The derived SNP that causes dry earwax was not found in all non-Africans

A new paper on Chinese genomics using hundreds of thousands of low-coverage data from NIPT screenings is making some waves. I’ll probably talk about the paper at some point. But I want to highlight the frequency of rs17822931 in Han Chinese. It’s pretty incredible how high it is.

Because the derived variant SNP, which is correlated with dry flaky earwax when present in homozygote genotypes, is also associated with less body odor, it has been studied extensively by East Asian geneticists. Basically, individuals who are homozygote for the ancestral SNP, which is the norm in Europe, the Middle East, and Africa, tend to have more body odor, and in societies and contexts where this is offensive these people are subject to more ostracism in East Asia as they are a minority (some of the studies in Japan were motivated by conscripts who elicited complaints from their colleagues).

The relatively low frequency in Guangxi is to be expected. This province was Sinicized only recently. As in, the last 500 years. And it still retains a huge ethnic minority population, and many of the Han in the province likely have that ancestry. But the question still arises: why do the Han have such a high frequency of rs17822931?

Here’s a plot of frequencies:

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Likely male-mediated Indianization in Southeast Asia

Pop     N R1a1
Cambodian     125 7%
Balinese     551 2%
Southern Han     166 0%
Northern Han     65 0%
Miao     25 0%
Hui     25 17%
Sala     43 21%
Bo’an     44 25%
Dongxiang     47 32%
Black, Michael L., et al. “Genetic ancestries in northwest Cambodia.”

In the comments below a reader has pointed out that there are Y and mtDNA results for Cham people.

This Austronesian group was once dominant in what was termed Annam by the French, the central regions of coastal Vietnam between the deltas flanking the northern and south (dominated by the Vietnamese and Khmer respectively). The Cham were a seafaring population and had extensive contacts with maritime Southeast Asian and the network of Austronesian peoples.

As such, the Cham were influenced by the currents of cultural change to their south, and as by the early modern era many had become Muslims. But a minority resident in Vietnam retained their Hindu religious identity, and this reflects a deep current of Indianization which took root among them in the centuries before 1000 AD. The boundary between ancient Champa and Đại Việt was also a civilizational boundary, between the elite culture of India and China.

The commenter states:

As far as I can see, this sample of Chams from Binh Thuan Province, Vietnam does not exhibit any clear South Asian influence in its mtDNA. This contrasts starkly with the significant (18.6% to 32.2%) South Asian influence that is apparent in the Y-DNA of the male subset of the same sample

This seems right. As you can see above I’ve found plenty of evident that R1a1a is found in Southeast Asia where it shouldn’t be. Notice that among northern groups in China R1a1a is pretty frequent too. Obviously from a different source, but the same general pattern. And in that case we have plenty of historical evidence of interaction with Indo-Europeans on the steppe.

I’m not very conversant in mtDNA. This paper argues that the Mon people of Thailand have some mtDNA affinities with India. I created this pivot table for readers to double-check (the “MO” populations are Mon).

The history of Southeast Asia, or perhaps more accurately the quasi-history of Southeast Asia since so many of the records are from China and elsewhere, indicates strong Indian influence in the period before 1000 AD. The standard model is that this is cultural diffusion. And by and large Southeast Asian peoples are are mostly indigenous. But, a non-trivial minority of their ancestry is recent, but pre-colonial, gene flow from the Indian subcontinent. Additionally, the imprint is easier to see in the Y chromosome than the mtDNA. The legends of marriages between Indian Brahmins and native princesses in places like Cambodia probably do reflect something real in the dynamics of the early Indianization.

Related: Indic Civilization Came To Southeast Asia Because Indian People Came To Southeast Asia. Lots Of Them.

Obscurantism in the service of transformation

The paper, Ancient Admixture in Human History, was peculiar as far as genetics publications go in that it foregrounds particular abstruse statistical methods developed due to the stimulus of genome-wide variation data. The surfeit of genomic data has resulted in the emergence of many subtle and almost impenetrable works laced with formalisms which daunt most biologists. But given time and effort, these newer methods relying upon greater analytic sophistication are decipherable.

To illustrate what I’m talking about, consider Mathematical Models of Social Evolution. This is a book with a fair amount of formality, but the topic, culture, social change, are often considerations which we ruminate upon verbally.

I open up to page 238 (I literally opened a random page).

…According to this approximation, the altruistic gene will increase whenever

    \[ \frac{g}{c} > \frac{2n}{\Omega} \]

In intrademic models in which groups are formed at random, \Omega = 1. In contrast, if groups were made up of full-sibs, \Omega = 2n. This provides a natural scale on which to judge the effectiveness of interdemic selection. If \Omega is near one, interdemic group selection is no more effective than intrademic group selection with random group formation, which is to say, it cannot lead to the evolution of strong altruism. If \Omega is large, then itnerdemic group selection is effective.

On first blush, the passage can seem impenetrable. But most of the people reading this are probably not intimidated by mathematical formalism. Many of you will know what intrademic and interdemic selection are. Some of you who are more numerically oriented may test some values to develop an intuition. The point is that the formalism is not there to intimidate. It is meant to illuminate. It is there so individuals thinking on the same problem can have a crisp currency with which they can exchange ideas.

Another major reason that this sort of formalism exists is that it’s clear when you think someone is wrong. A problem with many verbal arguments is that they are unspecified or vague in such a way that you’re not even sure if you disagree or agree with your interlocutor. The point is to get somewhere. Coherency. Contingency. And cumulativeness.

Applying a mathematical theory derived from evolutionary biology to cultural and social change strikes many people as strange. But there’s a method to this madness. Theory with data can give birth to a better understanding of the processes which define our world. A description of reality.

In contrast, let me quote Noam Chomsky:

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Chinese and Indian American population genetic structure

In Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past David Reich makes the observation that India is a nation of many different ethnicities, while China is dominated by a single ethnicity, the Han. This is obviously true, more or less. Even today the vast majority of Indians seem to be marrying with their own communities, jati.

Over the years I’ve collected many different genotypes of Americans of various origins who have purchased personal genomics kits, and given me their raw results. I decided to go through my collection and strip detailed ethnic labels and simply group together all those individuals from India, and China, who have had their genotypes done from one of the major services.

I suspect that these individuals are representative of “Indian Americans” and “Chinese Americans.” So what’s their genetic structure?

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Are there an other readers from 2002?

As some of you know, this blog started in early June of 2002. I just noticed that two people left comments who date from the summer of 2002…which means I have people here who have been reading what I’ve been writing for 70% of my adult life. I know people drop in and out, but are there any others?

Just curious.

Nomads, cosmopolitan predators, and peasants, xenophobic producers

Ten years ago when I read Peter Heather’s Empires and Barbarians, its thesis that the migrations and conquests of the post-Roman period were at least in part folk wanderings, where men, women, and children swarmed into the collapsing Empire en masse, was somewhat edgy. Today Heather’s model has to a large extent been validated. The recent paper on the Lombard migration, the discovery that the Lombards were indeed by and large genetically coherent as a transplanted German tribe in Pannonia and later northern Italy, confirms the older views which Heather attempted to resurrect. Additionally, the Lombards also seem to have been defined by a dominant group of elite male lineages.

Why is this even surprising? Because to a great extent, the ethnic and tribal character of the post-Roman power transfer between Late Antique elites and the newcomers was diminished and dismissed for decades. I can still remember the moment in 2010 when I was browsing books on Late Antiquity at Foyles in London and opened a page on a monograph devoted to the society of the Vandal kingdom in North Africa. The author explained that though the Vandals were defined by a particular set of cultural codes and mores, they were to a great extent an ad hoc group of mercenaries and refugees, whose ethnic identity emerged de novo on the post-Roman landscape.

In the next few years, we will probably get Vandal DNA from North Africa. I predict that they will be notably German (though with admixture, especially as time progresses). Additionally, I predict most of the males will be haplogroup R1b or I1. But the Vandal kingdom was actually one where there was a secondary group of barbarians: the Alans. It was Regnum Vandalorum et Alanorum. I predict that Alan males will be R1a. In particular, R1a1a-z93.

But this post is not about the post-Roman world. Rather, it’s about the Inner Asian forest steppe. The sea of grass, stretching from the Altai to the Carpathians. A new paper in Science adds more samples to the story of the Srubna, Cimmerians, Scythians, and Sarmatians. Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads. The abstract is weirdly nonspecific, though accurate:

For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.

The German groups which invaded the Western Roman Empire were agropastoralists. That is, they were slash and burn farmers who raised livestock. Though they were mobile, they were not nomads of the open steppe. Man for man the Germans of Late Antiquity had more skills applicable to the military life than the Roman peasant. This explains in part their representation in the Roman armed forces in large numbers starting in the 3rd century. But the people of the steppe, pure nomads, were even more fearsome. Ask the Goths about the Huns.

Whole German tribes, like the Cimbri, might coordinate for a singular migration for new territory, but for the exclusive pastoralist, their whole existence was migration. Groups such as the Goths and Vandals might settle down, and become primary producers again, but pure pastoralists probably required some natural level of predation and extortion upon settled peoples to obtain a lifestyle beyond marginal subsistence. Which is to say that some of the characterizations of Late Antique barbarians as ad hoc configurations might apply more to steppe hordes.

There has been enough work on these populations over the past few years to admit that various groups have different genetic characteristics, indicative of a somewhat delimited breeding population. But, invariably there are outliers here and there, and indications of periodic reversals of migration and interactions with populations from other parts of Eurasia.

Earlier I noted that Heather seems to have been correct that the barbarian invasions of the Roman Empire were events that involved the migration of women and children, as well as men. The steppe was probably a bit different. Here are the Y and mtDNA results for males from these data that are new to this paper:

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Almost no one is a genetic determinist except in your Communist imagination

Next summer I’m going to be giving a talk at the ISIR meeting. I’m a little bemused about this since, to be honest, I don’t talk much about behavior genetics and intelligence anymore.

Until August of 1998, I had rather conventional views for someone of my education and social background on psychometrics. Then I read Chris Chabris’ article in Commentary. From that, I began to conclude the “orthodoxy” that was presented in the elite media really wasn’t representative of what was going on in the field of psychometrics. It’s kind of like thinking that you get a balanced view of the Arab-Israeli conflict from reading Commentary.

Over the next few years, I read some books, review papers, and updated my views. Every few years I read a book or checked out a paper to see if anything had changed…and usually not to my eye as someone who is not in the field. About a decade ago I read What Is Intelligence?: Beyond the Flynn Effect. More recently I read Stuart Ritchie’s Intelligence and Richard Haier’s The Neuroscience of Intelligence. And other things here and there.

I’ll be reviewing Blueprint: How DNA Makes Us Who We Are, but I do wonder if it’s nothing more than an incremental improvement upon The Nurture Assumption: Why Children Turn Out the Way They Do.

Incrementalism isn’t a problem. I am a big fan of genomics. But its impact has been variable. And frankly in some fields less than you might think. I don’t believe it has changed our understanding of evolutionary process qualitatively (rather, it has allowed a finer-grained resolution to certain arguments around particular hypotheses). Educational attainment 3 is great. But does it change how heritable I think intelligence is in a qualitative sense? Not really. We already knew it was a heritable trait, and we’ve known it for a long time.

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How related should you expect relatives to be?

Like many Americans in the year 2018 I’ve got a whole pedigree plugged into personal genomic services. I’m talking from grandchild to grandparent to great-aunt/uncles. A non-trivial pedigree. So we as a family look closely at these patterns, and we’re not surprised at this point to see really high correlations in some cases compared to what you’d expect (or low).

This means that you can see empirically the variation between relatives of the same nominal degree of separation from a person of interest. For example, each of my children’s’ grandparents contributes 25% of their autosomal genome without any prior information. But I actually know the variation of contribution empirically. For example, my father is enriched in my daughter. My mother is my sons.

The sample principle applies to siblings. Though they should be 50% related on their autosomal genome, it turns out there is variation. I’ve seen some papers large data sets (e.g., 20,000 sibling pairs) which gives a standard deviation of 3.7% in relatedness. But what about other degrees of relation?

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Postcolonial imperialism

Rereading Edward Said’s Orientalism I am struck by the fact that he’s a very good writer compared to his heirs in postcolonial studies. As someone who cites Foucault, it is natural that there is a fair amount of vapid but lexically textured passages in Orientalism (you can open up any page and stumble upon a polished but inscrutable passage). But the general thesis and the review of the literary works seems moderately coherent actually. Far less of a screed than the more recent distillations. Who says evolution ascends upward in complexity?

As someone who isn’t well versed in literature I can’t really comment on the validity of the interpretations, but, there is one thing that I noticed in Said’s argument which prefigures modern postcolonialism: it abstracts and generalizes from a particular instance in human history, European interactions with non-Europeans in the early modern and modern period, and projects them across all of history. Like tachyons going back in time the manipulations and predations of early modern Europeans echo back through time and forward into infinite.

Here is a representative sample of what I’m talking about. The first section is a quote from Aeschylus:

Now all Asia’s land
Moans in emptiness.
Xerxes led forth, oh oh!
Xerxes destroyed, woe woe!
Xerxes’ plans have all miscarried
In ships of the sea.
Why did Darius then
Bring no harm to his men
When he led them into battle,
That beloved leader of men from Susa?

What matters here is that Asia speaks through and by virtue of the European imagination, which is depicted as victorious over Asia, that hostile “other” world beyond the seas….

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Open Thread, 9/30/2018

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

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

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

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

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

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

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

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

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

He’s trolling us.

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

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

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

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

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

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

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

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

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

Reproductive Longevity Predicts Mutation Rates in Primates.

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

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

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

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

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

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

Stuart Ritchie was not happy with Comfort’s review:

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

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

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

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

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