The expansion of modern humans ~50,000 as part of a regular Poisson process

Last of the giants: What killed off Madagascar’s megafauna a thousand years ago?:

The first job is to understand exactly when the megafauna died out.

Radiocarbon dating of over 400 recent fossils demonstrates that animals under 22 pounds lived on Madagascar throughout the last 10,000 years. For animals over 22 pounds, there are abundant fossils up to 1,000 years ago, but relatively few since. The biggest decline in number of large animals occurred rapidly between A.D. 700 and 1000 – practically instantaneous given the long history of their existence on the island.

According to new dates on fossil bones with cut marks on them, humans arrived on Madagascar 10,500 years ago, much earlier than previously believed. But whoever these early people were, there’s no genetic evidence of them left on the island. New analysis of the human genetic diversity in modern Madagascar suggests the current population derives primarily from two waves of migration: first from Indonesia 3,000 to 2,000 years ago, and later from mainland Africa 1,500 years ago.

So it seems that people lived alongside the megafauna for thousands of years. How did the humans interact with the large animals?

Our new study found dozens of fossils with butchery marks. Cut and chop marks provide compelling evidence as to which species people were hunting and eating. Evidence of butchery of animals that are now extinct continues right up to the time of the megafaunal crash. Some people on Madagascar hunted and ate the megafauna for millennia without a population crash.

The abrupt land use change might hold some clues. The transition from a forest-dominated ecosystem to a grassland-dominated ecosystem appears to be widespread….

This research about Madagascar is important. If it turns out correct, I think it gives us deep insights about the expansion of modern humans outside of Africa ~50,000 years ago, and why their arrival resulted in the extinction of so many other human lineages. A generation ago we might have posited that some massive bio-behavioral change is what triggered this, but I am coming closer to the idea that cultural changes are punctuated enough that that may actually explain things. The culture changes first, then genes follow the culture.

Perhaps one might posit a model with massive turnovers in the hominin lineage due to this cultural dynamic occurs periodically, as if it’s a Poisson process.

Open Thread, 04/12/2019

Just a reminder for people to check in on The Insight this week. Lots of talk about Denisovans between Spencer and myself. We’ve also got a follow-up podcast scheduled with a researcher working in Denisovan genomics in a few weeks (we’re on Spotify now by the way).

Our three new hires at George Mason economics. These look good.

Sri Lanka Suicide Bombings Targeting Christians Kill Hundreds. The most likely culprits seem to be a jihadist group active in southern South Asia.

A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences. I think the “Crusader genes” are hard to find in the Near East because the collapse of the Latin kingdoms was gradual enough that “Franks” and their scions mostly managed to get out and go back to Western Europe.

Whole-genome reference panel of 1,781 Northeast Asians improves imputation accuracy of rare and low-frequency variants.

Anxious Times In Pakistan’s Pagan Valley.

Why One-Third Of Biologists Now Question Darwinism. I’m writing a response to this piece for The Federalist. Rather than a response to Intelligent Design, I want to represent what evolutionary biology really is.

Evidence for Early European Neolithic Dog Dispersal: New Data on South-Eastern European subfossil dogs from Prehistory and Antiquity Ages.

Gene Wolfe, death of a master

Gene Wolfe, Acclaimed Science Fiction Writer, Dies at 87. Wolfe’s prose could be challenging to read. I actually read The Book of the New Sun trilogy twice because of some elements of impenetrability in the style, though there’s a reason Wolfe was acclaimed. In general, I’m not a fan of “science fantasy” or the “dying Earth” genre, but Wolfe really made it work.

One thing about Wolfe that is of interest is that like J. R. R. Tolkien he was a Catholic convert, whose religion influenced his work. Arguably more directly and consciously in the case of Wolfe. But it is subtle enough that it doesn’t distract or warrant notice. In fact, I’d argue that Severian is much less clearly a Jesus-figure than Paul in the Dune series to the naive reader.

I’m not someone who minds authors telegraphing their viewpoints and ideologies into narratives, no matter what it is. But I think there’s no point in putting it into “speculative fiction” if it’s too direct. For example, I think one reason C. S. Lewis’ Narnia cycle is less popular than Tolkien’s work is that it reads as Christian fantasy, rather than fantasy with inflections from the author’s Christian viewpoint.

Wolfe, like Tolkien, had strong personal views. But he did not let them saturate his stories. The Christian outlines and themes in The Book of the New Sun are clear after someone points them out. But they aren’t salient at all when you are reading it without foreknowledge.

Let the genomic die fly!

A new “polygenic risk score” (PRS) paper is making some waves, Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood. Since it is open access I suggest you read it.

But basically, they took ~2 million common variants (there are about ~100 million common variants in the world population) in ~300,000 individuals in 4 cohorts, and used it to predict weight. A genome-wide polygenic score statistic. The correlation with BMI of the score is 0.29. This is pretty modest. But it seems to me that the biggest and most important finding is that it seems to capture a lot of the people at the tails of the distribution.

I’m becoming more and more convinced that the best things these PRS scores can do in the near-term is to identify people who are possibly at these tails. In a complex trait context, the tails are where for diseases a lot of the people who are going to have issues later in life exist. People with BMI in the range 25-30 may have a modest increase in risks, but someone who is very obese, with BMI above 35, is at much greater risk. Over 40% of the people in the top decile here were obese. Only 10% of people in the bottom decile were.

This research comes out of the context of earlier work on the heritability of BMI. It’s around 0.75 or so. That means it runs in families. Combined with the fact that in the recent past, or in other nations, there is a great variation in median size and distribution, one can intuit that genetic dispositions and environmental context both help explain the variation we see around us. The modern American environment is clearly obesogenic. When most of the American population were involved in physical jobs on farms the environmental context was very different.

Over the next few years, there risk scores for BMI will get better, and expand to other populations. One thing that some people are pointing out is that we know it’s heritable, so why not just look at your family? As many of you know, Mendelian segregation means that siblings may have quite different risk profiles on the genomic level. Polygenic risk score prediction is I think going to be extremely interesting and informative in the case of traits which are known to be found within families across generations (e.g., autism), but don’t seem to impact everyone. Perhaps we’ll find for a given characteristic expression is random, due to some life event or cofactor such as infection. Or perhaps we’ll find that differences among siblings have some genetic basis in variants inherited from parents?

Addendum: One of the authors, Sek Kathiresan, has been answering questions on Twitter.

The telos of modern humans

Credit: Luke Jostins

Next week’s episode of The Insight is going to be on Denisovans. It’s a long one because so much has come out in the last few months on the specific topic, as well as the broader framing issues (e.g., the discovery of a new human species on Luzon).

One of the major points Spencer and I discussed is how important it is to understand general trends in the hominin lineage, that is, humans, before the great expansion ~60,000 years ago. For example, Neanderthals and Denisovans were very different in their paleoecology and biogeography. Neanderthals seem relatively homogeneous (probably due to repeated mass die-offs). In contrast, the “Denisovans” look to have been very deeply diverged within their clade. If the latest work is correct, and some Denisovan lineages split more than 400,000 years ago and persisted down to >100,000 years ago, then the differences between Denisovans may have been considerably greater than between any modern human lineages. For example, the Khoisan diverged from all other humans ~200,000 years ago, and there are possible deeper lineages, but not that much deeper.

Right now what you know about the Denisovans are from genomes in the Altai region. Imagine if we extrapolated to all modern humans from Altaians? It seems entirely likely that the Denisovan lineage was very diverse because it occupied very diverse territory geographically.

But diversity aside, one of the things I like to point out to people, is that there was an overall trend of encephalization among hominins. Neanderthal brains were growing larger too. We need to understand the natural history of all human lineages to understand what happened 60,000 years ago. I am coming to the conclusion that it wasn’t some incredible miracle of a behavioral big bang, but the inevitable outcome of systemic forces in hairless ape evolution that started ~2 million years ago.

Jon Snow and Daenerys Targaryen are genetically similar to full-siblings or mother and son

I’ve posted on this before. So I will post again just to reiterate something: in terms of genes, Jon Snow and Daenerys Targaryen are much closer to being full-siblings than they are to being aunt and nephew.

You get different numbers depending on how deeply you look at the pedigree of the two. But their relatedness is probably above 40% and below 50%. Others have confirmed:

The verbal reason without math and genealogies is simple: Daenerys Targaryen comes from an inbred lineage, and more importantly, two generations of brother-sister marriages. This means that Daenerys Targaryen and Rhaegar Targaryen were genetically much more similar than typical full-siblings. Because of this, Jon Snow and Daenerys Targaryen are much more genetically similar than typical aunts and nephews, because Jon Snow’s father was to a first approximation genetically a male and older version of Daenerys Targaryen.

Open Thread, 04/15/2019

After reading Jared Rubin’s Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not I can say I highly recommend it. Not necessarily because I’m entirely convinced by the thesis, which is quite subtle, but can be reduced to the proposition that religious elites in the Islamic world were never marginalized to the same extent that religious elites in the Christian world were, and so there did not emerge and economic elite which dictated changes in cultural and state amenable to their interests (and therefore, economic growth).

I don’t know if I’m going to fully review Rulers, Religion, and Riches, because I’m still thinking about all the arguments. But, I can recommend it because there are so many interesting subsections. Early on figure 1.1 and 1.2 show the most populous cities in Europe and the Islamic world in 800 and 1300. These data confirm that Europe lagged the Islamic world in 800, but had caught up by 1300. You should have already known this, but Rubin’s focus on data clarifies and solidifies much.

Though I was already sympathetic to the assertion that the timing of the Protestant Reformation was causally connected to the expansion of printing, again Rubin’s quantitative analyses convince me further. As a skeptical of Max Webber’s model, I find Rubin’s argument for why Protestantism was correlated with early modern economic growth much more persuasive (read the book!).

This week on The Insight I’ll be talking to Steve Stewart-Williams, author of The Ape that Understood the Universe: How the Mind and Culture Evolve. Most of the conversation revolves around evolutionary psychology, a topic I haven’t thought about much recently to be honest. The Ape that Understood the Universe is an irreverent, and broad-church, take on the discipline (there is not much mention of “cognitive modules” in the book).

On my other podcast, I dropped two recently that readers of this weblog might be interested in. First, one with Phillipe Lemoine, everyone’s favorite French philosophical “edgelord.” He has a blog post which I recommend to you, Polarization and misrepresentation of the outgroup.

Second, I talked to Zaid Jilani. Along with Leighton Woodhouse, he is behind the Extremely Offline podcast. Zaid is clearly a man of the Left, but he seems to have a traditionally liberal perspective on intellectual discourse. The most recent episode of their podcast featured a discussion between Mike Cernovich and Katie Herzog.

Was Thomas Kuhn Evil? Definitely overrated and not totally coherent, no?

Silicon Valley Housing Crisis Ensnares Stanford. More “cost-of-living porn.” Now I’m reading stories of hairdressers buying houses in Arizona and flying back on Southwest to San Francisco periodically.

Loss-of-function tolerance of enhancers in the human genome.

Genomic selection for lentil breeding: empirical evidence.

John Snow Emails 23andMe About His DNA Results. Genealogically he’s 12.5%. DNA is not magic!

Iran’s Revolution Reconsidered. I always thought it was known that the Iranian Revolution had an element of Platonism? Shia Islam did not turn as definitively against Hellenic thought as the Sunnis did after al-Ghazali.

Origin of elevational replacements in a clade of nearly flightless birds – most diversity in tropical mountains accumulates via secondary contact following allopatric speciation.

Macroevolutionary integration of phenotypes within and across ant worker castes.

Defining the genetic and evolutionary architecture of alternative splicing in response to infection.

By the I, I mentioned this on Twitter. 23andMe says I’m 97% “Broadly South Asian” and my parents are 99% “Broadly South Asian.” That broadly part clearly includes people with substantial East Asian ancestry, as is the norm among most Bengalis, especially those of us from the east. That’s fine, but the method they’re using is masking this from customers. I can see why they do this, but the PCA don’t lie, and we’re off-cline…. The admixture is just “old” (~1,500 years old).

Bayesian Estimation of Population Size Changes by Sampling Tajima’s Trees.

Multiple Deeply Divergent Denisovan Ancestries in Papuans. Many seem skeptical about the recent time estimate for late admixture. But the overall finding of structure is probably right on some level.

New Tides of History on Queen Isabella and the Reconquista.

Last week we dropped a podcast about the “missing heritability” with Alexander Young. He wrote a blog post exploring the issue. I also heard that PLOS has now invited him to write a comment on the topic! In a few weeks, I’ll be talking to John Greally about epigenetics.

Interview with Paul Coates, the father of Ta-Nehisi Coates. In the battle of ideas between the “ancients” and the “moderns”, sometimes the ancients were wiser.

New species of ancient human unearthed in the Philippines.

Coupled MCMC in BEAST 2.

Ritual purity as evoked culture

Jonathan Fast’s novel Golden Fire is set during the height of the Gupta Empire at the end of the 4th century A.D. The novel revolves around the origins and rise of Chandragupta II. But what remains with me after all these years is the depiction of social relations in an India where elite Hinduism as we understand it today is starting to take shape, and Buddhism is abating. Fast depicts a caste society, though not nearly as endogamous as exists today (this is probably correct from what the genetics tell us).

At one point, a former advisor to the king, a Buddhist monk, arrives at court. The current ascendant counselor is a Brahmin. When the monk, his old rival, arrives to address the king, the counselor turns around and faces away from the monk. Not only will he not speak to him, but he will not look at him. He explicitly contends that the rationale for this behavior is to minimize the ritual pollution that entails contact with a Buddhist who lacks caste.

This attitude persists in some ways in India. And South Asia more generally. Even after conversion, many Muslims continued to maintain habits of caste. My father’s mother’s family were converted to Islam from Hinduism in the early 20th century. They had been Bengali Brahmins and continued to maintain habits which reflected their origins without reflecting on or acknowledging their origins. They maintained separate dishes for guests, and would not drink out of other peoples’ cups. My father’s father was an ulem, a religious teacher. So he instructed all his children on the details of Hanafi shariah. But, the children were raised by his wife, and so all maintained the habit into adulthood of never drinking out of other peoples’ cups. Perhaps one way to describe her would be Muslim beliefs, Hindu customs.

I know the details of the origin of these practices (I also internalized my paternal grandmother’s habits in this area, to be honest) because one of my mother’s brothers converted to a reformist and fundamentalist variety of Islam, and he was conscious of the Hindu practices that Bengali Muslims maintained. He was ostentatious about drinking out of other peoples’ cups and eating off their plates because to him that was an important refutation of the separation between classes and castes which Hinduism fostered.

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Tutsis are genetically very similar to Masai

Many years ago, before I used ggplot, I did a little analysis of the genetics of the Tutsi. Actually, it was the genetics of a single Tutsi, or more precisely, someone who was 75% Tutsi ancestry (3 out of 4 grandparents).

I found that the Tutsi individual seemed quite distinct from the Bantu peoples in nearby Kenya. I suggested that it was likely that the Tutsi were then genetically distinct from the Hutu people amongst whom they lived. For many years this was part of the genetics section of the Wikipedia entry on the Tutsi, but recently the reference was removed and the page seems to have been re-edited.

That’s fine. I’m just a random blogger who had one sample. But as it happened recently about a dozen Diasporic Tutsis reached out to me. Over the last decade, the number of people who have been genotyped has increased greatly. So it wasn’t that difficult for interested parties to find these genotypes.

The mission they put before me is simple: “tell us about our genetics”. Over the next few weeks, I’ll do that. As there is no IRB, this won’t be published in a peer-reviewed journal (I am open to putting any researcher in contact with these Tutsis who reached out to me). I’m just going to put what I find out there so that Tutsis who do personalized genetic testing can make sense of what they’re finding out.

I received these genotypes today. A quick merge of samples I have reduced it down to 50,000 markers. I will work on creating a merge with a larger number of markers. But, I’ll report what I have found out so far as a first pass.

As you can see on the PCA plot above the Tutsi overlap almost perfectly with the Masai. Not with the Kenyan Bantu, or the Luo, who are more “African” shifted. But with the Masai. But, they are not as “Eurasian shifted” as the Somali.

Treemix confirms this:

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Open Thread, 04/07/2019

So Kingdoms of Faith: A New History of Islamic Spain is worth it for the first 2/3 of the book. The last 1/3 is a bunch of stuff about the Emirate of Granada that’s hard to keep track of. If you didn’t know that in 1500 most of the Muslim communities of the peninsula outside of Granada were in the kingdom of Aragon, then this book is worth reading, as it explains the reasons for this.

The Brown Pundits podcast is going to release a bunch of stuff in the next few days (already on Patreon page). Readers of this weblog will probably appreciate the conversation with Zaid Jilani the most. We talk about whether Matt Yglesias really believes the stuff he puts out there. Zaid has some insights. The podcast could have gone much longer because it’s interesting to talk to someone who doesn’t have paint-by-the-numbers answers to everything.

Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not is interesting because it’s starting to convince me of the importance of ideas and doctrine in religion in terms of material consequences! Need to think more deeply on this. But recommended.

China’s Hard Edge: The Leader of Beijing’s Muslim Crackdown Gains Influence. “He promoted education in Chinese instead of in Tibetan, and offered financial and other incentives to encourage interracial marriages.” Forced assimilation and demographic absorption have been a past Chinese tactic.

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits.

Gene-level heritability analysis explains the polygenic architecture of cancer.

Genome-wide association study reveals sex-specific genetic architecture of facial attractiveness.

‘There are no black people on Game of Thrones’: why is fantasy TV so white? People criticize Quillette for publishing predictable stuff…but the point that’s not brought up is how ‘respectable’ media regularly publish predictable clickbait to pay the bills.

A Mysterious Infection, Spanning the Globe in a Climate of Secrecy. Maybe we’ll die of infectious diseases rather than heart disease or cancer?

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles.

Genetic Associations with Mathematics Tracking and Persistence in Secondary School.

Genomic Prediction of Depression Risk and Resilience Under Stress.

U.S. Urges Immediate Halt to Military Operations in Libya. What’s going on in Libya again? Another mess we forgot….

This week on The Insight I’m talking to Alex Young about the missing heritability. He’s going to be putting up a blog post this week too.