Open Thread, 01/26/2020

I’ve been posting a fair amount about Southeast Asia. This an important part of the world. As outlined in Victor Lieberman’s Strange Parallels, there are similarities to Europe in terms of the ‘naturalness’ of nation-states. Especially in mainland Southeast Asia. Burma is dominated by Burmans. Thailand is dominated by Thais. Laos, but the lowland Lao. Cambodia by the Khmers. And Vietnam by the Kinh. Liberman’s hypothesis is generally geographical. He contends that the ‘protected’ geographic character of mainland Southeast Asia has analogs to Western Europe, which also was relatively sheltered by the impact of the Eurasian steppe.

One of the primary similarities between Europe and mainland Southeast Asia is that there is a combination of deep indigenous ethnocultural traditions as well as important external influences. Burma, Thailand, and Cambodia leverage Indian religious and political theory to maintain coherence. In contrast, Vietnam replicates much of the character of China. The “standard model” has been Indian influence is a function of “cultural diffusion.” But looking more deeply at the genetic data, it seems that 5-20% of the ancestry might be Indian. This is a minority element. But it is not trivial, especially in light of the likely dilutive effects of the Tai migration, as well as the Chinese in Thailand.

In Coronavirus, a ‘Battle’ That Could Humble China’s Strongman. One thing I will say is that public health professionals are focused on the tail risk. The risks are real. But please note that the worst-case scenario may not be the most likely scenario.

A Glittering Crossroads: In Damascus’s Umayyad Mosque, Roman paganism, Christianity, and Shiite and Sunni Islam all intersect. The Umayyad’s are Islam’s “first dynasty.” But they have a bad reputation among Muslims. The Shia hate them because their founder was an enemy of Ali, and eventually killed his grandsons. The Sunnis dislike them because they are perceived as impious Arab warlords, rather than Muslims. The latter view is colored by the commentaries of intellectuals who were patronized by the Abbassids, the successors of the Umayyads. But the piece above illustrates the reality that the Umayyads likely weren’t Muslims as we’d understand it for much of their history.

San Francisco Mayor London Breed endorses Mike Bloomberg for president. Weird.

The Saudi Connection: Inside the 9/11 Case That Divided the F.B.I. Money corrupts.

Medical data and machine learning improve power of stroke genome-wide association studies.

After Culinary and Literary Acclaim, She’s Moving to the Woods. ‘…every weekend from May to October, 10 people will each pay $750 to nearly $1,000 to relax in the woods and immerse themselves in what some chefs and writers have started calling “new gatherer” or “deep nature” cooking.’

Insight into the genomic history of the Near East from whole-genome sequences and genotypes of Yemenis.

Unrelated males in colonies of facultatively social bee.

Dynamic evolution of great ape Y chromosomes.

On the origin and evolution of RNA editing in metazoans.

Singer-songwriter David Olney dies on stage during performance at Florida festival.

Roger Scruton, a Provocative Public Intellectual, Dies at 75.

3000 years in the Levant, with Marc Haber. The Insight is cranking along.

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Indian ancestry maritime Southeast Asia

In the comments, people keep asking about Indonesia, and Java in particular. The reason is pretty simple: before wholesale conversion to Islam maritime Southeast Asia was dominated at the elite level by Indic social and religious forms. I say “Indic” because unlike mainland Southeast Asia Theravada Buddhism did not supplant other Indian religions, and in fact, while indigenous Buddhism that led to the Borobudur temple complex in the 9th-century went extinct, Hinduism persisted for quite a bit longer and persists to this day. Not only are there long-standing Hindu traditions in Bali, but far eastern Java remained a Hindu kingdom until 1770, and there remain Javanese Hindus (some of them are recent converts).

As several mainland Southeast Asian groups seem to have Indian admixture, what is the evidence for Indonesia? (the Singapore genome data offers up some Malays, and though some show recent Indian admixture, all of them have some Indian admixture). Luckily, there is a paper and data, Complex Patterns of Admixture across the Indonesian Archipelago. It uses the GLOBETROTTER framework, so I decided to reanalyze the data in a simpler manner, adding the Cambodians as a check (since from my previous posts you know a fair amount about that as a baseline).

Three points.

1) Definitely gene flow. But on the whole less than mainland Southeast Asia?

2) Lots of heterogeneity. Not surprising. The Sumatra samples seem to be taken from Aceh. This may matter a great deal.

3) In mainland Southeast Asia east of Burma there hasn’t been lots of colonial migration of Indians, nor a great deal of trade. The opportunities within maritime Southeast Asia for contact with outsiders are far greater. The inspection of results from Malaysia indicates continuous gene flow over a long period of time. In contrast, the results from Thailand and Cambodia indicate an early pulse.

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The Indian admixture into Southeast Asia is not just a function of distance

In the comments to the post below about Indian ancestry in Thailand, some observed that this should not be surprising due to reciprocal gene flow and proximity. Implicitly, I think what is being suggested here is that there is isolation by distance and continuous gene flow. Obviously some of this is true, but there details here which suggest that it is simply not just geography at work.

The reason I was curious about the Dusun people in coastal Borneo is that while Malays all seem to have Indian ancestry, many tribal Austronesian groups in maritime Southeast Asia do not. The Indian admixture into the Malays is not just recent. Some of it seems quite a bit older than the colonial period.

In the context of Southeast Asia, it seems that some of the more ancient Austro-Asiatic people, in particular, the Mon and Khmer, have Indian ancestry, and groups which mixed with Austro-Asiatic substrates, such as Burmans and Thai, also have this.

Additionally, some groups in the northeastern states of India have less “Indian” admixture than the Thai and Khmer. To show this, see this PCA:

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Thais may have more Indian ancestry than Cambodians and less than Burmese

Click to enlarge

There were some questions about the Indian ancestry of the Thai. The dataset released by the Reich lab has some Thai. I pulled that data, and some other Southeast Asian groups, and Tamils and Tajiks. The merging only left 62,000 SNPs, but that’s probably enough to answer this question. The PCA above shows the West Eurasian shift of some groups. The Thai definitely seem pulled to the Tamils, and are similar to the Cambodians, but with a bit more Indian ancestry and less “southern” Southeast Asian.

Below the fold are admixture and TreeMix plots. Basically you see what I’m talking about but in more detail. The Indian-like ancestry in the Luzon samples is really Spanish. The Ami and Atyal are Taiwanese aborigines. You see that they have the least West Eurasian ancestry. Even southern mainland Chinese seem to have some of that, indicating long-distance gene flow. But groups like Miao, Vietnamese/Kinh, and Dusun (Austronesians from Borneo) don’t the Indian ancestry that Thai/Lao/Cambodians/Malay have.

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A different time comes

When I was younger I read many of Frank Herbert’s Dune series of books. Though there was a notable decline after the first installment (or at least diminishing returns), I read the whole original series (and follow-ups), so I must have enjoyed it to some extent. I’m not really a completist, as such.

But an aspect of the world-building always bothered me.  The societies just seemed highly regressive, and that truly bothered me. My problem is best illustrated by the title of God Emperor of Dune. It struck me as almost sacrilegious that in the bright and shining future humans would still have emperors, whom they worshipped as gods. That they would organize themselves in such a hierarchical manner. The whole idea struck me as…Bronze Age!

“Everyone” knew, after all, that liberal democracy, and in particular the American flavor, was going to be the future. There would be changes on the margin, but the general structure which would allow humans to flourish had been established. We were at the end of history. We had figured out how best to be human.

As a young person, I simply did not reflect on the fact that every age, and every place, takes its own values and preoccupations for granted. And, people of every age and every place cannot imagine a different scenario. We are always at the center of the universe’s story, no matter who we are and where we are. But the reality is that no one truly has a privileged place. At some point, the eternal equilibrium will arrive. But not this day.

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All the commotion within Africa

Unless you’ve been asleep, you probably know by now that the Reich lab has come out with a paper that analyzes the remains of 4 individuals from western Cameroon, dating to 8,000 and 3,000 years ago (2 of each, with one of the older individuals yielding 18.5x coverage DNA!). The location and timing both matter.

This area of Cameroon is hypothesized to be the point of expansion for the Bantu migration. This expansion began about 3,000 years ago and swept east and south until the agricultural streams met back up in southern Africa.

Perhaps then the authors then “caught history in action” with a change between 8,000 and 3,000 years ago? No such luck actually. Here is the abstract, Ancient West African foragers in the context of African population history:

… One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region…However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today—as well as speakers of Bantu languages from across the continent—are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.

Basically, just like elsewhere in Africa where the Bantu expanded, you see massive discontinuity in this region of Cameroon (the modern agriculturalists in the area are Bantu-speaking). If you have ever analyzed African genetic data, the lack of high magnitude structure of the Bantu over wide areas is pretty shocking. The reason there’s little structure seems to be two-fold

  1. Rapid population expansion, so not much time to accumulate distinct variants (you see this in Northern Europe too)
  2. Minimal admixture with local populations, at least until you get to modern-day South Africa (then there is an admixture cline with Khoisan)

Meanwhile, you have these zones of relic hunter-gatherers here and there. These samples seem to be one of those cases. I think it’s analogous to the fact that hunter-gatherers persisted in pockets for thousands of years after the initial arrival of Neolithic farmers in Europe.

There are two types of things you can take away from a paper like this. General insights. And specific details. The plot at the top of this post illustrates a model that they generated with these data. It seems quite clear that the details are not crisp, and subject to a further specific revision. But the general insights seem robust and extend what we already knew.

First, there were several human lineages that diverged 500,000 to 1 million years ago. In Eurasia, these became Neanderthals and Denisovans. In Africa, one of the branches led to what we call “modern” humans. But a variety of lines of evidence indicate that within Africa there were also highly diverged human groups, analogous to Neanderthals and Denisovans. One could call them “African Neanderthal” analogs. But within the context of this paper, they are “ghost archaics.” But those aren’t the only “ghosts.”

Extant human populations sample only a fraction of the “modern” family tree, which seems to have diversified from one of the African human groups 300,000 years ago or so.

There is now a fair amount of circumstantial evidence that Neanderthals mixed with an African lineage that is an outgroup to most other Africans and descended-from-Africans. Because of its size and warm climate, I believe that Africa was quite a good habitat for humans, and there were a variety of them across the continent. Though I don’t discount deep-time back migration of Neanderthal/Denisovan groups into Africa, I think due to the different population sizes it is probably more the case that Africans went into western Eurasia than vice versa. Additionally, Southeast Asia seems to be a good target habit for any African species due to similarities of biome (e.g., Sundaland).

Finally, there is the fact that it seems non-African ancestry is closest to the Mota sample, dated to 4,500 years ago in Ethiopia. This makes geographic sense, though I do wonder if this is an artifact of continuous gene flow back from Eurasia, as much as the likelihood that this is near the exit path of African humans.

What about the details of this paper? Look a the supplements and notice all the admixture graphs. There are lots of potential fits to the data, and more data will come in. The paper is clear to not put too much faith in one set of weights for gene flows, and different graphs might explain the patterns in the data. Additionally, a highly dense African landscape of hominins might exhibit lots of continuous gene flow and isolation by distance. There’s a lot more to learn. Nothing is being closed in this case.

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Indian Y chromosomes in Thailand

The region of modern Thailand has gone through a major cultural shift over the last 1,000 years. Today the zone of Austro-Asiatic speech in mainland Southeast Asia is fragmented. To the east, there are the Khmer people of Cambodia, as well as various “hill-tribes” in Thailand and Laos who also speak Austro-Asiatic dialects. To the west, there are the Mon people of Burma.

But around 1000 A.D. the whole zone from the India ocean out toward the Mekong was dominated by Austro-Asiatic peoples. Modern-day Thailand was dominated by the Dvaravati polity, of which little is known, but possible Mon associations are assumed.

I have posted several times about the reality that it seems the whole zone between Burma and Cambodia seems to be impacted by a non-trivial proportion of South Asian (Indian) ancestry. A new preprint has a lot of Y chromosomes from various groups in Thailand. Below are frequencies I pulled out of two ethnic groups with large sample sizes (from table 3 in the supplements):

R1a+RLJ2HSample Size
Mon15%2%5%2%105
Central Thai13%0%3%5%129

These lineages are clearly more evidence of Indian males settling in this region.

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Open Thread, 01/20/2019

As I’ve been slowly but surely phasing out of posting much original content on Twitter I’ve been thinking about what has happened to the platform. One thing that I think seems obvious is that all communities degrade and degenerate until only the assholes remain. I saw this pattern in the early teens in “science writer” Twitter. I unfollowed a lot of those people in 2013-2014 because the constant drama was tiresome.

I was smug that “academic science” Twitter wasn’t like that. People were having discussions in good-faith.

It turns out that academics were no better, it’s just that writers had gotten on Twitter in full-force earlier. Just like ecosystem succession, the “climax” ecosystem is dominated by posturing smug assholes.

The problem for Twitter is that it’s democratic, open, and imposes a cap on complexity and nuance. At least with blogging, there was a niche for people who were earnest and wrote 1,000-word entries. Because of the format of Twitter, you couldn’t express a lot of complexity. You had to rely on good-faith engagement. If your interlocutor wanted to be an asshole, the medium really facilitates their behavior.

Unfortunately, unlike scientists, journalists seem to “have” to be on Twitter. I think it’s turning them all into smug assholes. Recently I’ve started seeing pieces in some web publications which are prose forms of what I see on Twitter.

Mohammed bin Zayed’s Dark Vision of the Middle East’s Future. When Western journalists profile M.B.Z. they want to paint a dark picture. But does it come across that way to the fair-minded reader?

How U.S. Firms Helped Africa’s Richest Woman Exploit Her Country’s Wealth. The ruling clique in Angola had a period where they were “Leftists,” or were aligned with the Soviet bloc. But if you read about the history of this faction, that was fake.

Why Do Trump Supporters Support Trump? Michael Lind has a new book out, The New Class War: Saving Democracy from the Managerial Elite . Lind is an unabashed Hamiltonian, and an admirer of Henry Clay’s “American system.” He is in some ways the inverse of Matt Stoller, though arguably both are to the Left of the Center (Stoller far more Left). Anand Giridharadas, in the review linked, is not a fan. Unlike both Stoller and Lind, Giridharadas says uninteresting and fashionable things. You will never see Giridharadas go off the script in a novel or unsurprising way. This is in contrast to both Stoller and Lind.

I bought the Lind book just now. Like I bought Stoller’s book. Mostly because these two individuals are at least sincere, as opposed to mouth-pieces for factions.

Ancestral Haplotype Reconstruction in Endogamous Populations using Identity-By-Descent.

The Chinese Population Crisis. The one-child-policy was not good. On the other hand, look at the trajectory in other East Asian nations, and it’s pretty clear its impact was on the margin. China was always going to have this problem.

Capitalism Draws Fire, Despite Strong Global Economy. This piece in WSJ has an infographic: “Percentage of people surveyed who believe they and their families will be better off in 5 years – Global average in 2019: 47%.” This looks to be the average of nations, not weighted by population. India, China, Indonesia, and Brazil, are all optimistic nations, 70-80%. These four are over 40% of the world’s population!

Studies of human twins reveal genetic variation that affects dietary fat perception.

Novel phylogeny of angiosperms inferred from whole-genome microsynteny analysis.

A scalable method for estimating the regional polygenicity of complex traits.

In Huawei Battle, China Threatens Germany ‘Where It Hurts’: Automakers.

Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq.

Genetic analysis of male Hungarian Conquerors: European and Asian paternal lineages of the conquering Hungarian tribes.

Saudi Society Is Changing. Just Take a Look at These Coffeehouses.

A New Model of Genetic Variation and Evolution Evaluates Relative Impacts of Background Selections and Selective Sweeps.

The fate of standing variation and new mutation under climate change.

Genome-Wide Search for Candidate Drivers of Adaptation Reveals Genes Enriched for Shifts in Purifying Selection (SPurS).

Windows out of Africa: A 300,000-year chronology of climatically plausible human contact with Eurasia.

Mate selection provides similar genetic progress and average inbreeding than optimum contribution selection in the long-term.

Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations.

The origin of domestication genes in goats.

Why ‘Star Wars’ Keeps Bombing in China. I’m an “80s-kid”, so a lot of the motifs of “Star Wars” played a big deal in my “playing” during my elementary years. But I never got into the whole series, so I kind of get why the Chinese are shrugging.

Crater Left by One of Earth’s Biggest Ever Meteorite Impacts Finally Found.

Missouri charmer led double life, masterminded one of the biggest frauds in farm history.

Some people are mad about my posts on Tutsi genetics. Do you know who is not mad? Tutsis reaching out to me, angry that the autocratic government of Rwanda is promoting lies. In any case, there are some academics who are uncomfortable about what I did. This reminds me of the fact that a friend who works in human rights in D.C. for a minority group told me of the various groups she engages with, academics are the most cautious and cowardly (she talks to journalists, think-tankers, lobbyists, etc.).

What Americans Don’t Understand About China’s Power. It’s not China’s rise, but our quiescence.

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Ideas may matter in the aggregate, but not on the individual scale

Scott Atran’s In Gods We Trust: The Evolutionary Landscape of Religion convinced me of many things. One of the things it convinced me is that aggregate espoused beliefs had a marginal consequence on the individual level. There were several reasons for this. Some of the elements of “higher religion” which were asserted by some beliefs, e.g., the rejection of free will in Calvinism and Sunni Islam, seem to have not been internalized in their actions by believers themselves (even if espousing those beliefs). In other cases, such as the Trinity, most believers had a very tenuous grasp on the details of what that belief entailed (e.g., the term “essence” is no longer as resonant in the modern age, even among intellectuals).

On a particular level, Jared Rubin’s Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not makes a reasonable argument for why ideology matters when it comes to religion and society. I’m not entirely convinced by Rubin’s argument, but it’s a legitimate one.

More broadly, the field of “cultural evolution” has convinced me that norms, values, and practices, can bind groups together to produce cohesion, and result in inter-group differences in characteristics which redound to their success in competition.

Where does this leave me? In David Abulafia’s The Great Sea the author mentions Amalfi’s repeated alliances with Muslim polities and corsairs. Similarly, Hungarian Protestants marched with Turks, Lithuanian Tatars with Catholics, and the Hindu generals of Muslim Mughals ruled the subcontinent for their potentate. Practicality and reality make strange bedfellows. But, on the whole, there are systematic trends and biases. It seems possible that though ideology has a weak to nearly zero individual impact, there are subtle differences on the margins in the aggregate which compound to produce large differences on the macro scale.

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The Belgians did not invent the Hutu and Tutsi ethnic groups, who have different origins

Since I resurrected the analysis of Tutsi genotypes last year I’ve been getting a fair number of emails and messages from people. The issue is that periodically someone, usually, but not always, a white male, will explain that “actually, Tutsis and Hutus aren’t real ethnic groups, and were invented by the Belgian colonialists….” Many people from this region of the world are privately very skeptical of this viewpoint (they tell me so, but don’t want to get into a huge public spat with all-knowing-white-gods). After all, they are from this region, and Hutus are Tutsis are physically often quite distinctively different. They simply do not buy the social constructionist narrative as explaining everything that they see with their own eyes.

But we’ve seen this before, haven’t we? “Well actually, the Lombards weren’t ethnically different from the Romans, they were a Germanized group of mercenaries who created an identity de novo.” Also, “well actually, ‘caste’ is an ancient Indian concept but modern caste-jati groups were reified by the British in the 19th-century….” (genetics tells us both assertions were wrong).

Historiography of the early 21st-century will observe that many white semi-intellectuals took on the metaphorical role of Hamlet in world history, tortured and self-hating souls who put themselves at the center of every dramatic event. All roads lead back to Hamlet.

As it happens, I now have a single Hutu to compare the dozen or so Tutsis to.

Click to enlarge

On the PCA plot above you see the Hutu is near the Luhya and Bantu agriculturalists from Kenya. The Tutsis are shifted toward various Near Eastern populations. Nothing surprising.

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