5) Many of the native ethnic groups of China proper don’t seem to be that different than Han Chinese. In fact, they resemble Han in their own region. This might be gene flow, or, it might just be that the Han for whatever reason were the demographic winners over the last 4,000 years in China proper and marginalized the other groups.

 

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• Category: Race/Ethnicity, Science • Tags: China 
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51aBlSPDX8L._SX342_BO1,204,203,200_ One of the more interesting things about reading a book like The Making of Modern Japan, which is a relatively deep dive into the political and social history of Japan from 1600 on, is that it gives you an interesting window onto your own country. For example, I know from American history that there was a period of Southern dominance from the early 1800s down to the decades before the Civil War, followed by marginalization of the South in national politics. I had not known that for 50 years after the Meiji Restoration Japanese politics was dominated by a group of men who emerged from the Choshu and Satsuma domains, which were at the far west of Honshu and in southwest Kyushu respectively. These men were arguably the founders of modern Japan, and they were geographically and socially (i.e., they came from the samurai class by and large) very narrow in their origins. I had assumed that Japanese history, and the loci of power, had shifted gradually east in a unidirectional sense, from Kansai to the Kanto plain and what became Tokyo (Edo).

AinuGroup

Ainu 1904

The reason I’m fascinated by the resurgence of Choshu and Satsuma is that this is the region of Japan where the Japanese as we understand them began. That is, the Yayoi culture, which spread across Honshu between 500 BC and 500 AD, from the south and west, to the north and east. Long present before them on the Japanese islands were the Jomon people, a relatively advanced hunter-gatherer culture. They are presumed to be related to the Ainu of Hokkaido. More intriguingly, in the second half of the first millennium the Tokohu region of northern Honshu was inhabited by a non-Japanese people termed the Emishi. Some of these people apparently accompanied a Japanese embassy to the court of Tang China, and their hirsute appearance was commented upon.

A fair amount of DNA evidence seems to suggest that the Ainu and Jomon are connected and that some of the ancestry of modern Japanese descend from the Jomon. Additionally, the Yayoi were probably rice farmers from Korea. I have some Korean data, so I ran TreeMix a bunch of times. As you can see usually the Japanese and Koreans are rather close. Japan is placed closer to the Yakut though. This makes sense if the Jomon were Siberian.

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In May there was a publication that confirmed using Bayesian methods that the Japanese are a dual origin population. Instead of simple inspection and confirmation of a particular pattern, they tested an explicit set of models; replacement of Jomon by Yayoi, Jomon to Yayoi continuity, and Yayoi absorption of the Jomon. They found that the hybridization model was 29 to 63 times more likely than the replacement and continuity models. It’s great precision on what we already knew. And, if you look at their dates, the Yayoi begin to admix with the Jomon thousands of years before they show up in Japan archaeologically! They have some clever ways around this, but it seems that they’re trying to square a circle.

So today I was talking to Greg Cochran and he said someone should do some D-statistics on Ainu. Well, after I got off the phone with him I found this paper, Unique characteristics of the Ainu population in Northern Japan. They didn’t use D-statistics, but they employ and f3 and f4 ratio tests (see this paper for what all this means).

jhg201579f1 On the PC plot to the left you see a cline running from Chinese, to Koreans, to Japanese, to Ryukyuans (Okinowa and other islands). Then, on the larger PC (explains 3 times more proportion of the variance), you see a cline out toward the Ainu. In the TreeMix plots above there were gene flow edges from Southeast Asians and Yakuts into the Southern and Northern Chinese populations respectively. One could hypothesize that this reflects demographic absorption of indigenous groups by an expanding group of Han agriculturalists. The Yayoi were almost certainly part of this broader set of groups on the move. To the east you have the Japanese, but also the Han in all directions, and the various Southeast Asian groups as well.

jhg201579f2 The second PC plot is very interesting. It has a huge data set from all over Japan and a much thicker marker set (that’s why the Koreans aren’t on the plot, they didn’t overlap with it). What you see is a cline toward the Chinese, and then an axis defining the Ainu and Ryukyuan. The Ryukyuans have been found to have more Jomon-like ancestry in previous research, so it’s entirely unsurprisingly that they’re somewhat Ainu-shifted. But, observe that they are somewhat parallel to the Ainu. In all likelihood the Japan developed some population structure. The Ryukyuan and Ainu would be the northern and southern ends of the Jomon distribution, respectively. Additionally, there’s a subtle pattern in the results from the Japanese from the main islands: the Tohoku region. The authors observe that these samples, highlighted in red, seem skewed. And not toward the Hokkaido Ainu. In all likelihood that means that the Emshi were another branch of the broader Jomon population, distinct from the Ainu, and those peoples to the south. Additionally, there’s probably a “Jomon-cline” within Honshu, with more the further you go from the far west of Japan.

jhg201579f3 For the f4 ratio tests to determine admixture across a specified topology, they used the one to the left. It seems reasonable enough to me. By all phylogenetic results that I’ve seen the highest probability seems to be that the Ainu are a branch of Northeast Asian people if any. Roughly they find that the Jomon ancestry for mainland Japanese is a bit less than 20%, and for Ryukyuans it is a bit less than 30%. Reference population matters, so these are not gospel estimates. Probably they are a slight underestimate if I had to guess, as the Ainu are not perfect proxies for the Jomon.

Finally, they used rolloff to estimate admixture dates. For the mainland Japanese it was about 1,500 years ago. For the Ryukyuans it’s closer to 1,000 years ago. This dovetails well with the order in which the Yayoi occupied these regions. I wouldn’t, and they don’t, take the dates as gospel. They probably are underestimates (see The Spatial Mixing of Genomes in Secondary Contact Zones for some good arguments and results which indicate these methods underestimate time since admixture). But, they’re far closer to the archaeology than what the other paper above found, and don’t require a lot of special conditions to make the genetic inferences align with the rest of reality.

Japanese actress But the most interesting part of this paper is not the phylogenomics. I’ll just quote:

We also identified SNP loci that are differentiated between the Ainu and Mainland Japanese by using pairwise Fst values. The pairwise Fst values ranged from 0 to 0.8903, with a mean of 0.0407. The majority of the SNPs (approximately 400 000) have Fst values of less than 0.02. We picked 6413 SNPs that were within the top 1% and had Fst values higher than 0.36. The Fst values and annotations for these top 1% SNP are listed in Supplementary Table 1. Within those top 1% of SNP, some of them were found in genes reported to be associated with facial structure in Europeans2…and hair and tooth morphology in East Asians…The distribution of Fst values for SNPs in those genes are shown in Figure 4. Two out of five genes for facial morphology (PAX3 and COL17A1) contain highly differentiated SNPs, as with the hair/tooth morphology gene (EDAR). The results of gene annotation analysis on those top 1% SNPs showed enrichment for biological processes and cellular components involving collagen (Supplementary Figure 8).

The derived variant of EDAR is found in high frequencies in both East Asians and Amerindians, so it has to be somewhat old. But in places like Korea it’s very close to fixation. To me the high pairwise Fst on this gene is a tell that the Ainu did look very different when they were numerous and not admixed, even if they shared Pleistocene ancestry with the incoming Yayoi. That being said, when I looked at the list of genes that back with high Fst hits in their supplemental table a lot of them looked very familiar. So we should be cautious about over-imputing form these results. But perhaps with a better exploration of the genomics of these phenotypes we can figure out the details of the epicanthic fold…though I suppose phenotyping adults would be a little strange in Korea.

Finally, the very last sentence kind of annoys me: “If we consider a very unique genetic status of Jomon people, then it is understandable that Ainu people, who inherited the highest proportion of Jomon DNA, are quite unique among all extant East Eurasians.” I am curious how the Ainu and the Jomon relate to other Asian, an non-Asian, people. Normally I don’t do anything like this, but I sent an email asking for the genotypes to test myself.

 
• Category: Race/Ethnicity, Science • Tags: Japanese 
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Kalash women in traditional clothing

Kalash women in traditional clothing

Ayub Khan with a German general

Ayub Khan with a German general

If you read Nell Irvin Painter’s The History of White People you will learn that the white race is a social construction of relatively recent vintage. When I read her work in 2011 I was a touch annoyed by it, because a lot of interesting empirical data was shoehorned into her thesis and preferences. In relation to her putative topic, she wasn’t a big fan (I don’t doubt that Painter likes white people as humans, but she obviously thinks that the invention of the white race was not a good thing). I have serious reservations and objections to these sorts of Manichaean frameworks. And yet over the last few years I have come to a very different but new perspective: I believe white people emerged biologically only in the past 5,000 years, on the edge of history and prehistory. I think a plain reading of the race concept in biology is entirely defensible so long as you integrate population thinking. But, human races are not primordial. They aren’t even Pleistocene.

Book-cover-UK This brings us to the Kalash of Pakistan. They are pagans who live in the fastness of the Chitral. Their cousins on the other side of the border, in Afghanistan, are the Nuristanis, who were foricbly converted to Islam in the last decade of the 19th century. The Man Who Would be King takes place among the Nuristanis, who were then termed Kafirs. It was written in 1888, before the conversion to Islam. The Kalash were in British India, so spared from conversion. It seems unlikely that they will persist beyond this generation due to the social-political milieu of modern Pakistan, where religious toleration only exists for economic elites who can withdraw into their own private world. It was this context which drove Gerard Russsell to include the Kalash in his book Heirs to Forgotten Kingdoms: Journeys Into the Disappearing Religions of the Middle East. The Kalash are not Middle Eastern, and are very different from various heterodox groups of the Middle East (who often have connections to the astral religion of Late Antiquity), but there is an urgency in recording their culture before it disappears.

Another major salient aspect of the Kalash is that they are mostly white. That is, if you took a Kalash man and dressed him in jeans and a baseball cape wouldn’t think twice if you saw him in a country music video. Let me quote from Man Who Would be King:

“‘In another six months,’ says Dravot, ‘we’ll hold another Communication and see how you are working.’ Then he asks them about their villages, and learns that they was fighting one against the other and were fair sick and tired of it. And when they wasn’t doing that they was fighting with the Mohammedans. ‘You can fight those when they come into our country,’ says Dravot. ‘Tell off every tenth man of your tribes for a Frontier guard, and send two hundred at a time to this valley to be drilled. Nobody is going to be shot or speared any more so long as he does well, and I know that you won’t cheat me because you’re white people — sons of Alexander — and not like common, black Mohammedans. You are my people and by God,’ says he, running off into English at the end — ‘I’ll make a damned fine Nation of you, or I’ll die in the making!’

And later:

… Dravot gives out that him and me were gods and sons of Alexander, and Past Grand-Masters in the Craft, and was come to make Kafiristan a country where every man should eat in peace and drink in quiet, and specially obey us. Then the Chiefs come round to shake hands, and they was so hairy and white and fair it was just shaking hands with old friends. We gave them names according as they was like men we had known in India — Billy Fish, Holly Dilworth, Pikky Kergan that was Bazar-master when I was at Mhow, and so on, and so on.

The genetics on the pigmentation loci make it clear why the Kalash are so fair. They are fixed at SLC24A5 for the derived variant. In fact their pigmentation genes are rather similar in allele frequency distribution to Sardinians (check SLC45A2 and OCA2/HERC2). In a European context the Kalash are not notably fair skinned, but a substantial number can clearly pass as white without difficulty because for all practical purposes they are white physically. The observations of Kipling’s narrator in Man Who Would be King holds true today, white Western journalists who need to pretend to be native in Afghanistan take on a Nuristani identity. Even if most Nuristanis and Kalash are not blue eyed and blonde haired, enough are that it is not totally implausible that a fair Northern European could pass as one of them.

Though the Nuristanis and Kalash are at one end of the distribution in South Asia, they’re not total aberrations. Many Pathans, for example, basically look white. Above I posted the photo of Ayub Khan, military dictator of Pakistan in the 1960s. He was an ethnic Pathan. Khan loomed large in my father’s recollection of this period. When he arrived in Pakistan to complete his master’s degree he was surprised that most people were not white like Ayub Khan!

Which brings me to the question, if a subset of people on the Northwest fringes of the Indian subcontinent are physically white, are they then related to the peoples of Europe to an inordinate level? In the 19th century the presumption was they were, insofar as these were “Lost White Races,” with some theorists positing connections between high caste Indians and Europeans as Aryans. These sorts of mental frameworks are not particularly unique to Europeans. I’m mostly finished with The Making of Modern Japan, and the Japanese immediately made an analogy in appearance between the Europeans entering their waters and the Ainu people to their North. And then there is the legend of Alexander. In particular, that the Kalash are descended from the Macedonians and Greeks who marched with Alexander. That in truth they are a lost European tribe. I get questions about this pretty much every three to four months. I always answer in the negative. There is no strong evidence of a specific connection. I’ve even made it into the Wikipedia entry for the Kalash:

Discover Magazine genetics blogger Razib Khan has repeatedly cited information indicating that the Kalash are an Indo-Iranian people with no Macedonian ethnic admixture.[47][48][49] A study by Hellenthal et al. (2014) on the DNA of the Kalash peopl evidence of input from Europe or the Middle East (the researchers could not pin down a precise geographic location) between 990 and 210 BC, a period that overlaps with that of Alexander the Great.[50][51]

Screenshot from 2015-08-08 17:24:22 The paper cited to offer up an opening to the possibility of Kalash connections to the Macedonians comes up frequently. It’s known to me, and though the group associated with it is top notch, and the results are certainly impressive, their interpretations are not bullet proof (and the authors are reasonably tentative). I went back and re-read the Hellenthal et al. paper, and checked out their awesome website where you can repeat their analyses. The screenshot to the left shows the Kalash admixture event. They have Greeks and Bulgarians in their data, but the gene flow is from Northern Europe.

Enough talk though. I have data, and will do some more analyses myself. The preliminaries. I took the Reich lab Haak et al. data set (it’s a subset of this), and yanked out a bunch of populations. Additionally, I took the four Yamnaya samples with the best quality genotypes, and created a data set where all their genotypes are included and those that they are missing are excluded (the –mind option in Plink). What I’m saying here is that the variation in the data set is skewed toward the good SNP calls in the ancient Yamnaya samples. After some more quality control I got down to 85,000 SNPs.

First, here is some PCA….

Rplot10 You can’t see it on the thumbnail, and the colors are confusing if you click it, but the Kalash sit square on the northwest edge of South Asian populations. Exactly where you’d expect them to be if they were indigenous to South Asia, and not European transplants. The earlier genetic markers I talked about were a narrow set related to pigmentation. This is genome-wide, sampled out of the 30 million polymorphisms. If you took the pigmentation related loci, Kalash would probably cluster on the edge of Europe. What this shows is that not all genes are representative of genome-wide patterns. SLC24A5 seems to have been subject to selection within South Asia, in situ.

Next I want to zoom in a bit to make a point. You probably want to click to enlarge, but from the top right to bottom left: Greeks, Lithuanians, Yamnaya, Pathan/Kalash.

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You notice in this plot that the Kalash are closer to Lithuanians than Greeks. I think a fair minded person would say that the Kalash look more like Greeks than Lithuanians, that is, they’re brunette whites. But genome-wide data show that they are closer to Lithuanians! This is in line with the results you saw above from the Globetrotter genetic admixture methodology. Kalash affinities in Europe are not with Southern Europeans, but Northern Europeans.

Next, we’ll look at PC 3.

Rplot17 Click the image to see it bigger, what PC 3 in these data map onto is a Papuan (up top) and South Asia (bottom) axis. The Kalash are one of the most South Asian populations on this axis! Don’t make too much of this, as there aren’t any South Indian groups. But, it shows that there is something distinctive about the Kalash which is like many other South Asians, and not like Europeans. Not surprisingly the Iranian samples are somewhat shifted toward the South Asians.

The above plots are a bit cluttered. So let’s look at a subsample. Below is a zoom in. PC 1 separates East Asians (off to the left of the plot, not visible) from Europeans. PC 2 separates Yamnaya from everyone else (they are below the bottom edge). I’ve highlighted a few populations.

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You can see that the Lithuanians are the most Yamnaya-shifted population. But the Kalash and other Northwest South Asian groups are Yamnaya shifted as well. Not surprisingly, the Druze and Sardinians are the least Yamnaya shifted. The Greeks are not notably Yamnaya shifted, though they are in comparison to the Sardinians.

Now we’ll run Treemix. The parameters -m = 5 and -k = 500. I ran a bunch of iterations. The plots are below.

KalashOut.10 KalashOut.9 KalashOut.7 KalashOut.8 KalashOut.6 KalashOut.4 KalashOut.5 KalashOut.2 KalashOut.3 KalashOut.1

The Kalash are drifted a lot. So they are a long branch often. But you see that most often they are near the other Northwest South Asians. There is no gene flow parameter from Europe. Though that’s probably a function of the other gene flow events being more much significant. So let’s cut down the data set to the same extent as with the PCA.

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The Kalash are much closer to Europeans in these plots than some South Asians. But why? Clearly it is partly a function of the positioning and affinities of the Yamnaya. Additionally, the Kalash cluser with the Pathans, and to some extent other Northwest South Asians. Geography is stamped genome-wide.

Let me quote from the supplements of Hellenthal et al.:

The Kalash are a geographically and genetically (39) isolated population that have lived in a remote valley within present-day Pakistan for many centuries (40; 66). In the original (Full) analysis, the Kalash possess our oldest estimated date of most recent admixture, of 600BCE (990-210BCE), between sources best represented today by Germany-Austria (though within a range of potential European-related sources, e.g. represented by Turkey in the CentralAsia analysis; 35%) and the nearby Pathan (65%). Intriguingly, this period overlaps that of Alexander the Great (356-323BCE) whose army, local tradition holds, the Kalash are descended from (40). The history of this group is not known: our analysis suggests a major admixture event from a source related to present-day Western Eurasians, but we cannot identify the geographic origin of this ancient source precisely.

In the “Central Asia” analysis of Note S7.4 (but not in the “full” analysis), a very similar ancient admixture signal (always dated older than 90BCE) is seen in five nearby Pakistan populations: the Makrani, Balochi, and Brahui, and more weakly in the Pathan and Sindhi, but not identified in the most northerly groups. Ancient admixture involving sources related to East Asia is inferred in the easterly Burusho and tentatively (within a second signal) the Kalash. These older events are similar in date to that seen in the Kalash but involve less strongly European-like, and more West Asian like, sources (Figure 4; Figure S18), and pre-date recorded history for the region.

The power to detect the events seems a bit weak. Probably better phasing (they had 425,000 markers and used population-based methods) and sample coverage would help. But I think what they’re seeing here are two migration events. First, one with affinities to northern West Asia, which is the majority of the “Ancestral North Indian” (ANI) signal. It is overwhelming in the south and northeast of the subcontinent. A secondary wave probably relates to the Indo-Aryans. It is substantial in the northwestern regions, and less so as you proceed into the Gangetic plain, and present only among Brahmins and other migrants in southern India. It probably correlates well with lactase persistence. I suspect that the Jatts may actually have substantial ancestry from post-Aryan waves based on genetic results I’ve seen.

Where does this leave us in relation to the Kalash? Why is it that they look so much like European whites when phylogenetically they aren’t much more like European whites than many people around them. A few years ago I discussed Indian genetics with John Hawks, and one objection I had to the idea of a European-affiliated Indo-Aryan migration of any substantial demographic heft is that European pigmentation alleles are so rare in South Asians. I’m particularly thinking of European variations of SLC45A2 and OCA2/HERC2. I now understand that my assumptions were wrong. 4,000 years ago Europeans did not look like Europeans!

First, as outlined in Population genomics of Bronze Age Eurasia, Massive migration from the steppe was a source for Indo-European languages in Europe, and Eight thousand years of natural selection in Europe, the genetic character of Europeans as we understand it is a recent phenomenon. Second, as outlined in Genetic Evidence for Recent Population Mixture in India, the genetic character of South Asians is also a recent phenomenon. In fact, both are of the same period, with the finishing touches probably around ~3,000 to 4,000 years ago.

What does this mean? Well, it could be that the “white” phenotype emerged several times in variously related people. In other words, the similarities between the Kalash and Southern Europeans is due to convergence, not common descent. This is reasonable, since all the best evidence now suggests that in many ways the most ancient Southern European populations, such as Sardinians, are among the most distant from South Asians of the European groups. Of course some of the alleles for pigmentation are common. For example, SLC24A5 has a very explosive haplotype structure with little variation. It’s new across its whole range. There are some suggestions though that it is most diverse in the Middle East. It may have swept across all of Western Eurasia recently. Part of the expansion was demographic no doubt, but, part of it was also selection. So being part of the common network of demes, Southern Europeans and Northwest South Asians drew upon some of the same variation as part of their adaptive response to selection pressures.

200px-DarwinsRadio(1stEd) For skin color the standard explanations are out there. The sun, sexual selection, and changes wrought by agriculture. But can they really explain all these concurrent shifts across Eurasia? In Darwin’s Radio the science fiction author Greg Bear posits a genetic time-bomb within us all introduced by a virus that produces species wide saltation. So Neanderthals turned into modern humans almost immediately. It’s a science fiction story. But what about the idea of a disease which selects strongly for the derived variant of SLC24A5? The change in skin color is just a side effect. In fact in South Asia it’s not optimal, though with clothing and avoiding direct sun during the midday, people can deal with it. Instead of a great white race sweeping across Eurasia, I’m positing a great white plague. And not just for white people. What about the sweep around EDAR, which results in many of the characteristics so distinctive about East Asians. It’s a major development gene, but perhaps it too is a reaction to a disease?

linear-300x300 All these things lead me at a strange place. I think human population structure is a big deal. It’s real, it matters. Genetics, and genetic variation matters. But, I also think that a lot of it isn’t very deep in terms of time. That is, a lot of the genetic variation is mixed and matched of recent vintage. Rather than phylogenetic trees, there are reticulated graphs. But not only is the history of our species’ phylogeny radically conditional on the last 10,000 years, many of the salient physical characteristics are also recent, and seem to be popping up everywhere at the same time. And yet, remember Luke Jostins’ plot which showed parallel increase in encephalization across hominin lineages for millions of years? This may not be the first time that inevitable processes were driving many lineages toward the same end points.

 
• Category: Race/Ethnicity, Science • Tags: Genomics, Kalash 
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There was a question about East Asian genetic structure. There have been a fair number of papers published on the issue. But over the years I’ve assembled a pretty large personal data set from public sources, as well as stuff people have sent me. I decided to look at the East Asian individuals and how they relate to each.

First, I focused on the major ethno-national groups (or ones of particular interest and relevance, such as Mongols). Second, I LD pruned the data set down to 96,000. Third, I did some outlier removal. For example, I wanted to include some Kalmyk data, but it turns out all the Kalmyk have European admixture at some level. And a subset of individuals from Cambodia and Vietnam are ethnic Chinese. Those were removed.

I ran ADMIXTURE K = 5 unsupervised. Treemix k = 500 and global rearrangements on, and rooted with Cambodians.

Eigenvalues 7.59041, 4.04862, 3.00559, 2.60692 and 2.01554.

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First, the evidence of gene flow into the Han ethnicity, or the absorption of the Han of local substrate, is clear in these results. Second, I’m pretty sure that the weird affinity between Yakut (the northernmost Turks) and Cambodians has to do with admixture into both groups from non-East Eurasians that is old. In the case of Cambodians something Indian-like, and for Yakuts something more like “Ancient North Eurasians.”

 
• Category: Race/Ethnicity, Science • Tags: Asian Genetics, Genetics 
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51qciM4cBhL._SX258_BO1,204,203,200_*The past after the word*

If science is hard, history is harder. Harder in that the goal is to understand what happened in ages which are fading away like evanescent ghosts of our imagination. But we must be cautious. We are a great storytelling species, seduced by narrative. The sort of empirically informed and rigorous analysis which is the hallmark of modern scholarship is a special and distinctive thing, even if it is usually packaged in turgid and impenetrable prose. It is too pat to state that history was born fully formed with the work of Thucydides (or Sima Qian). In fact Thucydides’ pretensions at historical objectivity despite obvious perspective and bias lend credence to the assertions of those who make the case that the past is fiction (in this way Herodotus may actually have been more honest). The temptation is always great to paint an edifying myth which gives succor to national pride or flatters our contemporary self-image. The fact that modern nation-states in the technological age have vigorous debates about details as to the nature of periods of history in the recent past, when the people who lived during those times are still here to bear witness, is telling in terms of the magnitude of the task before us. Fraught questions must be answered with far fewer resources.

Much of history we see only vaguely through chance and contingency, known through happenstance and the whims of our ancestors. In the West the documents which shed light upon antiquity come to us through tunnels of finite transmissions, a furious period of textual transcription in the last few centuries before 1000 A.D. The Carolingians, the Byzantines, and the Abbasids all engaged in sponsoring the capital intensive project of taking ancient texts and making copies for posterity. The vast majority of the works of antiquity we have today can be traced back to this period[1]. Biases and concerns of the elites who sponsored these projects were critical in determining the nature of the source material which serves as the foundation for our understanding of the deeper past which we take for granted today. We know how little was copied because the extant material make copious reference to a vast body of work which was circulating in the ancient world on assorted topics (and even many of the works we do have are only portions of multi-volume endeavours, such as that of Livy).

brotherhoodBut what about pushing beyond what the text can tell us, and transitioning from history to prehistory? Here is where matters become opaque and conditional upon the nature of the texts (or lack thereof). This is clear when you observe that there are very early periods of human history when our knowledge of individual actors and daily life is actually greater than later epochs due to regress of civilization, or, changes in technology which mitigated against preservation of texts[2]. The “Dark Ages” of Greece between the Mycenaeans and the Classical Greeks are the purview purely of archaeology (and even during the Mycenaean period most Linear B were of a bureaucratic nature; I do not know of narrative literature such as we have for Egypt or Babylon). For the Classical Greeks the rupture was traumatic enough that their Mycenaean past became the subject of legends. The citadels of the Bronze Age warlords were viewed as “cyclopean” works, as if only giants could have created them. Similarly, the period in Britain between the end of central Roman rule and the Christianization of the Anglo-Saxons, about two centuries, is perceived only faintly because of the paucity of written records (this also explains why this period is often utilized as the setting for historical fantasy).

9780192807281_p0_v1_s260x420 Yet when text is silent one still has material remains. Their collection and analysis are the domain of archaeology, a historical science. The fact that history as we understand it deals in the written word, and so limits its focus to the period when we have texts, is itself a historical coincidence. Ideally traditional history and archaeology should work in concert, and critically, words have a way of deceiving and misleading. Most obviously we have a major ascertainment bias in our understanding of the past when we listen only to the perspectives of those who can speak through words, because they who were literate or had access to literate professionals were a very small subset of the broader human experience. Archaeology has less of this bias, because all classes leave behind their material evidence (though if one wants textual representations of a broader cross section of the Roman populace, the novel The Golden Ass is a good place to start). An excellent illustration of this for me, as readers know, is the extended argument in the book The Fall of Rome, which brings material evidence to buttress the position that the decline and fall of the unitary Roman state in the 5th century coincided with a genuine degradation of what we might term civilization. Revisionists looking purely at textual materials have long argued that the classical view was misleading, and to reduce their argument down toward its essence, suggest that classical civilization evolved and transformed, channeling its energies into different activities (e.g., the rise of Christian theology as a successor to the classical liberal arts, see Peter Brown’s The Rise of Western Christendom). But what material remains tell us is that there was indeed an economic and demographic collapse, despite apologia that one can make as to the reshaping of high culture in texts. One may choose to weight these facts, or not, but the facts nevertheless remain, no matter how many glosses one wishes to upon them. The Rome of 600 may have had many more Christian theologians than the Rome of 400 (which was then a mainly non-Christian city), but the Rome of 400 probably had a population on the order of 10-20 times greater.

41hdiv6SmHL._SY344_BO1,204,203,200_ In a world without text, which is almost all of human history, the material remains are all that we have to grasp upon. Though we can attempt to glean the minds of people long gone from paintings and scratches in stone, the reality is that what they hunted with, what they ate with, and the dwellings in which they lived, are going to give us concrete information where leaps of imagination are unnecessary. Moving beyond the text can allow us to truly illuminate the vast dark oceans of human history with more than our dreams, from the dawn of our species, down to even recent periods when literacy was the privilege of the few, and the experiences of the many were dead to us. Despite this, the paintings have only a few colors on the palette, because archaeology is filled with enormous gaps in perception. Pots not cloth. Caves not tents.

Which brings us to biology, and specifically genetics, as it turns out that DNA is actually one of the material remains that one can extract from archaeological field sites. It’s a robust macromolecule, and today researchers believe that it is feasible that some information can be drawn from remains as old as 1 to 2 million years, though that’s a best case scenario. When it comes to questions of demographic change genetic insights are key, and present data in a way that allows for more rigorous analysis. As has been the case in previous posts I must now give a nod here to L. L. Cavalli-Sforza and The History and Geography of Human Genes. Cavalli-Sforza’s magnum opus reopened the book in attempting to understand history through demographics. It was the first page, and the first chapter. Prior to this before World War II there was a cottage industry which attempted to do what Cavalli-Sforza achieved in the late 20th century. But these endeavors were hobbled by two problems. First, they was not scientific, often relying upon intuition derived from their erudition (they were not hypothetico-deductive, though that’s overrated if you have lots of data). Second, the reliance upon intuition meant that many of the conclusions dovetailed rather neatly with the ideological preferences of the day, National Socialism most horrifically, but much more widely than that was a shoddiness of nationalism inflected prehistory. Scientific romance without the genocide (see Pat Shipman’s The Evolution of Racism). After World War II archaeologists reversed course and decoupled cultural evolution and change from demographic variation. Works such as the Races of Europe became anachronistic when decades before they’d have been mainstream, and there was a strong bias toward a null hypothesis that pots, that is cultural traditions, migrate, but people do not.

 

k7442 Into this intellectual climate stepped Cavalli-Sforza and his students, triggering a minefield in academic explosions (see The Human Genome Diversity Project: An Ethnography of Scientific Practice). Molecular anthropology in its earliest incarnations focused on deep time. In particular, there was a recalibration of time depth of the origin of apes and humans, where the molecular biologists clashed with paleontologists, and came out the victors (see The Monkey Puzzle for a history of these controversies). Then, there was the “Out of Africa” debate (see The African Exodus). Though these were somewhat fractious and personalized arguments, the emotions around the implications of these contests of ideas were often limited to scholars (though the scholars themselves may not have felt the fallout was limited; apparently at Stanford in the late 1990s a cultural anthropologist gave a presentation where he juxtaposed a photo of Cavalli-Sforza with Josef Mengele). What Cavalli-Sforza did was bring genetic science toward addressing more contemporary phenomena, to answer questions which come to the cusp of the present, tackling issues of relevance to living human people on the scale of nations and peoples. Over many decades his lab collected enough information from hundreds of genetic loci to arrive at the sum totality of inferences which were eventually presented in The History and Geography of Human Genes.

CosttoSequenceaGenome-e1409924136899 Let’s take a step back here. Cavalli-Sforza and his colleagues had access to hundreds of markers at best. Note that ~2% of the human genomic codes for proteins, but there are 3 billion positions in terms of bases. Today anyone who wants to pay can get millions of positions through SNP-chip services. My son has billions of positions, because he’s been whole-genome sequenced. For phylogenetic purposes you don’t need billions, millions, or even thousands, depending on the nature of the questions you have in mind. But, it puts in perspective how far we’ve come in literally 20 years. Even 5 years.

As is the nature of science there was much that Cavalli-Sforza got wrong in The History and Geography of Human Genes. But there was much that he got right, because the results were so clear and strong on particular points of contention. In short, very broad patterns on the continental level jumped out when analyzing even hundreds of neutral (that is, not subject to natural selection) markers. For example, the data confirm a gradient of genetic diversity which implies human origins from an African locus, as well as the relative homogeneity of Europe (aside from Finns, European populations have a surprisingly low between-population pairwise genetic distance in most cases). But, more subtle counterintuitive relationships were often not robust (e.g., North and South Chinese do not bifurcate in the manner that he reported in the 1990s). And, most critically for the purposes of this post inferring past demography from current phylogeographic patterns had serious limitations.

*The present as a window into the past*

downloadm511NSSGQNWL._SY344_BO1,204,203,200_ The basic idea behind historical population genetics (archaeogenetics) which was pioneered by Cavalli-Sforza at the HPGL at Stanford was to look at patterns of diversity and relatedness among modern populations, and intersect that with what was and is known about history, as well as geography, and then allow those intersections to peal back the palimpsests of human history (see his The Great Human Diasporas). Though Cavalli-Sforza focused initially on autosomal markers scattered through the genome, in the period between 1995 and 2005 there was a great deal of work using uniparental data., the markers on the Y and mtDNA. The mtDNA is passed through women only, is copious in terms of quantity on a cellular level, and has a highly mutable region of utility for molecular phylogenetics. The Y chromosome exhibited some technical difficulties in comparison to mtDNA, but with the emergence of better extraction techniques as well as a focus on highly mutable microsatellite regions, it came to be set next mtDNA as a critical tool in the forensic reconstruction of human population history. In addition, both had the virtue of being nonrecombining, so that the generation of a phylogenetic tree was not an artificiality, but a reflection of the nature of the transmission of these two regions of the genome (congenial to a coalescent framework as well).

Human_migrationIn the end this line of research often resulted in a transposition of a phylogenetic tree upon a world map, outlining patterns of human migration. It also aligned well with another line of research which explicitly modeled the expansions of humans out of Africa as a “serial founder bottleneck” process. That is, each population which left Africa progressively branched out in a unidirectional manner, resulting in reduced genetic diversity as one progressed out of Africa.

Ramachandran, Sohini, et al. "Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa." Proceedings of the National Academy of Sciences of the United States of America 102.44 (2005): 15942-15947.

Ramachandran, Sohini, et al. “Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.” Proceedings of the National Academy of Sciences of the United States of America 102.44 (2005): 15942-15947.

In its broadest strokes this model is not without validity. It does seem that most of the ancestry of modern humans can be traced to a population which flourished around or in Africa ~50-100 thousand years ago. Much of the inter-continental racial variation that we see in extant populations does nicely fit onto a bifurcating tree-like model (e.g., Non-Africans branch off from Africans, West Eurasians and East Eurasians diverge, Amerindians branch off from East Eurasians). The problem though is that the branches themselves turn out to be brambles which turn back in on themselves, and in some cases twist with other branches, creating lineages with very diverged ancestral roots. The yield of the earliest efforts by Cavalli-Sforza and his heirs was on a very coarse continental grain, where the effects of the dynamics were so striking that they would exhibit themselves across most neutral markers without much difficulty. But, when the questions were narrower, and the temporal and spatial scope more constrained, the earlier methods were not perceptive enough to smoke out the real dynamics.

Li, Jun Z., et al. "Worldwide human relationships inferred from genome-wide patterns of variation." science 319.5866 (2008): 1100-1104.

Li, Jun Z., et al. “Worldwide human relationships inferred from genome-wide patterns of variation.” science 319.5866 (2008): 1100-1104.

By the middle years of the 2000s researchers had gone back to a focus on recombining autosomal markers. But now they had a whole human genome to compare it to, as well as SNP-chips which quickly yielded large troves of data with little effort. In 2008 a paper was published which took the origin HGDP data set collected by Cavalli-Sforza and his colleagues, and utilized the new technologies to make deeper inferences. First, instead of hundreds of markers you had 650,000 SNPs. Second, the emergence of powerful new analytic and computational resources allowed for the complemention of tree-based and PCA visualizations of genetic relationship with model-based understandings of genetic variation and population structure. By “model-based,” I mean that the algorithm posits particular parameters (e.g., “3 ancestral populations”) and operates upon the data (e.g., “650,000 SNPs in 1000 individuals”) , to generate results which are the best representation of the fit of the data to the model.HGDPme This different from PCA, which has fewer assumptions, and represents genetic variation geometrically (each axis represents an independent dimension of variation within the data). Model-based clustering is very clear and aesthetically appealing. It gives precise results. But, the model itself is not necessarily right.

Anyone who uses these methods understands their limitations. If you use PCA to project variation of the data set, then the composition of the data you input is going to influence the largest principal components. Therefore, if you are asking questions on a broader spatial scale you should be careful about the possibility that you are overloading the sample set of interest with particular populations. More data in this case might result in less insight. Similar issues crop up with model-based clustering you don’t appropriately weight the populations. Another major problem is that the models are imposing limitations which might produce false inferences (false in that they do not accurately reflect demographic history). Most simply you might ask for many more population divisions than is realistic for the demographic and genetic history of the data. Consider a data set of Irish from Cork and Nigerians from a small village. PCA would no doubt show you two very tight and distinct clusters. With a model-based framework you could look for divisions and structure beyond K = 2 (two ancestral populations). The method is devised in such way that you would get results. But, they wouldn’t be very informative, and they’d be forced. They wouldn’t be robust. The model would be a poor fit to reality.

*From model to reality*

Obviously no model captures all elements of reality. But when the model deviates so much from reality that you get a false sense of what is true then that model is not nearly as useful. Being wrong is a definite bug. Aside from model-based admixture analysis, which posits a finite number of ancestral populations which come together to produce the genetic variation in the data set, you notice that the 2008 paper also had a tree representation of genetic variation. These two together give real and substantive results that can be useful. But, they mislead to the point of falsity in many specific cases.

nihms137159f3

Reich, David, et al. “Reconstructing Indian population history.” Nature 461.7263 (2009): 489-494.

This can be illustrated by the instance of South Asians, who are about 20% of the world’s population. A 2009 paper, Reconstructing Indian Population History, utilized both the higher autosomal marker density sets and new analytic frameworks to come to some specific conclusions which resolve many confusions about the nature of the genetic history of the peoples of the Indian subcontinent. So what did we know before? If you go back to the ideas of the old physical anthropologists they observed that many South Asian groups had an affinity to the peoples of West Eurasia (Europeans and West Asians). This varied as a function of geography and caste. In other words, there was a cline to the northwest, as well as up and down the caste system. You can see it in a PCA, where Indian groups vary in distance from Europeans, while Europeans form a very tight cluster. It also shows up in admixture based analyses. There is usually a K value where a South Asian modal cluster emerges, and it is near fixation in South Indian non-Brahmins, declining in frequency as one moves toward Pakistan, or, in North India up the caste hierarchy (the residual are West Asian and European clusters, except Bengalis, who have East Asian admixture). In The History and Geography of Human Genes South Asians form an outgroup to Europeans and Middle Eastern populations using older distance measures.

So far all good. One can imagine then a cline of genetic variation, with South Asians at one end, and West Eurasians at the other. On a PCA between East Asians and Europeans South Asians usually fall in the middle, but closer to Europeans. But there have long been major problems with this model when you drilldown into the details. The mtDNA and Y chromosomes of South Asians give very different results. The former classes them as distinct from West Eurasians, with distance affinities to East Eurasians. The latter on the other hand are quite a bit more like West Eurasians. Second, South Asians exhibit a lot of variation as a function of both geography and class in terms of their relatedness to word populations. If South Asians were deeply rooted in the subcontinent, as the migration maps above would imply, then we’re talking about massive barriers to gene flow which have persisted for tens of thousands of years. An alternative explanation is that South Asians are the product of recent admixture between two very different groups, which is what is often the norm when there is a lot of inter-individual variation in ancestral components and PCA position within a putative population group (e.g., African Americans). Finally, tests of natural selection geared toward detecting very recent sweeps have indicated a commonality between South Asians and Europeans and Middle Easterners on the haplotype of SLC24A5, which implies either extreme connectedness, or, recent admixture and migration (on the margin these two models are going to be hard to distinguish, since connections are mediated through migration).

I will sidestep the technical issues at this point, and just offer up that the work on South Asians has presaged much of what we’ve learned over the past decade when it comes to the genesis of modern population structure. The puzzles about South Asian genetic variation are resolved when you admit a model where a West Eurasian population mixed with a local indigenous group with distant affinities with other East Eurasians (see Genetic Evidence for Recent Population Mixture in India). The high level of between population variance within South Asia is due to the recent nature of the admixture event and the high genetic distance between the source populations. This may actually be the story of much of the world over the last 10,000 years. Instead of a regular branching process, imagine branches that periodically fuse back together, in a reticulated pattern. Another way to conceive of it is that the last 10,000 years have been a story of the destruction of population structure accrued over the past 100,000 years. A survey of this field can be found in the review Toward a new history and geography of human genes informed by ancient DNA.

*Inference made concrete, ancient DNA*

Up until now we have been talking about increasing the power of analysis of genetic variation in existent populations. Processes like bottlenecks and positive selection leave footprints in the genomes of modern peoples. But these methods of inference have limits. And, to a great extent they necessitate a simplicity of population dynamics to allow for them to have utility in painting a portrait of the past. Researchers had to assume that the past was simple, or the methods that they had wouldn’t be able to tell them as much as they claimed. The complexity of the demographic palimpsest could never race beyond ability of the genetic methods to peel it back, so there was a ceiling on the number of layers imposed upon the model.

41ePHetk1dL._SY344_BO1,204,203,200_ Ancient DNA was a game changer, because it did not come with these limitations. Instead of just inferring the past from the present, the past could now be inferred from the past! That is, a temporal transect in time could be generated which explicitly explored the trajectory of genetic variation across time and space. As if to recapitulate history the earliest work was with mtDNA, just as it had been with “mtDNA Eve” in the 1980s. The sequence target here is small and mtDNA is copious. The immediate upshot though is that massive discontinuities were detected. Populations replaced each other repeatedly in many regions. Pulse admixture events being inferred with novel methodologies on extant populations now could be understood to have been the natural result of migration and population change over the past ~50,000 years. Thanks to the work of researchers such as Svante Paabo and Eske Willerslev the number of samples we have from ancient DNA for humans has grown to such an extent over the past 5 years that a bright line is shining into what had been a dark cavern of prehistory.

*European man, made and unveiled*

Because of both the concentration of researchers in Europe, as well as suitable preservation conditions in Northern Eurasia, ancient DNA has totally changed how we understand the genetic history of this continent most especially. Two new papers have expanded the sample set to 170 individuals, and many major questions have now been answered, and other new questions have been triggered by perplexing results. A few years ago I was talking to Spencer Wells about the age that we are privileged to live in. Spencer is a history and genetics buff (he was one of Richard Lewontin’s last grad students). So naturally as genetic science has emerged to shed light on history we’ve tracked its developments very closely. Spencer professionally, he’s a genetic anthropologist. Many questions which in the past would have been unanswerable are now answerable. Truth is coming at us so fast that it is hard to even respond to all of it (if you wait too long to publish, everything might have changed).

Carl Zimmer’s piece in The New York Times, DNA Deciphers the Roots of Modern Europeans, is accurate as to the current state of the accelerating research in this area. This is the equivalent of having a Rosetta Stone. The ancients are now coming back to life. They speak! Everything has changed. In Nature Ewen Callway quotes a scientist stating in plain language, “Christ, what does this mean?” I’ll try and flesh out further what it means, but the papers themselves do a good job. These are first steps, but they’re very big steps. There’s only so much more to go, and truth will be at hand.

First, the two papers, Massive migration from the steppe was a source for Indo-European languages in Europe, and Population genomics of Bronze Asia Eurasia. As might be suggested by the title the latter paper has coverage of populations outside of Europe, while the former focuses on Europe. The samples sizes are 69 and 101 respectively. The first paper uses a methodology which yields many SNPs, while the latter relied upon whole-genome sequencing (variation is variation, so really this is a minor detail for the results, though it matters a lot for the working scientists who are generating the data). Both agree broadly on the major results. Additionally, there is a third work, a preprint, Eight thousand years of natural selection in Europe, which has results in line with the second paper above (it has a section on selection as well as phylogenomics).

*European genetic structure is younger than the pyramids*

51IZQjMbVlL._SY344_BO1,204,203,200_

The old debate whether Europeans are descended from farmers or hunter-gatherers was always somewhat incoherent. All humans are descended from hunter-gatherers. Rather, the issue was whether modern Europeans descend primarily from people who were resident within the continent of Europe at the end of the last Pleistocene, or, whether they descend from peoples who developed agriculture in the Middle East ~10,000 years ago. That is, did farming spread through cultural diffusion or migration? Plants or people? The answer is actually not straightforward, but, the results are not controversial today.

First, migration seems to have been the dominant dynamic which defined the spread of farming, especially early on. These first farmers who arrived in Europe were genetically very different from the hunter-gatherers of Europe’s north and west. Some of their ancestry had been isolated by long distances for tens of thousands of years before contact. The people of the Iberian peninsula today have less genetically in common with the hunter-gatherers which were present in the region when the farmers arrived than do modern Northern Europeans, who harbor a greater fraction of ancestry which derives from the Pleistocene people. The main qualifier I’d put on this though is that the farmers themselves seem to have picked up European hunter-gatherer admixture on their way out of the Middle East. The fraction is on the order of ~50%. The other component has been termed “Basal Eurasian,” because this element is an outgroup to all other Eurasians, including the European hunter-gatherers. That is, the Basal Eurasians are an outgroup to a clade that includes such as diverse populations as Andaman Islanders, Australian Aborigines, Japanese, and European hunter-gatherers.

Lazaridis, Iosif, et al. "Ancient human genomes suggest three ancestral populations for present-day Europeans." Nature 513.7518 (2014): 409-413.

Lazaridis, Iosif, et al. “Ancient human genomes suggest three ancestral populations for present-day Europeans.” Nature 513.7518 (2014): 409-413.

The figure to the left is from the paper Ancient human genomes suggest three ancestral populations for present-day Europeans. WHG = “Western (European) Hunter-Gatherers.” EEF = “Early European Farmers.” You can see that EFF is a compound. I don’t think there’s too much clarity right now with where the EEF got its WHG-like ancestry. It could have been structure in the Middle East. Or it could have been in Southeast Europe. In the supplements of Haak et al. they test a Hungarian sample, and it does seem that the EEF individuals are closer to it than the Western European hunter-gatherer samples. So there might have been structure in the ancestral European population, but the confidence here is low. And from what I can tell Basal Eurasian is still something of a mystery, almost occupying the role of “Planet X” before the discovery of Nepture. To make the patterns make sense they have to exist, but much isn’t known about them in detail. And of course there seems to be a huge lacunae right now in terms of exploring the population genetics of the Middle East in a similar fashion as has occurred in Northern Eurasia (my understanding is that Carlos Bustamante was an important person in getting Latin American populations in the 1000 Genomes; unfortunate that there wasn’t someone else to advocate for including a Middle Eastern group, since this is such an important part of the world for human history).

With all that said, if one assumes that the West Eurasian admixture in EEF was from European hunter-gatherers, then it is clearly obvious that most of the ancestry of modern Europeans can date to the Pleistocene (i.e., EEF + Yamnaya likely means more than half the ancestry is WHG-like if you look back 10,000 years). But, this proportion obscures the fact that massive migrations and population turnovers have occurred, so that a simple model of expansion out of Ice Age refuges no longer holds. Cavalli-Sforza has long argued that pure proportions of ancestry are less important than the dynamic, as population growth driven “waves of advance” will over time dilute the initial genetic signal anyway (though the final proportion of non-WHG-like ancestry is actually higher in much of Europe than Cavalli-Sforza conceded in the early 2000s). Whether the ancestry of modern Europeans derives predominantly from those of European hunter-gatherers, the idea of dominant local continuity in a given region has been thoroughly refuted. The hunter-gatherer ancestry in the British Isles, for example, may be mostly from admixture into agricultural groups far to the south and east during the initial waves of advance, not from the people who initially recolonized Northern Europe in the early Holocene.

k8488 The second demographic turnover event which has been highlighted by the papers cited so far is from the east. The migration from the steppes. This event had disproportionate, even dominant, impact across much of Northern Europe. Culturally it is often rooted in the Yamnaya complex, which gave rise to various disparate and wide ranging “daughter” societies. David Anthony’s The Horse, the Wheel, and Language surveys the archaeological terrain thoroughly. If you are interested in this topic, and haven’t read it, do read it. In this work Anthony outlines the spread of Indo-European languages via expansion of a mobile pastoralist elite. He was involved in the retrieval of some of the samples in these studies, and from what I am to understand he was personally surprised that the genetic data imply not just elite migration, but a folk wandering. Not just a band of brothers, but whole peoples on the move.

Haak, Wolfgang, et al. "Massive migration from the steppe was a source for Indo-European languages in Europe." Nature (2015).

Haak, Wolfgang, et al. “Massive migration from the steppe was a source for Indo-European languages in Europe.” Nature (2015).

Focusing on the genetics, these people seem to themselves be a compound of disparate elements. First, some of their ancestry derives from a population which Haak et al. term “Eastern Hunter-Gatherers” (EHG). And the other half derives from a population with affinities to those of the Near East, but different from that of the EEF. There is some disagreement between the two papers in Nature as to the details, but Allentoft et al. admit that they did not have EHG samples, which may have impacted their ability to detect admixture. Allentoft et al. also diverge from Haak et al. in the emphasis they place on the ancestral component among the Yamnaya which some term “Ancient North Eurasian” (ANE) based on the location of the most ancient individual of this line (see Upper Paleolithic Siberian genome reveals dual ancestry of Native Americans). What does seem clear is that this element is deeply diverged from other West Eurasian populations, on the order of ~20 to 30 thousand years. And, they contribute about half the ancestry to the EHG (the rest is WHG-like). The descendants of the Yamnaya people brought this component all throughout Europe, with the exception of the Sardinians and Sicilians, likely isolated because of their position on the Mediterranean littoral (Sicilians have later Near Eastern admixture as well). But this is not limited to Europeans, as a substantial proportion of Native American and West and South Asian ancestral heritage (at least the Kalash) also exhibit connections to this component. Allentoft et al., like Haak et al., points out that there was likely structure in this broader group. That is, the ANE themselves were diversified, with the ancestors of the element in Native Americans and Europeans different from that which contributed to the Siberian component. In fact I have talked to researchers who believe that the term “Ancient North Eurasian” is misleading, as there is little clarity on the distribution of this group (the highest inferred fractions in Eurasia are in the North Caucasus). It is feasible that the Kalash have a different ANE source than Europeans.

A key issue to note, and that confuses some people, is that the ancestry of groups such as Yamnaya exhibited commonalities with other groups across Eurasia. Therefore, if you replaced similar groups then the change in admixture components utilizing model-based programs may not be as extreme as you would think. To illustrate what I’m getting at concrete, the population transfer between Greece and Turkey during the 1920s was far more impactful as a dynamic than simple before and after admixture estimates would suggest to you (since genetically the two groups were very similar). The figure from Haak et al does not use admixture components that break out naturally, but their inferred demographic mixes taking into account the genetic character of the putative ancestral populations. The blue component refers to WHG, but WHG-like ancestry is also in both the green (Yamnaya) and orange (EEF) elements (this is why I’m saying it is likely that modern Europeans are mostly >50% WHG-like).

One temporal dimension that Haak et al emphasizes in particular, but seems clear in Allentoft et al. as well, is that non-Yamnaya ancestry slowly begins to rise again by the Bronze Age. Why? I will address that below. But, Allentoft et al. has broader Eurasian samples, including likely Indo-European populations in the trans-Ural and trans-Altai regions. In both of these areas the successor cultures had EEF-like ancestry. That is, like the Corded Ware population, and unlike the parent Yamnaya group. This strongly implies back-migration by this complex from Eastern Europe, as far east as western China, during the Bronze Age.

warbefore In The New York Times piece David Anthony states two things which puzzle me as an interested lay person without his expertise. First, he seems to think that the amalgamation of the Yamnaya and EEF-descended populations was not a warlike process. Specifically he says “It wasn’t Attila the Hun coming in and killing everybody,”. This is a useful image, but let’s be honest and note that the Huns were not primary producers, and did not aim just to increase pasturage by killing settled peoples as Genghis Khan had wanted to do (see The End of Empire: Attila the Hun & The Fall of Rome). Rather, they conquered and subordinated other barbarian groups, as well as extorted tribute from the East Roman Empire. The demographic impact of the Huns was not directly from them, but the fact that they and their successors (in particular the Avars) facilitated the migration of other groups, first, the Goths, and later the expansion of the Slavs. By the time of Attila barbarian leaders were well aware that the conquered were vital as economic producers whose capture and subjugation would allow them to engage in status competitions of conspicuous consumption. I do not believe that this was quite the case in the Copper and Bronze Ages beyond the limes of the civilized world, which was then an small archipelago of literacy in a sea of barbarism. Both the above papers indicate massive demographic disruption across Europ. Though war as we understand it is necessarily inevitable for our species, between the rise of agriculture and the modern period it seems to have been very common. It is not a coincidence that the Scandinavian Corded Ware culture are also called the Battle-Axe culture. Yes, many archaeologists believe that they were primarily a status symbols. I’m willing to bet many archaeologists are wrong. It’s been known to happen.

gokturk_empire_by_still_ates The second issue which Anthony brings up is the connectedness of the various post-Yamnaya cultures, in particular that of the earliest Indo-Europeans on the fringes of western China, 4,000 miles from their likely point of origin. The genetic characteristics of these eastern groups is also such that it is likely that there was gene flow from Europe, mediated by a common steppe culture. Anthony states that “I myself have a hard time wrapping my head around explanations for that”. This totally confuses me, because he’s a professional archaeologist, so he must know that widespread gene flow and cultural ties cross the vast swath of the Eurasian heartland is not surprising at all! To Carl Zimmer I pointed out the example of the Goturk Empire of the mid 6th century A.D., which expanded rapidly from the core Altai zone, and prefigured the later distribution of the Turkic people, from the Nile to the fringes of the Arctic sea. Language and lifestyle mediate relationships and demographic contact. The peripatetic character of steppe peoples is well known and attested from the historical and semi-historical record. Groups such as the Huns, Avars, and Alans, had inchoate origins in the heart of Eurasia, and moved back and forth along lines of cultural affinity as needed. Alans were serving under the Mongols in China in the 13th century, but 800 years earlier they had accompanied the Vandal tribe to North Africa, and maintained a separate identity there until the conquest of Justinian. It seems entirely plausible that this pattern of hyper-mobility arose with agro-pastoralism along the whole range of continuous ecological appropriateness, only ending with the rise of gunpowder empires and the crushing of the Oirat by the Manchus (with the tacit approval of Russia).

*Northern European archetypical physical characteristics are younger than the pyramids*

Spencer Wells, a new look in the world

Spencer Wells, a new look in the world

Phylogenomics is tangled and complicated still, even with all these new results. I’ve only scratched the surface above. You really need to read the papers, and their supplements, to even get a sense of what’s going on (yes, ideally you’ll know what an f3 statistic is!). But, the population genomics which give us a sense of the character of natural selection and phenotype over time is much clearer. The suite of traits which we associate with white Europeans is quite possibly very recent, as late as post-Bronze Age. White supremacist scholars of the early 20th century who posited that ancient Egypt (in fact, all civilizations) were founded by blonde Nordic people turn out to likely be wrong because these civilizations probably predate the existence of blonde Nordic people, both in their genetic structure, and in their physical type (at least in any number).

nature14507-f4 The genetic architecture of pigmentation is something geneticists know a fair amount about, because genome-wide association has been very fruitful in this area. Unlike traits such as height there is a large amount of between population variation in pigmentation. And, that variation is due in large part to a few genes of large effect. At SLC24A5 there is a SNP which accounts for around 1/3 of the melanin index difference between Europeans and Africans, using an admixed African American population to test the effect. As I have observed before SLC24A5 in its derived form is as close to fixed as you can get in Europeans. In the 1000 Genomes data set of thousands of individuals I found a few samples with a heterozygote and the ancestral copy. In the Middle East this allele is also near fixation, though not quite. As you can see from the figure I adapted from Allentoft et al., among South Asians the derived allele is also at high frequency. My whole family is a homozygote for the “European” variant. There is some suggestive evidence that this haplotype derives from the Middle East. It was only at low frequency among European hunter-gatherers[3]. But, by the Bronze Age had it gone to fixation in Europe, as well as on the Eurasian steppe.

Of more interest to me is the trajectory of SLC45A2. The derived allele is nearly fixed in modern European populations, though not nearly to the same extent at SLC24A5. In Iberian and Sardinian populations the ancestral type is in the range of ~10%. During the Bronze Age in Europe it was only at ~50% frequencies, which is in the range of modern Middle Eastern populations. It was even at lower frequency in the steppe, from which the putative Indo-Europeans migrated.

Finally, in this panel for pigmentation they included a major SNP in OCA2-HERC2 region. This locus is famous for being involved in blue-brown eye color variation, explaining 75% of the variance, and also exhibiting the third longest haplotype in the European genome. Naively projecting from these SNPs one could credibly argue that the ancient hunter-gatherers of Europe at the beginning of the Holocene were dark-skinned and blue-eyed! The Bronze Age European samples, which in this case are biased toward Northern Europeans, had a range of genetic variation equivalent to modern Southern Europeans. The people of the steppe did not seem to have blue eyes at all.

skin2

These results align perfectly with those in Mathieson et al. One thing to observe is that the Paleolithic samples, which have a much deeper time depth, are “ancestral” at all these positions. Even if the sample size is small (N =4), they’re from diverse times and places. Does that mean that they were much darker than even the Holocene hunter-gatherers of Europe? As some have pointed out we can’t just straight-line extrapolate from the genetic architecture of today to the past. Remember that Neanderthals exhibited pigmentation polym]orphism, but of a different sort. A deeper functional analysis may yield the possibility that Paleolithic Europeans had alleles which also resulted in lighter skin, but they were different ones from the ones segregating as polymorphisms today. I have already stated that I doubt much of modern European ancestry derives form before the Last Glacial Maximum. The reason that modern genetic variation in terms of predicting phenotype gives these sorts of results is that they may have arrived at the same trait value via a different set of polymorphisms. Genotype-phenotype maps derived from modern populations may be a poor predictor of the relationship 30,000 years ago. Why would one think that selection upon variation in pigmentation began at the cusp of the Holocene?

But, I do think we can predict with more confidence the nature of phenotypes for populations which are genetically much closer to modern ones. Bronze Age Europeans fit that bill. And, I know something personally about what the appearance of individuals during this period might have been based on genetic architecture: both my children exhibit a genotype profile on pigmentation loci similar to many Bronze Age Europeans. That is, they’re fixed for the derived variant of SLC24A5, and are heterozygotes at SLC45A2 and OCA2-HERC2 (my son, but not my daughter, is a heterozygote at KITLG; it does seem to make a difference in hair color). In terms of just their complexion they could pass as indigenous Southern Europeans, but definitely not Northern European.

*Culture leads genes by the leash*

Another major finding of Mathieson et al. and Allentoft et al. is that the derived allele found across West Eurasians that allows them to digest lactose sugar as adults has been sweeping up in frequency over the last 4,000 years. This allele spans a diverse array of populations, from Basques to South Asians. With pigmentation it seems that we need to consider jointly the impact of ancestry and selection (in South Asia derived SLC24A5 frequencies are definitely a function of both selection and descent). But with LCT it seems likely that selection is paramount. The predominant genetic character of Eurasia was established by the Bronze Age, but the frequency of the lactase persistent allele was still far lower. Tests of natural selection which focus on patterns of haplotype variation long detected a huge hit from LCT so this is not surprising.

51r8Ph-vcaL._SY344_BO1,204,203,200_ Intriguingly Allentoft et al. indicates that though the Bronze Age steppe populations had low frequencies of the derived allele, it seems that they did have a higher frequency than contemporary populations. This suggests that the origin of this haplotype, which spans the whole range of Indo-European speaking populations, and also into Finnic groups and the Basque, may still be attributed to the Yamnaya complex. In 10,000 Year Explosion Greg Cochran proposed the hypothesis that the favored mutation for LCT enabled the spread of Indo-European pastoralists. These results are not strong support for that direct causal relationship; rather, it strikes me that the ascendancy of the pastoralists drive the selection pressures for the allele in question. Biology did not drive culture, culture drove biology. The milk-drinking Celts and Germans encountered by Julius Caesar 2,000 years ago may still have been in the middle stages of adaptation to the agro-pastoralist lifestyle slowly being perfected by their ancestors.

*As the white man is, so shall we all be*

A new look as well

A new look as well

It is a running joke of mine on Twitter that the genetics of white people is one of those fertile areas of research that seems to never end. Is it a surprise that the ancient DNA field has first elucidated the nature of this obscure foggy continent, before rich histories of the untold billions of others? It’s funny, and yet these stories, true tales, do I think tell us a great deal about how modern human populations came to be in the last 10,000 years. The lessons of Europe can be generalized. We don’t have the rich stock of ancient DNA from China, the Middle East, or India. At least not enough to do population genomics, which requires larger sample sizes than a few. But, climate permitting, we may. And when that happens I am confident that very similar stories will be told. Using extant genetics we can already infer that modern populations in South Asia are a novel configuration of genotypes and phenotypes. The same in Southeast Asia, the Americas, and probably Africa. Probably the same in East Asia. Perhaps in Oceania. Even without admixture humans evolve in situ and changed, but with admixture the variation increases, and the parameter space of adaptation becomes richer and more flexible.

In Isaac Asimov’s later Foundation books he touched upon the existence of racial diversity in the future (from what I recall his earlier works from the pulp era were whites-only galaxies). At one point Hari Seldon encounters someone whose physical appearance seems to be East Asian, and they discuss the strangeness of people with East Asian ancestry being termed “Easterners” and those with European appearance being “Westerners.” With a loss of memory of the ancient distribution of these populations on the home planet only the shadow of a semantic recollection exists as a ghost in the galaxy-spanning Empire based out of Trantor. But of course tens of thousands of years in the future, even barring genetic and mechanical modification, it is unlikely that modern racial types will persist in any way we would recognize them.

But these results coming out of ancient DNA are telling us that what is likely to be true for the far future was also true for the recent past. White Europeans are a new type. But so are brown South Asians. Ethiopians have a recent ethnogenesis, as do most North African groups. The Bantu expansion has reshaped the face of Africa on the edge of the historical horizon. And so forth. In the big picture Young Earth Creationists are wrong, but in the specifics the idea that the sons of Noah populated the world ~5,000 years ago is not looking as crazy as it once did! Human genetic variation across Eurasia today may be mostly clinal, but in the recent past it was not. Rather, it was characteristic by sharp discontinuities and isolated local populations with diverged ancestry from their neighbors.

*And culture made man in its image*

51L3op-B8fL._SY344_BO1,204,203,200_ About ten years ago it was common in paleoanthropology to assume that human beings emerged almost fully formed ~50,000 years ago, and wiped out all the others in a genocidal wave of advance. Richard Klein advanced this model in The Dawn of Human Culture. Klein’s thesis was that some stochastic event, a mutation, resulted in the punctuation of a new species, our own. This singular genetic process allowed for the emerged of fully formed linguistic faculties in our lineage, which allowed for the development of the cultural flexibility, which made the rest of the human lineages evolutionary dead ends. It was a single and elegant story. It appealed to the principle of parsimony. The reality of “archaic” admixture was a difficulty for Klein’s model, evidenced by the fact that he voiced his skepticism of genetic claims of admixture in The New York Times after most others had moved on. For Klein a biological change explained the rise and success of our species, not a cultural one.

At the time I found the thesis compelling. We were after all a very special species. Modern Homo made it to Oceania and the New World. Something must have happened. Something big. What else could explain our rapid expansion and marginalization of other lineages? I’m a biologist, and so biology is an appealing causal mechanism.

linear

*The luck of the English facing the ocean*

At about the same time the evidence for Neanderthal admixture came out, Luke Jostins posted results which showed that other human lineages were also undergoing encephalization, before their trajectory was cut short. That is, their brains were getting bigger before they went extinct. To me this suggested that the broader Homo lineage was undergoing a process of nearly inevitable change due to a series of evolutionary events very deep in our history, perhaps ancestral on the order of millions of years. Along with the evidence for admixture it made me reconsider my priors. Perhaps some Homo lineage was going to expand outward and do what we did, and perhaps it wasn’t inevitable that it was going to be us. Perhaps the Neanderthal Parallax scenario is not as fantastical as we might think?

41z97bDZvUL._SY344_BO1,204,203,200_ Consider the case of Europe around 1600. In England and northern Germany (or what was to become northern Germany) you have two Protestant and genetically similar populations. But by 1850 it looked as if England was going to demographically overtake Germany in a broader genetic sense. James Belich’s Replenishing the Earth reviews the history of this period, when England spearheaded a demographic revolution far out of proportion to what one might have predicted in the year 1000. But by 2000 Germany, or Germans, had caught up somewhat. How? Millions of Germans migrated to the United States, starting in very large numbers in the mid-19th century, and were “picked up” by the demographic revolution which was the United States. The point is that contigencies of history, cultural and social, rather than biology, explain the trajectory of the gene pool over time. Much of the human past, and the sharp fluctuations in gene frequencies, might be driven by the long and forceful arm of culture.

In the treatment above I note that the EEF farmers who by and large replaced the indigenous hunter-gatherer groups in modern Southern Europe were themselves a compound. The hunter-gatherer ancestry within the EEF was far more successful than that of those they replaced, but the only reason that this was so was geographic coincidence. The WHG-like groups absorbed into the EEF were positioned further east, and so closer to the initial locus of expansion of Neolithic farmers. Similarly, the Neanderthal admixture into modern populations was almost certainly localized to particular groups. This is not to say that there are no biological differences between human populations which may explain a wide range of phenomena. Anyone looking at the skull of a Neanderthal and a modern human knows there are. There are also likely bio-behavioral differences between extent populations. Gene-culture coevolution is a real process, even if the details need to be worked out. But the interplay between biology and culture is complex, and in many cases cultural changes are driving the biological change, and then fixing differences which are advantageous to the “winners” (lactase persistence seems rather to be a perfect case of this). But just as in the individual case we must also remember that winning is often in part a function of being lucky. Naturally selection, generally thought of as a deterministic process, is also to some extent stochastic[4].

*From genetic islands to a roiling sea of humans*

One of the most shocking things for many of the geneticists working in the area of ancient DNA, and encountering the variation of the past, is the high level of population structure. That is, you have groups co-resident for many generations who nevertheless exhibit genetic distances of intercontinental scale. But as I stated above David Reich himself found the same results for India. And, in Africa you have long symbiotic populations, such as the pygmy groups of the Congo, and their agricultural neighbors, who are genetically very different, and have been for tens of thousands of years. Allentoft et al. dryly observe that “These results are indicative of significant temporal shifts in the gene pools and also reveal that the ancient groups of Eurasia were genetically more structured than contemporary populations.”

castesofmind About 10 years ago I read Nicholas Dirks’ Castes of Mind. Dirks is an eminent scholar who is now the chancellor of UC Berkeley. He emphasizes the power of European categories and systematization in creating the modern caste system. I don’t want to reduce his argument to a caricature. Obviously caste predates European colonialism. Dirks would admit this. But in Castes of Mind it is hard to shake the feeling that he believes that the British imposition of formalization made it what we truly understand it to be today. That caste has to be understood as a contemporary and early modern phenomenon, rather than an ancient one that was a structural feature of South Asian society.

The genetic evidence is clear now, and it paints a very different landscape. Many of the caste, even jati, boundaries we see today are thousands of years old. Endogamy long predates the British. It may predate the Aryans! Rather than the British, or Aryans, inventing caste, this form of ethnic segregation may date to the initial admixture event, to be reinvented and modified with each new population which arrives and imposes its hegemony on the subcontinent. In The New York Times David Reich states “You have groups which are as genetically distinct as Europeans and East Asians. And they’re living side by side for thousands of years.” He then he goes on to say “There’s a breakdown of these cultural barriers, and they mix,” alluding to the rise in WHG ancestry in farmer samples over time. Of course it is interesting to remember Reich’s work on India has highlighted exactly how persistent caste has been, and how it maintains genetic variation in a localized region that is often nearly inter-continental in magnitude.

We can never know if 6,000 years ago the LBK people, the first farming culture of Northern Europe, imposed a caste-like system of segregation when encountering the indigenous hunter-gatherers. Nor can we say with total confidence whether their relationship exhibited a symbiosis analogous to that between the Bantu agriculturalists and pygmies of the Congo (though do note that in these scenarios the Bantu communities are higher status, and the individual pygmies often have a semi-slave status). But, we need to look to what cultural evolutionary models and empirical results can tell us to make sense of these patterns. Ancient DNA can tell us very concretely the details of changes in allele frequencies. We can somewhat confidently reconstruct the faces and complexions of our ancestors. The questions population genomicists ask and answer in relation to animal models are relatively cleanly addressed by these data sets, assuming the sample sizes are large enough. But humans are the cultural animal par excellence, and that is the critical new variable which will require a new set of scholars to come together and create a truly multi-disciplinary understanding of the human past, present, and perhaps future. Powerful genomic techniques which produce results which have implications for the study of human history needs to leverage the full array of scholars who study human historical science.

1 – The three-fold copying is an important matter, because the different cultures had different preferences and goals. The Arab effort for example focused mostly on the philosophical production of the ancients. Without the Byzantines we would have far less of the humanistic production of Classical Greece, in particular the theatrical tradition.

2 – Much of what is known about the diplomatic history of the Bronze Age Near East has been preserved in cuneiform tablets. Though unwieldy, this form of writing on clay tablets is obviously more robust and less dependent upon copying than parchment and papyrus which came later.

3 – I would be curious to know if it is the same haplotype as is currently common in Eurasia.

4 – New mutations will usually go extinct, even if they are favored, in the initial generations. It is only when the frequency becomes high enough due to chance that selection will inevitably drive its frequency up, perhaps to fixation.

 
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FT_15.06.03_califProjectionsShare Hispanic as a catchall is a ridiculous term. I was thinking about this a few days ago when I saw this article, Google’s staff worldwide still overwhelmingly white and Asian men, where it actually notes the underrepresentation of “Hispanics.” Why does this matter exactly for an international corporation like Google? Presumably people of Middle Eastern descent (and no, I don’t count Ashkenazi Jews who are not Israeli as Middle Eastern!) are also underrepresented. But through an American prism having a surname from the Iberian peninsula really, really, matters* (also, it can transform people who are 100% white into underrepresented minorities; e.g., a friend who is the grandchild of Jewish refugees to Mexico who proudly checks Latino on demographic boxes to gain diversity points). The term arose almost by happenstance during the Nixon administration in the early 1970s. Though at least unlike the term “Asian American” there is some sort of cultural-historical coherency, as it generally connotes people of Latin American provenance, who are shaped by the events and migrations after 1492.

In any case, I just want to point to a Pew piece today, Will California ever become a majority-Latino state? Maybe not. The key to remember is that the sensitivity to assumptions is a major issue with all ~50 year projections. And yet the news media, and the general populace, tends to take these extrapolations as fact. “Proven.” It might strike you as ridiculous that seven years can radically overturn earlier initial conditions and qualitatively change predictions such as the “inevitable Hispanic majority” in a state as marinated in Latino culture as California, but that’s the takeaway, it is ridiculous. One should have only marginally more confidence in this projection than the one from 2007.

Remember, historically inevitable forces have a way of being not inevitable. History over timescales that mortals care about tends to be highly contingent. We make our own history. It does not proceed as the tides rise and fall and the sun marches across the sky.

* Latino is often preferred by some as it is more inclusive of Brazilians.

 
• Category: Ideology, Race/Ethnicity • Tags: Hispanic 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"