The social and demographic dynamics of Al-Andalus

A slight detour from Rulers, Religion, and Riches took me to Brian Catlos’ Kingdoms of Faith: A New History of Islamic Spain. I’ve enjoyed Catlos’ work before, and he has an engaging narrative style. His books are quick reading and I recommend them, incuding his monographs.

But, there is always a weird aspect to his work and analysis that has always struck me: his overall narrative often works at cross-purposes with specific assertions he makes in passing. As an example, Catlos rightly points out that in Spain under the rule of the Muslim Arabs particular and specific religious confession was not a major issue, since most people lived lives not dominated by religion. But as you keep reading you notice that the overall arc of history is strongly shaped by confessional identities.

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South Asian Genotype Project, Spring 2019 update

It’s been a while since I updated the South Asian Genotype Project. Well, I updated almost everyone (‘projectmembers v2’ tab is one what you want). A few people had strangely formatted text files, so I’ll go add them tomorrow. Thanks to everyone who has submitted so far!

One of the main things that I’ve been curious about is undersampled groups. I finally got an Uttar Pradesh Kayastha in the data set (well, technically my second…but the first is a friend). I also got a submission of a Bengali Brahmin with origins in the west, and another in the east (in fact, from Comilla, which is where my own family is from). And, I got the submission of another West Bengali Kayastha.

Finally, I got another Maharashtra Kayastha.

If you click the image above you see some obvious things:

  • Bengali Brahmins don’t seem to be geographically structured. The eastern and western individuals are near each other on the PCA. Additionally, they are very close to Uttar Pradesh Pradesh Brahmins. Not the main Bangladesh cluster.
  • In contrast, the West Bengal Kayastha is positioned close to the Bangladeshis, though outside of that particular cluster.

In other words, to some extent Bengal’s landscape reflects both aspects of the South Asian genetic variation: it is strongly structured by caste, and, geography also plays a role. People from western Bengal have less East Asian ancestry and more affinity with peoples to the west on the Gangetic plain. But Bengali Brahmins are genetically entirely dissimilar from other Bengalis.

The dissimilar position of Kayastha groups across South Asia is in contrast to Brahmins. Though Brahmin groups in Bengal and South India seem to have mixed with local groups (they are always somewhat shifted to the regional substrate), overall their genetic character indicates shared common ancestry. In contrast, the different Kayastha groups seem much more likely to be a case of local populations who arose to fill a particular occupational niche that emerged with polities which required a bureaucratic class.

Deep Denisovan population structure

The Denisovan session at the American Society of Physical Anthropology meeting was very interesting. In Science Anne Gibbons reports on the findings, Our mysterious cousins—the Denisovans—may have mated with modern humans as recently as 15,000 years ago:

The elusive Denisovans, the extinct cousins of Neanderthals, are known from only the scraps of bone they left in Siberia’s Denisova Cave in Russia and the genetic legacy they bequeathed to living people across Asia. A new study of that legacy in people from New Guinea now suggests that, far from being a single group, these mysterious humans were so diverse that their populations were as distantly related to each other as they were to Neanderthals.

The finding of two Denisovan lineages in Southeast Asia adds to results reported in Cell last year by Sharon Browning of the University of Washington in Seattle and her colleagues. They had suggested that New Guineans had a separate source of Denisovan DNA than people in East Asia, suggesting at least two mixing events.

“I’m skeptical,” added Cosimo Posth of the Max Planck Institute for the Science of Human History in Jena, Germany. He suggests the hints of a late mating could reflect an encounter of previously isolated modern populations rather than of moderns and Denisovans. In this scenario, modern humans mated with Denisovans, then the modern populations diverged, with each branch retaining a different set of Denisovan genes. The moderns then reconnected, mixing the two sets of Denisovan DNA together again.

Here is one thing that I think is important to remember: unlike Western Eurasia parts of Eastern Eurasia were better insulated from extreme climatic events. Neanderthals show strong evidence of repeated die-offs and population expansion so that in general Neanderthal relatedness is more a function of time than location (i.e., Neanderthals tended to go extinct in much of their range periodically, to be repopulated from refuges).

In contrast, the Denisovan range likely went far into Southeast Asia. It is not surprising that this is a highly structured population, with deep lineages. This is exactly what we see in Africa for the same time period. Tropical Southeast Asia is not as extensive as Africa, but it was more expansive during the Pleistocene due to lower sea levels. Hominins with low population densities occupying a huge range of territory almost certainly had developed local lineages and traditions.

As should be clear in the quotes we shouldn’t take these presented results as definitive. But they are suggestive and align well with earlier work that there were several Densiovan admixtures across Eurasia.

The population turnover in westernmost Europe over the last 8,000 years

The figure above is from The genomic history of the Iberian Peninsula over the past 8000 years. If you had seen something like this five years ago, you’d be gobsmacked. But today this is not atypical, especially in light of the fact that Spain seems to harbor many good sites in relation to the preservation of ancient DNA. In the figure above you see an excellent representation of the different streams of ancestry and settlement within Spain over the last 8,000 years. You can conclude from it, for example, that only a small proportion of the ancestry of modern Spaniards derives from people who were residents of the peninsula during the Pleistocene. Similarly, you can also conclude that a minority, though non-trivial, proportion of the ancestry of modern-day Spaniards derives from people who arrived during Classical Antiquity and the Moorish period.

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Society creates god, god does not create society

Several years ago I read Big Gods: How Religion Transformed Cooperation and Conflict. This was after a long hiatus from reading about the topic of religion from a broad evolutionary perspective. In the 2000s, I read Darwin’s Cathedral: Evolution, Religion, and the Nature of Society, In Gods We Trust: The Evolutionary Landscape of Religion, and A Theory of Religion, to name a few works. These are all very different treatments of religious phenomena, from an evolutionary, cognitive, and economic, perspective respectively. But, they are united by examining religious as a ‘natural’ process, and culture as a reducible and analyzable phenomenon.

This is distinct from what you’d find in “Religious Studies”, a field with a more humanistic and historical perspective. Some of the early practitioners in this field, such as Mircea Eliade, were influenced by perennialism, so the epistemological stance tends to differ from the more positivist and scientific frameworks above.

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Open Thread, 03/18/2019

Going back to finishing Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not. My general attitude so far is that I’m skeptical, but the author presents a plausible thesis. Additionally, the book is worth reading because of its engagement with the whole literature in this area. It’s got a good bibliography you can follow-up.

We had Shadi Hamid on the Brown Pundits podcast. Really appreciate Shadi’s interest in engaging with a diverse array of people. A real intellectual for our time, and unfortunately all too rare in many places these days (I think Shadi should go on the Extremely Offline podcast, even though he is extremely online).

There’s a Fake Outrage Machine on the Right, Also. Basically, they’re trying to get a professor fired for saying in some forum several years ago that cops should be killed. This is egregious, but one of the features of academia, as it is today, is that egregiousness is defended.

Some people are making the analogy to the professor who is under fire at Sarah Lawrence, who wrote an op-ed suggesting there needs to be more intellectual diversity in academia. That’s a pretty weird comparison, but I guess it tells you something. If you are conservative your very existence is scary. If you are on the Left, suggesting people should be killed is scary. But look, there are literal Communists in the academy. No one is demanding they be fired, and unless you add all sorts of caveats being a Communist often means you believe in violent revolution against a class of people. Being liberal in the broad sense is illustrated only when it’s hard, not when it’s easy.

A conservative assault on academia may need to occur, but it shouldn’t be around small things like a professor here and there. Go for the money. That’s the heart. Crazy professors are like stray strands of hair.

The Stanford professor who rejected one of Elizabeth Holmes’ early ideas explains what it was like to watch the rise and fall of Theranos. If you listened to The Dropout, you get the feeling that Dr. Phyllis Gardner was the hero we didn’t deserve. It must have been difficult to watch what has happened over the past 15 years for her. She knew it was fake all along.

Immune Gene Diversity in Archaic and Present-day Humans. Starting to think that the low diversity and population sizes of northern humans were a long-term problem, and one reason they were absorbed by southern modern humans. Not totally sure though.

Jomon genome sheds light on East Asian population history.

Shared polygenetic variation between ASD and ADHD exerts opposite association patterns with educational attainment.

The Scandals of Meritocracy. Virtue vs. competence. Would you rather have a boss who is evil but competent, or good but incompetent? The reality is you have to balance the two. Richard Nixon was probably smarter that Dwight Eisenhower in raw g, but Eisenhower was probably a better person.

Indian population is growing much faster in the north – and the south is paying the price. Much of South India is below replacement. Kerala’s fertility is similar to Japan’s. The Gangetic core of North India is well above replacement. The state of Bihar has 100 million people and a total fertility rate of 3.41. That’s similar to Pakistan’s.

Classic Mechanism of Epigenetic Inheritance Is Rare, Not the Rule. Some geneticists are in “but we all knew that” mode. But the reality is that going by the popular press the public doesn’t know that. The unfortunate reality is that scientific revolutions don’t come around that often.

DNA Friend. Amusing parody site.

Genome-Wide Polygenic Risk Scores and prediction of Gestational Diabetes in South Asian Women.

Fooled By Randomness is my favorite Nassim Taleb book.

Graham Coop has released a textbook, Population and Quantitative Genetics. Since I periodically get emails to delete comments from kids in high school and college, I knew younger people read this weblog. I’d recommend a resource like this to see if you are really interested in population and quantitative genetics.

Check out the Population Genomics blog.

A History of the Iberian Peninsula, as Told by Its Skeletons.

Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula.

Population histories of the United States revealed through fine-scale migration and haplotype analysis. White Americans are the garlic people.

The Ubiquitous Sequencing Age

Several years ago Yaniv Ehrlich published A Vision for Ubiquitous Sequencing. We’re inching in that direction. In The Atlantic Sarah Zhang has a piece, An Abandoned Baby’s DNA Condemns His Mother, while The New York Times just came out with, Old Rape Kits Finally Got Tested. 64 Attackers Were Convicted:

Still, even with such successes, the problem of untested rape kits persists. Advocates for rape victims estimate that about 250,000 kits remain untested across the country.

Unfortunately, until recently, the ‘forensic genetics’ employed rather primitive 1990s technology. But that’s changing, though both money and expertise need to be brought to bear. Companies such as Gencove and Othram are bringing that expertise to a broader market, with the latter company focusing specifically on the forensic market.

So ubiquitous sequencing is happening. Soon. What does that mean? We need to think about privacy. We need to think about data. We need to reflect on the broader implications of this world beyond specific targeted tasks such as forensic identification.

Open Thread, 03/14/2019

Again, recommend Nature’s Metropolis: Chicago and the Great West. Great book.

Creating Christian Marriage in Early Islamic Arabia:

…perhaps the earliest, of a churchman saying definitively that marriage isn’t marriage without a specific Christian ritual comes from an unexpected corner of the late antique world: the Persian Gulf island of Dayrin (modern Tarut in Saudi Arabia) under the rule of the early Muslim caliphate. On this island in 676, Patriarch George I—chief bishop of the Church of the East, one of the two main churches of the Syriac Christian tradition—issued a canon that only unions that received a priestly blessing would be recognized as legitimate, lawful marriage….

…Patriarch George’s writings suggest that East Arabian Christians habitually drank at Jewish taverns and participated in “pagan” funerals—pagan, that is, in their “un-Christian” ostentatiousness. Significantly, interreligious mixing extended into family relations too. George complains of Christian women marrying “pagans,” here meaning Muslims….

I’m not a total revisionist. But not the date. 676. Contrary to traditional Islamic historiography I think it is highly plausible, even probably, that these men would not have been “Muslims” as we’d conceive of them. Rather, Islam, as we’d understand it really, makes sense only from 750 AD and later, with the emergence of the Sunni ulema, the turn against philosophy in mainstream Islam, and the focus on religious legalism. No Bukhari, no Islam.

This brings me to another issue that emerged in a discussion with a reader about Brown Pundits. Some Hindus say that their religion is founded in the Vedas. Similarly, though traditional most Muslims (Shia and Sunni) ground their faith in customs and traditions which accrued organically in the centuries after the death of Muhammad, they will assert that the fundamental basis of their religion goes back to Muhammad and that Islam qua Islam exploded out of the deserts of Arabia under the Rashidun.

From the perspective of the nonbeliever, I think both narratives miss important cultural genealogical features of the development of “Hinduism” and “Islam.” Hindus believe that their religion is the tradition of the Aryans. I hold that the Aryan, Indo-European, traditions that are present within Hinduism are calcified fossils, artifacts which symbolic meaning, but that the core of Dharmic traditions, whether Hindu or Buddhist or Jain, are not fundamentally from the Indo-Europeans. Some intellectual historians suggest that the Sramanic traditions, the counter-Hindu movements, are a revolt of the indigenous non-Aryan components. But I think the same is arguably true of Puranic Hinduism. All of these religions are qualitatively different from the sacrificial ritualism of the pastoralist Aryans.

Similarly, with Islam it is no secret that I am sympathetic with the argument that the emergence of the mawālī, non-Arabs, within Islam after 750 A.D. fundamentally transformed from the religion. Whereas proto-Islam under the Umayyads crystallized was the cult of the ruling caste, an Arab peculiarity, under the Abbasids, who saw the waxing of Iranian culture within the Caliphate, Islam became the religion of the state, and eventually the dominant element of the society. Though I would argue that the influence of Iran and Turan on Islam is probably quantitatively less than that of non-Aryan India on Hinduism, the transformation is great enough that I think one can make a similar case that Islam, a post-Christian Arab ruling sect, was “hijacked” by Iranian and Turanian modalities under the Abbasids.

Again, to be clear, I am not interested in “explaining” to Muslims or Hindus that “actually….” their religion isn’t what they think it is. I’m trying to get a better sense of cultural development and relatedness from the perspective of non-believers.

Biotic interactions affect fitness across latitudes, but only drive local adaptation in the tropics. This surprised me at first blush.

A week ago I had a conversation with Thomas Chatterton Williams for the BrownCast. One thing that we both agreed on: we hate Twitter, but we can’t leave it. Also, lots of people on Twitter are very stupid. I used to think commenters on this blog were stupid, but the reality is that you are geniuses among the dull compared to the Twitter mobs.

Why Elites Dislike Standardized Testing. The reality is that the gains to test-prep are not that great. ETS works really hard on this. But if you read Twitter or many mainstream commentators they act as if test-prep is driving the inequalities. It’s not. The world is full of bullshit.

The Life History of Human Foraging: Cross-Cultural and Individual Variation. Very important paper.

A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background Rate Variation. I don’t know much about the details of phylogenetic methods, but the first author is an old grad school classmate of mine. He knows his shit.fopen

Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution.

Genomic architecture of phenotypic plasticity of complex traits in tetraploid wheat in response to water stress.

Siete Habanero Sauce, 4.5 stars out of 5.0

Tried out Siete Habanero Hot Sauce today. I really like it!

That being said, I have my biases. I like them hot. It’s moderately hot…it won’t burn a hole through your alimentary system, but it will kick you gently in the mouth. Second, it’s not a very sweet sauce, but a savory one. That makes sense in light of the avocado oil.

But the most exceptional and pleasant aspect of Siete Habanero Hot Sauce is the fact that somehow the spice kicks in later on. Instead of barging in the front door you can taste the creamy avocado before there is a “finish” of habanero spiciness. It’s something I always look for in a hot sauce since it allows for full flavor appreciation.

Swidden rice farming does not lead to high population density

Admixture on K = 5

I’ve been looking at the data from the recent Munda paper. Standard stuff, admixture, treemix, and f-statistics.The northern Munda samples were collected in Bangladesh. So I thought: I can test the hypothesis that the East Asian ancestry in Bangladesh is to a large part Santhal. After looking at it every which way, I think that in fact, the Munda may not have ever been very populous in much of northeast India. The Santhal is just not a good donor population to Bengalis, at least not when comparing mixes such as Dai + Tamil.

Additionally, the Santhal are really not that well modeled by mixing South Asians with any particular Southeast Asian group, though it works. I think that’s suggestive of the possibility that the Austro-Asiatic group which gave rise to the Munda don’t exist in their current form anywhere in Southeast Asia. Additionally, the Lao samples that are provided in the new paper I think may have Indian ancestry via admixture from Austro-Asiatic Mon or Khmer groups.

Basically, there is so much bidirectional gene flow that I think it’s really hard to get a grip on what’s going on. Additionally, the Burmese and northeast Indian populations (e.g., the Mizos) clearly have a strand of ancestry that derives from relatively recent migrants that came down from the region of eastern Tibet, and perhaps Sichuan or even further north. And this component shows up in Bengalis as well.

On top of this, there is the “Australo-Melanesian” substrate that is present all across Southeast Asia, and probably was present in modern southern China in the early Holocene, which has distant affinities with the “Ancient Ancestral South Indians” (AASI).

At this point, I keep my own counsel. But there may be an interesting story to tell related to how efficient and effective different forms of agriculture were, and how that interplayed with genes and language.