Open Thread, 3/19/2018

Some people have asked me what I think about Imagined Communities: Reflections on the Origin and Spread of Nationalism. I haven’t finished it, but now I understand why it is one of the most assigned books for undergraduates: it’s concise yet facile superficiality would appeal to a know-it-all twenty year old. What’s more disturbing, though I guess not surprising, is that Imagined Communities communities is a book that I’ve seen name-checked for years by various public intellectuals. Did they read the book?

It’s not that the book is incredibly wrong. It’s just that there’s not that much there in my opinion.

Been enjoying sampling the Philosophize This! podcast.

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Haven’t blogged it because I haven’t read the supplements.

Relationship between Deleterious Variation, Genomic Autozygosity, and Disease Risk: Insights from The 1000 Genomes Project.

Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase. This is big.

‘Serial Bomber’ Is Suspected in Explosions That Have Put Austin on Edge. Twitter was useless yesterday as most of the people seemed more enraged at the media for not laying the blame on white supremacists or Muslim radicals, as opposed to those getting killed or injured.

Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits.

Feeling like I should reread The End of History and the Last Man. Feels like history has started again….

Some people ask me about how I read fast. Part of the answer is that I read a lot in a specific area at the same time. Also, you can read fast if you know a lot about a topic. For example, a substantial portion of Who We Are and How We Got Here involves going over four and three population tests. I know what those are, so I read those sections quickly.

Finally going to hunker down and figure out which plugin is causing the 500 error on this website.

Just a reminder, please subscribe to the podcast on iTunes or Sticher and review it (positively). I’ll stop with the flogging when people no longer tell me “Oh, I didn’t know you had a podcast!”

This week we’ll I’m interviewing Milford Wolpoff (that is, what’s going live).

The western wolves are back, did you notice?

Tensions rise on the range after wolf kills cow in California for the first time in a century:

A wolf has killed a California rancher’s cow for the first time in more than 100 years, raising tensions in the newly reclaimed wolf country in California’s rugged northeastern corner.

California now has two packs in the north. This isn’t world-altering. Perhaps it was inevitable. But sure crept up on me.

Oregon now has nearly 100 wolves. There’s even a pack which wanders the mountains above the town I grew up in!

The gray wolf habitat is forest, so much of California won’t see a swarming of wolves because it is desert or cultivated. But it seems very unlikely that the Shasta pack doesn’t presage an expansion of wolf territory west toward the Pacific, and then down into vast timberlands reaching toward San Francisco. And wolves will surely move south along the western edge of the Sierras.


Denisovans, Neanderthals, Yetis, oh my!

An excellent open access paper is out in Cell which explores the distribution of archaic hominin, and in particular Denisovan, ancestry, Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture:

Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

Before you get caught up in the results, you should check out the methods. They’re pretty ingenious. Though with novel results like this people also really need to work their way through them as well (the authors present a lot of simulation results to validate the method, so I’m sure that will convince most; it certainly sways me).

The plots at the top of this post show the different distribution of Neanderthal and Denisovan admixture, by matching regions of the genome that they’ve identified as archaically introgressed. The ultimate logic is to look for variants which aren’t found in Africans, and are found in non-Africans, and scan over segments of the genome hoping that you can pick up the haplotypes that would slowly be chopped up over time through recombination that came in from Neanderthals or Denisovans.

At the top-left of the figure, you see “Northwest Europeans.” The segments tend to concentrate at the bottom-right of the panel. That means that they match the Neanderthal reference sequence to a high degree, but not the Denisovan. This makes sense since everything we know from earlier work indicates that Northwest Europeans don’t have Denisovan ancestry.

On the bottom-right you see Papuans. They’re very out of place because they are the only population in the list where Denisovan ancestry is greater than Neanderthal ancestry. This is visible in the match patterns.

South and East Asian populations exhibit a pattern with high (relative) levels of Neanderthal matches, but also a minor amount of Denisovan matching. This aligns with earlier work, which reported low levels of Denisovan admixture among populations with eastern Eurasian ancestry broadly.

The surprise is that the variation in matching to the Denisovan Altai genome exhibited a north-to-south cline. In particular, Northeast Asian populations seem to have a mix of two types of Denisovan. One, which is close to the Denisovan sequence that is normally used as a reference, and one which is diverged from it. The Papuans and South Asians seem to have Denisovan ancestry which is not so much like the Altai sample. This is not very shocking of course.

Finns barely miss the p-value cut-off (Bonferroni-corrected threshold), but they clearly have some Denisovan from East Asian gene flow, and some of it looks to be similar to the Altai Denisovan. Curiously, the Vietnamese (Kinh) don’t show any Altai Denisovan, but the Dai do. The Japanese have a lower proportion of the Altai Denisovan than the two Han Chinese samples. And very strangely the 1K Genomes samples from the New World, a substantial proportion of which have Amerindian admixture, show no Denisovan.

Pontus Skoglund immediately made a very interesting observation:

And Alexander Kim followed up:

In the thread to Skoglund’s original comment Africa Gomez notes that the authors suggest that high linkage disequilibrium in New World populations, due to recent admixture between diverged groups, may reduce the power to detect the Denisovan ancestry. So perhaps that’s that?

But for a moment, let’s set that aside. The best evidence right now is that the Denisovan admixture into Papuans, and therefore South Asians, occurred not too after the Neanderthal admixture event. That mixture is reasonably well dated because of ancient genomes which are closer to the period of admixture. But what about the second event with the Altai Denisovan? If what Skoglund says is true the date for that might be closer to the Last Glacial Maximum, and not when modern humans came to dominate the region. And I say dominate because there’s evidence that anatomically modern humans may have ventured quite far into eastern Eurasia before they finally swept aside more established lineages.

A few years back researchers found that one of the mutations that allow for Tibetan high altitude adaptation seems to have come in from a Denisovan genetic background. Spencer Wells, who knows a thing or two about Central Asia, has always half-seriously suggested that the legends of the Yeti derive from populations of archaic humans who persisted in the uplands of the heart of Eurasia.

But perhaps they weren’t pure Denisovans in any case. Work out of David Reich’s lab has suggested that Denisovans themselves, or at least the Alta Denisovan, harbors a deep ancient lineage diverged from modern humans, Neanderthals, and Denisovans, in low fractions. The “Altai Denisovan” admixture may have come into Northeast Asians via a mixed population, which arose when modern humans came to dominate eastern Eurasia, but only transmitted the Altai Denisovan ancestry later.

A preview review of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past

So I read the final version of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. It’s good. You can finally set aside The History and Geography of Human Genes, though with the rate of change in the field of ancient DNA I wouldn’t be surprised if there was a major revision of Who We Are and How We Got Here in two to four years.

I’m writing up a full reaction for National Review Online, so I’m not going to say too much here in specifics. And, since the book is still not out for a bit over a week I think it would be kind of rude of me to spill the beans on anything too juicy (though if you read this blog closely there won’t be any huge reveals).

So let me say something in the generality first. I’ve told the story of my friend Barry* before. Barry is a smart guy. He has a Ph.D. in the physical sciences from an eminent university in the Boston area. Barry works as a senior research engineer at a major semiconductor firm. Barry is interested in many things about the world. In 2011 I mentioned in passing to Barry over dinner that researchers had published in Science last year the fact that most humans alive today carry appreciable Neanderthal DNA. Barry was shocked. This was news to him. When I expressed shock that someone like Barry would be ignorant of this fact, Barry suggested perhaps I needed to expand my horizons as to the nature of things that the typical educated and interested person knows about science at any given time. That’s fair enough.

Someone like Barry is a perfect audience for Who We Are and How We Got Here. Barry hasn’t taken much biology, so the review of concepts such as recombination (even if the author doesn’t use that word) and mutation are useful. But more importantly, Who We Are and How We Got Here catches someone like Barry up to the state-of-the-art knowledge that we have in terms of human history, deep and prehistoric.

But it’s not just Barry. I’ve talked to plenty of people who work in evolutionary genomics who are not totally up-to-speed on the ancient DNA revolution. They too would benefit from reading Who We Are and How We Got Here front to back. I know people who work in the field of cultural evolution, who would also benefit from reading Who We Are and How We Got Here. I know behavior geneticists who would benefit from reading  Who We Are and How We Got Here. And so forth.

If you can’t find it in yourself to read 200-page supplements top to bottom, Who We Are and How We Got Here also is what you need.

Last summer I had the pleasure of having lunch with the author of Who We Are and How We Got Here, David Reich. If you read the prose it’s hard not to hear his precise and careful words echoing in your mind. Who We Are and How We Got Here is not rich with the same stylistic flourish and engagement as one might find in a popularization by Steven Pinker or Richard Dawkins. And I don’t think that was its intent, judging by how much space is given over to the four-population test! This is a serious book that is earnest in focusing on the substance of the science first, second, and last.

David expressed his discomfort with the opportunity cost that writing this book entailed for him when we spoke. While focusing on the book for the past few years he hasn’t had much time to do original analysis himself. His body language indicated the deep discomfort this caused him, and in Who We Are and How We Got Here he admits frankly that devoting himself to the book resulted in him not performing many analyses and publishing many papers.

One reason to write Who We Are and How We Got Here is that a book will reach outside the circle of those consuming and participating in the ancient DNA revolution. And a revolution it is! David Reich is already a highly eminent academic by any measure.  Who We Are and How We Got Here will do nothing to elevate his standing among his peers, because amongst them his stature is measured by the scientific papers published and projects in which he is involved.

So why make the sacrifice and write this book? Let me quote David Reich himself:

…I finally thank several people who repeatedly encouraged me to write this book. I resisted the idea for years because I did not want to distract myself from the science, and because for geneticists papers are the currency, not books. But my mind changed as my colleagues grew to include archaeologists, anthropologists, historians, linguists, and others eager to come to grips with the ancient DNA revolution.

I would expand the purview here more broadly: all public intellectuals should know about the human past in its fullness. It’s a shadow that hangs over us and frames our arguments about the present. How we came to be where we are matters unless you are the most clinical of logicians. If you are Gilbert Ryle, turn away!

In Who We Are and How We Got Here Reich recounts an encounter with an impudent undergraduate at MIT who wondered at the end of a lecture how it was he got funding for his abstruse projects. He responded with the standard pitch that goes into NIH grant proposals, that to understand human disease, one must also understand human population structure, and to understand human population structure it helps to understand human population history. After recollecting this anecdote Reich observes that he wishes he had responded differently. He concludes:

The study of the human past-as of art, music, literature, or cosmology-is vital because it makes us aware of aspects of our common condition that are profoundly important that we heretofore never imagined.

To me, this goes back to the Greek distinction of techne vs. telos. Science as an instrument in expanding the limits of human longevity and health is important, but it is not the only thing that science is capable of. If we turn science into pure instrument, we lose something essential and integral in its purpose.

These are old, ancient, universal disagreements. In ancient China, there were groups of philosophers who outlined a vision that had little use for the fripperies of the past. Legalists who wished to turn the whole society into an instrument of production and power, for whom techne was prominent. The Legalists expressed a cold calculating face of practicality and instrumentality, but the universal altruists who followed Mozi ultimately had some of the same inclinations. How could men make merry with music when there was still suffering in the world? Shouldn’t nonproductive cultural practices be curtailed before we achieve the Utopia of plentitude?

Because the disciplines of Confucius won the ancient culture wars the Legalists and Mohists are remembered as crass caricatures. But the Confucian respect and reverence for accumulated human wisdom, the customs, and folkways of the past, were wise, insofar as a Confucian system persisted in China for over 2,000 years.** They gelled with deep human dispositions.

If we are to view human beings more than production and consumption machines shackled to the modern capitalist hedonic treadmill, then we need to consider the past as part of who we are. It is part of the treasury of human existence, which is more than just feelings of the present, but echoes down through the generations, through family lines, and cultures, and even in our genes. Humans without root float freely, but they are never truly free.

* I’m changing names, though if you know me from college or know me personally, you know who I’m talking about.

** Obviously this is a coarse generalization, one could argue that Legalism was laundered through State Confucianism!

Open Thread, 3/14/2018

I finally met my old friend Ramez Naam in the flesh. Ramez’s publisher sent me his book More Than Human: Embracing the Promise of Biological Enhancement in 2005. One thing led to another, and somehow he’s guest blogging on Gene Expression!

CRISPR as we know it did not exist in 2005. Things have really changed since then, and for the better, at least from the perspective of genetic engineering. It’s as if some of the stuff in More Than Human is coming to life.

I also recommend his book The Infinite Resource: The Power of Ideas on a Finite Planet.

Ramez is more optimistic about the future than I am, though cautiously so. I hope he’s right, and I’m wrong. I fear he’s not.

My concern is not with technological innovation. That will happen. It’s with maintaining social stability due to the immiseration of what was the middle class in developed societies. Also, the bourgeois version of the New Class seems to lack empathy toward the future lumpen….

SEC Charges Theranos Founder Elizabeth Holmes With ‘Massive Fraud’. “Fake it ’till you make it” will keep happening if there are no follow-up criminal charges. Holmes may not have gotten away the con, but she was a paper billionaire for a while and funded R & D with the cash that they raised on lies. One moral some are going to take away is that she took a big risk and failed, but it was one that perhaps needed to be taken.

Adaptive landscape of protein variation in human exomes.

Genetic dissection of assortative mating behavior.

Conor Lamb Wins Pennsylvania House Seat, Giving Democrats a Map for Trump Country. I’m pretty bullish on a Democrat takeover of the house. The country will swing back. That being said, I’m also bullish on the idea that the Democrats are their own best enemy, and divisions and lack of coherency in their plan going forward will mean they won’t be able to capitalize on their electoral windfalls over the next few years.

This week’s episode of The Insight is up, 23andMe, the FDA, and Our Genomic Future. We have some potential guests lined up. One of whom is Stuart Ritchie, author of Intelligence: All That Matters.

Please subscribe via iTunes or Stitcher, and leave us 5-star reviews! 

St. Patrick’s Day is coming up. I’ll be avoiding drunk people on the streets of Austin. But I also want to point out that my “side-hustle” DNA Geeks has an M222 t-shirt available. In case you don’t know, that’s the legendary Niall of the Nine Hostages’ possible haplogroup (a sublineage of R1b). About 10% of Irish men are M222.

‘Tomb Raider’: Fans Slam Criticism of Alicia Vikander’s Body. There are two points that I want to make. First, at 5’5 inches, Alicia Vikande is of a very normal height (Angelina Jolie was two inches taller). She’s not physically imposing, and she has a very narrow waist as well. Her figure is “boyish.” Second, since the 1990s there has been a shift in male action stars toward being more shredded/athletic as opposed to jacked-up and exaggerated in their physicality. This is a very different Lara Croft for a very different time.

I decided to check out the new public library today. Saw the book The Invention of Humanity: Equality and Culture Differences in World History. I hate the overuse of the term “invention” in book titles, but when I noted the beginning covered China, I got it. Too often books that are Eurocentric turn out to be more data than narrow/inference, and they rig the data ahead of time to support their thesis (see, Inventing the Individual).

I also got Constructing the World (a David Chalmers book), The Bible and Asia: From the Pre-Christian Era to the Postcolonial Age, Creators, Conquerors, and Citizens: A History of Ancient Greece, The Third Reich: A History of Nazi Germany. That’s ranked in order of likelihood that I’ll get through them.

Also, Philip Jenkins has a new book, Crucible of Faith: The Ancient Revolution That Made Our Modern Religious World. Jenkins is a great scholar, I admire his work a lot. But I think I’m going to take a break from religious history, since I know a fair amount about the topic.

Polygenic scores and tea drinking.

Exposing flaws in S-LDSC; reply to Gazal et al.. Working your way through this literature is often pretty useful, so start at this commentary.

National Geographic has a special on race and what not. One piece being shared is kind of interesting, These Twins, One Black and One White, Will Make You Rethink Race. Here’s an important quote:

In genetic terms, skin color “is not a binary trait” with only two possibilities, Martin notes. “It’s a quantitative trait, and everyone has some gradient on this spectrum.”

Historically, when humans have drawn lines of identity—separating Us from Them—they’ve often relied on skin color as a proxy for race. But the 21st-century understanding of human genetics tells us that the whole idea of race is a human invention.

If you’ve read this blog you know I’ve blogged about “black and white twins” for over ten years. Also, I think a lot of the debunkings of race are pretty facile. But that’s not what I want to talk about. Rather, one of the things that are unmasked unwittingly in pieces such as this is how deeply Eurocentric these conversations are. It’s as if public intellectuals and journalists that write on this topic either don’t know any non-white families or they pretend that they don’t. The “humans” and “Us” implicitly points to white European systems of racial classification (e.g., East Asians relied on skin color somewhat, but since they are not much darker than white Europeans, they also included hair color, to distinguish the Dutch from the Portuguese, and large noses and body hair, to distinguish from themselves).

Twins with different skin tones are striking. But almost any South Asian, black American, or Latino, or Southeast Asian, or even East Asian, can tell you that there is a wide range of pigmentation within many families. Basically, unless you are in a homogeneous European social environment, where most everyone has very light skin on a global scale, you will see the variation of pigmentation within families. Both my parents have large sibling cohorts, and in both of them there are cases where the difference in complexion between siblings is in the same range as the two fraternal twins highlighted in the piece.

Of course, journalists who work for National Geographic or The New York Times know people of varied ethnicities and probably see that there is pigmentation variation within those families. They just pretend as if they don’t for these sorts of pieces which debunk race, and the readers pretend they don’t know this information as well as they take it in in a self-satisfied manner and nod sagely.

I haven’t had much time to read Enlightenment Now: The Case for Reason, Science, Humanism, and Progress. But those who say it’s quite like The Better Angels of Our Nature seem correct from how how far I’ve gotten.

My timeline has been swarming with debunkings of Enlightenment Now from all ideological angles. The best responses to these can usually be found in Saloni’s timeline (from her), who is “Pinker’s bulldog.”

Ex-Muslim TV‘s Twitter account is irritated that some of its stuff is now labeled “sensitive material.” The day before this came up I noted that one of my posts that Jerry Coyne retweeted about Islam and apostasy was also labeled “sensitive material.”

Basically if Muslims find it offensive, it might be subject to scrutiny from Twitter. This may or may not be defensible from Twitter’s perspective in a business sense, or ethically. But it’s just the reality we have to deal with, though I would like to know which school of Islamic jurisprudence Twitter relies on to gauge sensitivity and offense. I suspect it will be the Hanafi fiqh due to its liberal utilization of qiyas, which allow’s Del Harvey’s minions more free play.

The nation-state is dying. What will come out of its ashes? I suspect empire by another name….

The day we saw Stephen Hawking

In the spring of 1996, several of my dormmates decided to trek north to the University of Portland, to attend a speech by Stephen Hawking. We were still in that phase where we barely left campus, so intense was our social world. So this was a major undertaking. I don’t recall how we found out about the speech. This is before the internet was a widespread means of distribution of this sort of information (though I think we found out from my dormmate who was a journalism student).

I remember the anticipation and excitement. It was like we were going to a rock concert.

The talk Hawking gave was a typical one about cosmology. He also gave some shout outs to Linus Pauling, who was a native Oregonian.

Like many people, I had read A Brief History of Time. Also, perhaps like most people, I didn’t recall much from that book (I read the book years before going to the talk, in my defense).

Even by the mid-1990s, I was aware that Stephen Hawking was part of a somewhat out of control hype-machine. Though he was an eminent physicist, he was not necessarily the most brilliant physicist since Einstein (one of the claims on one edition of A Brief History of Time I saw at one point). We didn’t have Wikipedia, so I didn’t know about his somewhat messy personal life.

What we did know about Hawking was that he was a man of incredible brilliance who didn’t let his medical condition stop him. We admired him. We admired his achievements. He was heroic. By the time my dormmates and I saw Hawking in the flesh, he was already very frail. The only movement that we could perceive was that you could see he was breathing because of some barely perceptible movement around his neck.

At the end of the talk, people mulled around during the Q & A, trying to get as close as possible. I still have a vivid recollection of seeing Hawking up on the dais, in bright light.

Afterward, on the trip home, we reflected that it seemed unlikely that the great physicist had much time left, seeing as how he was nearly immobile. We felt privileged to be in his presence when he gave a talk. That was enough. Of course, he lived on for more than 20 years.

The barbarian invasions, illuminated by genetics

My own comprehension or understanding of the fall of Rome and the barbarian invasions probably began when I was about nine years old when I read a book about the various peoples who crashed the gates of civilization. First and foremost in the various descriptions were the Huns, a mysterious and fearsome race who in previous times had almost a talismanic role in the history of this period. Like the Mongols later on, they were more a force of nature that illustrated the hand of an angry God in the world than a people with their own agency.

But their identity was, and is, mysterious. Though contemporary descriptions seem to describe them as alien and repulsive in physiognomy, by the 19th century these antique descriptions were filtered through the racialist framework ascendent in the West of that period to cast them as foreign Asiatics. By the 20th century, a reaction set in and attempts to adduce the Huns’ possible connection to Central Asia seem to have diminished, though no one could deny the proposition either.

The fact that the ethnolinguistic affiliation of the Huns is mysterious to us should give a clue that they weren’t related to the standard Germanic or Iranian groups which operated on the fringes of the European Roman world. If the latter surprises you in the context of the European frontier of the Roman Empire, the Sarmatian tribes which pushed into Hungary and harried Rome defenses were related to groups like the Scythians, and branches eventually gave rise to the Alans (who ended up in the North African kingdom of the Vandals!) and Ossetians.* The German peoples have been observed by the Romans since the time of Cimbri invasions, and the later eruptions were easy to slot into that ethnographic framework.

In contrast, the Huns are mysterious precisely because they were a new cultural force. They seemed to be pure nomads like the Sarmatians, but not out of the Iranian steppe cultural milieu. Though they may have been a linguistic isolate, the most likely probability is that they spoke a Uralic (e.g., Hungarian) or Altaic language (e.g., Turkish). Like later steppe nomad hordes which burst out of Inner Asia into the Eurasian oikumene the genius of the Huns was in part organizational, as they accrued to their confederacy a motley of German and Iranian tribes. One standard narrative of the Gothic migrations is that their peregrinations were triggered by the movement of the Huns and their allies to their east and north.

An extreme social constructionist might assert that the term “Hun” simply brackets a new way to organize mobile barbarians beyond the Roman frontier. That they were not ethnically distinct. Though I don’t know anyone who holds to this extreme view, it’s not entirely impossible.

But now we have some genetic data. Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria:

…we generated genomic data from 41 individuals dating mostly to the late 5th/early 6th century AD from present-day Bavaria in southern Germany, including 11 whole genomes (mean depth 5.56×). In addition we developed a capture array to sequence neutral regions spanning a total of 5 Mb and 486 functional polymorphic sites to high depth (mean 72×) in all individuals. Our data indicate that while men generally had ancestry that closely resembles modern northern and central Europeans, women exhibit a very high genetic heterogeneity; this includes signals of genetic ancestry ranging from western Europe to East Asia. Particularly striking are women with artificial skull deformations; the analysis of their collective genetic ancestry suggests an origin in southeastern Europe. In addition, functional variants indicate that they also differed in visible characteristics. This example of female-biased migration indicates that complex demographic processes during the Early Medieval period may have contributed in an unexpected way to shape the modern European genetic landscape. Examination of the panel of functional loci also revealed that many alleles associated with recent positive selection were already at modern-like frequencies in European populations ∼1,500 years ago.

The admixture plot is key. They have enough markers that intercontinental genetic differences should be discernible. The male and female symbols should be familiar to you, but they also classified the samples by the cranial deformation (a practice associated with the arrival of the Huns to Europe). Blue ~ no deformation, green ~ intermediate, and red ~ deformation.

You can see that the individuals with cranial deformation, who are females, are genetically very distinct from everyone else. And, in particular, the males who exhibit no deformation are pretty homogeneous. Both PCA and admixture suggest that the males resemble typical North-Central Europeans. That is, Bavarians. The women on the PCA plot are shifted toward Southeastern Europe, where anthropologically the deformations were much more common.

The authors analyzed the features of these women and determined that they were likely darker than the males in eye color. This is entirely reasonable in light of their more Southern European genetic character.

There are a few other random samples too. In the admixture plot, FN_2 is a Roman soldier from ~300 AD from the Munich area. About two centuries before the Bavarian samples. The authors note it is curious this individual seems to exhibit Spanish ancestry (IBS being the Spanish samples). And yet this ancestry did not impact the region. Anyone who reads a history of the Roman Empire and its fall and regression knows that the area of southern Germany, Austria, and Hungary south into the Balkans became highly barbarized. It seems likely that many Roman peasants died or fled back to the safety of the empire.

PR_10 is a Sarmatian from the southern Urals. The individual has more “Finnish” ancestry, but that’s not atypical for Russian samples. The South Asian ancestry is something I’d dismiss normally, but I think this might be shared Yamnaya heritage.

Finally, VIM_2, like AED_1108 (a Bavarian female with cranial deformation), has East Asian ancestry. This individual was sampled in Serbia, dates to the 6th century, and is presumably a Gepid, a relatively obscure German tribe.

The presence of East Asian ancestry in these individuals highlights the likely cosmopolitan character of the barbarian zone stretching from Hungary to Bulgaria. It should definitely increase our likelihood that the Huns spoke a Turkic language of some sort. By the time most Turkic peoples arrive on the scene in Western Eurasia, they’re highly admixed, but they invariably have some East Asian ancestry. I highly doubt that the Huns arrived in Europe with the Southern European ancestry, TSI (Tuscan). So that is probably admixture over the century and a half since they arrived that allows for this individual to be predominantly TSI (though the individual may also have been a later Oghuz migrant). The ancestry of the Huns should have been more like a mix of East Asian and Sarmatia. The latter sorts were the first “West Eurasians” they’d run acros unless they had originally come from further south in the Tarim basin.

In the decades before the Huns turned West, they harried the East Roman Empire, pushed its limes back toward the sea, and extorted tribue out of it. After the collapse of Attila’s Empire, they seem to have retreated back to the territories to the east where they could be self-supporting, as opposed to extorting protection money out of states more powerful than them. Because the Huns become less of a problem for the Roman Empire, we don’t hear much about them by the late 5th century. And yet that does not mean they disappeared. The human and biological ecology of this region seems to have been amenable to the intrusion of Eurasian nomads, by the end of the 6th century the Avar confederacy was dominant in the interior Balkans and toward southeastern Germany.

Though this paper is not exactly revolutionary, it confirms that individuals from a post-Hunnic cultural configuration are mostly indigenous, that some evidence of East Asian ancestry persist, it shows that many of the arguments about Late Antiquity as to the ethnological character of peoples will be resolved. Unlike prehistory, where we have no written records, this period has clear and distinct cultures which we have a grasp of. The empty spots on the map are smaller.

* Some captured Sarmatians were settled in Britain on the frontier looking north. There are conjectures that Sarmatian motifs may have influenced Arthurian legends.

Turks are Anatolian under the hood, somewhat more Greek than Armenian

My post, Are Turks Armenians Under The Hood?, attracted a little bit of controversy. The main criticism, which was a valid one, is that I did not sample Anatolian Greeks. A reader passed on three Anatolian Greek samples. I also added a Cypriot data set. To my mild surprise, the Anatolian Greeks and Cypriots cluster together, at the end of the Greece cline toward West Asians. Therefore, for further analysis, I pooled the three Greeks with the Cypriots.

Additionally, there are two Balkan Turk samples. Even on the PCA it’s pretty clear that they’re genetically very different from the other Turks (one of them is from what has become Bulgaria), though the shift toward East Asians indicates that Turkification is very rarely a matter purely of religious conversion to Islam and assimilation of the Turkish language (obviously it initially is for many people, but these people then intermarry with those with some East Asian ancestry).

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The population genomics of South Asia is complicated, and politics doesn’t make it easier

Many people have been sending me links to this article, By rewriting history, Hindu nationalists aim to assert their dominance over India. Here’s a key section:

The RSS asserts that ancestors of all people of Indian origin – including 172 million Muslims – were Hindu and that they must accept their common ancestry as part of Bharat Mata, or Mother India. Modi has been a member of the RSS since childhood. An official biography of Culture Minister Sharma says he too has been a “dedicated follower” of the RSS for many years.

Sharma told Reuters he expects the conclusions of the committee to find their way into school textbooks and academic research. The panel is referred to in government documents as the committee for “holistic study of origin and evolution of Indian culture since 12,000 years before present and its interface with other cultures of the world.”

Sharma said this “Hindu first” version of Indian history will be added to a school curriculum which has long taught that people from central Asia arrived in India much more recently, some 3,000 to 4,000 years ago, and transformed the population

There are several threads here. First, it is a fact that the ancestors of South Asia’s non-Hindus were Hindu. There are minor exceptions, such as the Parsis, who are ~75% Iranian. One can quibble as to whether many tribal and peasant populations were truly Hindu in a formal and explicit sense. But I think this is a semantic dodge. Muslims would recognize these beliefs and practices as Hindu, no matter if one was a Brahmin monk or a member of a tribe which still sacrificed animals.

I’ve looked at the genotypes of a fair amount of South Asians of Muslim background. The overwhelming (usually exclusive) proportion of their ancestry is South Asian. It’s a fact that the ancestors of non-Hindu South Asians were Hindu.

But, the article and a dominant theme in Hindu nationalism today are that distinctive historically important groups like Indo-Aryans are indigenous to South Asia. This is set against a narrative of invasions and migrations from the outside, which is presumed more friendly to a multicultural paradigm (I have a hard time keeping track of the political valence of all these things). To some extent, the reality of invasions and migrations cannot be denied, whether it be Alexander, the Kushans, or the various Muslim groups. But these historical invasions left little genetic imprint.

When 2009’s Reconstructing Indian Population History was published things changed for the impact of the earlier migrations. By the time the ancient Greeks were recording observations of India in Classical Antiquity, it was already noted as the most populous nation in the world. I was initially skeptical about the result in Reconstructing Indian Population History, that there was massive admixture between West Eurasians (ANI) and indigenous South Asians (ASI) because that would imply massive migration. Additionally, phenotypically the pigmentation genes didn’t seem to work out if the source population was European-like.

Nearly 10 years on we have a lot more clarity. Ancient DNA has changed our understanding of the past. Massive migrations were common. And, the pigmentation and genetic profile of modern Europeans is recent, within the last 4,000 years. The source population(s) for “Ancestral North Indians” (ANI) may not have been Europeans in the way we’d understand them. In fact, a follow-up paper, Genetic Evidence for Recent Population Mixture in India, hinted at two admixtures. There’s a fair amount of circumstantial evidence now that one component of “Ancestral North Indian” relates to West Asian populations and another component to the more classical steppe Indo-Aryans. The former is more widespread across the subcontinent than the latter, which is concentrated in the northwest and among upper castes.

I do understand Indians who want to interpret their own history through the lens of their own cultural priors. The problem is that genetic science has proceeded so fast in the last few years that many propositions which were speculative in the 20th century are testable in the 21st century. Some Hindu nationalist friends and acquaintances express embarrassment and worry about the track that Indian nationalists are going on. I don’t know what to say, but Americans have their own delusions and blithe acceptance of propaganda, so I’m not going to be one pointing fingers. Other Indians have told me via Facebook that they “believe in the results from the 2000s” (when they were more congenial to their viewpoints?). I guess that’s one strategy; just keep up with the science until it starts refuting your model.

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Yellowbird ghost pepper sauce, 4.5 out of 5 stars

Yellowbird is a small-batch artisanal hot sauce brand out of Austin, TX. I’ve talked some smack about their habanero sauce before.

Well, today I swung by the local hot sauce shop, as I was out of the spice, and needed some more. I chatted up the clerk and we were talking Yellowbird, how the serrano sauce tasted so good, and how the habanero one was second-rate. I asked him about the ghost pepper variety, and he told me to try a sample. So I did. And I liked what I tasted!

This is not the spiciest sauce in the world. But very few non-extract hot sauces are killer. And, unlike extract sauces, Yellowbird ghost pepper sauce doesn’t taste artificial or metallic. Real hot sauces have complex flavors. Though not as spicy as something like Dave’s Insanity, this will leave most civilians sweating.

But there’s more than spice! Yellowbird ghost pepper sauce has a rich and nuanced flavor profile despite the powerful spice level, with a strong sour punch that hits you in the face before you even realize how hot it is. The savor is pretty flat from the beginning to end, but I tend to get a sweet kick at the end. I’m not a big fan of sweetness in hot sauces, but it isn’t pervasive and overwhelming and serves as a nice accent before you start to get the sweat on as capsicum binds to your receptors.