The ancient DNA oligopoly and the stories people tell about David Reich

There is a very long piece in The New York Times Magazine, Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps?. It’s the talk of DNA-Twitter for obvious reasons. The very fact that you have a long piece in The New York Times Magazine on this topic means that David Reich is almost certainly going to made into something of a villain. The reason I say this is that these sort of narratives pitched to a general audience have to exhibit novelistic drama and plot, and so there are “spots” preexistent for both antagonists and protagonists. If the writer doesn’t create that narrative, the piece would probably never see the light of day. Who would read it?

So before the first pixel loaded, I knew:

1) David Reich was going to be the antagonist
2) And indigenous people, along with supporting archaeologists were going to be protagonists

This does not speak to whether this is “true” or not. It is simply how it was going to work out if the piece was ever going to be published because those are the elements of a story that would appeal to readers of The New York Times. This is a product strongly shaped by consumer demand.

One thing I want to address is a critique, expressed by some academics in the piece, that researchers in ancient DNA do not have the number of samples to make the generalizations that they make. This seems reasonable on the face of it, but one thing you have to consider is that when you obtain an individual’s DNA you get a window onto their whole pedigree. A single individual is actually a pedigree if you have its genome. A genome provides an enormous amount of data. It is an endpoint of a historical process of sexual reproduction that extends back many generations. This is how you can use a single whole genome to infer whole population histories. One of the consequences of humans being “evolutionarily young” is that we all bear the stamp of some common processes and events.

From a naive perspective, you can say things like “how do you know this person is related to other people in the area?” And taken in the aggregate there are cases where unrepresentative individuals will yield results that mislead researchers. But on the whole over the last decade or so these groups have developed certain intuitions and guidelines, and have been rather good at making inferences based on a few data rich individuals. They make mistakes. But most objections about the nature of the data are really unfounded (albeit, widespread).

Scientist as devil

Many of the aspects of the piece do ring true. There are only a few huge laboratories in the ancient DNA space which tend to hoover up samples and collaborators. I have a suspicion I know who this is: ‘One geneticist compared competing with the big labs to battling an entire navy ‘with a little dinghy, armed with a small knife.”‘ For Holocene period analysis, the two big players are the Reich group and that of Eske Willerslev (Johannes Krause is going to make a splash with Late Antiquity). Though Eske’s group is mentioned offhand, it is curious that he himself is not mentioned at all.

Young Eske

In many ways, Eske is a much more colorful figure than Reich, and many of the issues applicable to the work of the latter and his relationships with indigenous peoples and archaeologists apply to the former. But in the United States David Reich is a brand name to the general public that Eske is not, and there can be only one devil in the underworld. But from a narrative perspective, Reich presents less raw material. He is a soft-spoken and delicately built vegetarian computational biologist. Eske Willerslev is the scion of Vikings whose background is in fieldwork as an anthropologist. His autobiography, written in Danish, is apparently very colorful!

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The state of Neanderthals in early 2019

PNAS has published a paper, Limits of long-term selection against Neandertal introgression. It’s from a preprint which I blogged this summer. What are the major takeaways here?

It’s been about 10 years since the draft Neanderthal genome was published. At around that time everyone realized that there was archaic introgression into the modern human genome. More precisely, reticulation in the human phylogeny was a major thing in the time scale of 50,000 years and earlier.

But there were a lot of details to clear up. For example:

  1. Did % Neanderthal admixture vary outside of Africa?
  2. Was there really only one single admixture?
  3. Has natural selection shaped the proportion of Neanderthal genetic material in our genomes?

The reason the new paper above is interesting is that they used differences between Neanderthal populations (of different relatedness to the source into moderns), as well as modeling different demographic scenarios through simulation, to show that:

  1. Neanderthal % is Europe is no different than Asia, rather, there is West Eurasian gene-flow into Africa
  2. Selection against Neanderthal genes seem to have occurred very early, and little later one
  3. Selection seems to be strong around regulatory elements
  4. The lack of variation due to basal Eurasian admixture indicates they may have been part of the admixture

This is not the final world. Rather, it illustrates that though the first pass result stands, a lot of details are being worked out, and that this dynamic field is sensitive to the samples available and theoretical frameworks that leverage those samples.

Liberty and justice for all

Saudi Teenager Who Fled Family Embraces All Things Canadian. (O.K., Maybe Not Winter.):

She wants to go to college to study architecture. She would like to take English classes. She is wondering about how to harness her newfound media stardom.

In Saudi Arabia, Ms. Alqunun was a first-year university student, studying basic science and math. One of 10 children of a well-off emir, she said that life had been financially comfortable, but that she had no freedom.

Things grew even harder, she said, when her father left the city and put her under the guardianship of her older brother. She described her life as one of strict rules and abuse at the hands of her family. After she cut her hair in a way her family did not approve, her brother locked her in a room for six months, she said. A few months ago, when she removed her niqab, he beat her and locked her up again, she said.

Rahaf Mohammed Alqunun is like many people who read this weblog. The “life of the mind” is important to us, the freedom to learn, to experience. To make use of one’s liberty to flourish.

When reading the biography of an early fighter for the liberties of American women, Elizabeth Cady Stanton, I perceive a clear distillation of myself, despite differences of race, sex, and time. The genius, the power, of the early Enlightenment movement and the universalisms that it unleashed is that is that it refracts our common individual yearnings, and propagates them throughout humanity. To me, this is the culmination of the visions of the “Good Society” propagated by the religions and ethical systems of the Axial Age thousands of years ago: “There is neither Jew nor Gentile, neither slave nor free, nor is there male and female, for you are all one in Christ Jesus.” I may not believe in the Christ Jesus, but I believe in common humanity.

This is not to say that I am here promoting a flat, formless society, defined by our most pressing near impulses. Human societies tend to exhibit order, hierarchy, and tradition. Men and women are different from each other, just as people of different religions and social classes tend to have different values and habits. We are not all the same, but there are common threads which bind us together in our humanity.

The society of the Kingdom of Saudi Arabia is one where women, half the population, are chattel to men with power, whether it be their father or their brother. Their “guardians,” who tend them like they are valuable sheep. The fundamental problem with the society of KSA is that it is not in balance, with its surfeit of petro-profits perpetuating a system of sex-slavery that most of the world has long moved beyond.

Today we have moved to a global consensus that holding other human beings as property without the rights of humanity on account of their origin or life circumstance is wrong. That such deprivation of liberty is without justice. Our brothers’ blood cries out from the lashes received. As this century progresses I believe we will see that the same is true of women in the KSA.

Open Thread, 01/15/2019

Update: Forgot to open comments on this. Fixed.

Robert Alter has a new translation of The Hebrew Bible out. I really like Alter’s work. In particular, Genesis: Translation and Commentary. But read all his stuff!

NPR has an interview with him up right now. He admits that he did the translation in longhand!

Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences.

Changing environments and genetic variation: inbreeding does not compromise short-term physiological responses. At least in Arabidopsis lyrata.

Saudi Woman Who Fled Home Embraces All Things Canadian. (O.K., Maybe Not Winter.). Women in Saudi Arabia basically live in a form of slavery, in that they are somewhat the property of the paternal lineage.

Almost all of the actresses who’ve played Cleopatra have been white. But was she? This is in Vox. There are some good writers at Vox, but they also produce click-bait for mildly above average IQ liberals. So I’m curious when articles like this come up how they justify giving their audience the conclusions they want.

At one point, the author says “The researchers believe Arsinoe’s remains, found in Ephesus, Turkey, indicate that her mother (also likely Cleopatra’s) was African.” The link goes to the BBC, and a 2009 article: “But remains of the queen’s sister Princess Arsinoe, found in Ephesus, Turkey, indicate that her mother had an ‘African’ skeleton….”‘ Looking even deeper, I found the conclusions about Arsinoe’s mother comes from old measurements of the skull. In other words, Vox is citing research on skull-shape which indicate African ancestry!

This is really weird. But I guess not surprising. A conclusion in search of an argument.

Arab Christians clash violently with police in Haifa over ‘McJesus’ sculpture. Honestly, not surprising that they got angry. Can you imagine if a McDonald’s had a depiction of Muhammad?

Evolution of the mating type locus with suppressed recombination.

Hunter-gatherer genomes reveal diverse demographic trajectories following the rise of farming in East Africa.

7-month-old Japanese girl with full head of thick hair becomes latest Instagram sensation.

Scientists Are Using CRISPR to Make Spicy Tomatoes.

Exploring deep-time relationships between cultural and genetic evolution in Northeast Asia.

Reading Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not. Skeptical of the thesis, but fascinated by empirical data.

Looks like Quillette event in Toronto was a success. Several friends went, and asked if I was going, but alas, I’m a family man now and can’t just go jetting off to events at the last second! Lots of familiar faces to people who read this weblog in the photos….

The genetic palimpsest of the Horn of Africa

Over the last few days I’ve been looking at genetic data related to the Middle East, and as part of that process, I added some Ethiopian samples (in particular, Beta Israel). Which has brought me to thinking about the issue of the origins of the Ethiopians. In 2012 Pagani et al. published a paper which concluded modern Ethiopian peoples by and large emerged out of an admixture event that occurred around ~3,000 years ago. The Sub-Saharan African ancestors of Ethiopians seem to be most similar to the peoples of Sudan. The dating of this admixture is really recent historically. In fact Homer mentions Ethiopians, which suggests that people in the Near East and Eastern Mediterranean may have had some awareness of various populations in this region while the mixing between different ancestral streams was occurring at that very moment (recall most admixture datings pick up the last signals, not earlier ones).

Pagani and those working with him published follow-up paper which indicated that the Eurasian ancestry in Ethiopians is most similar to that in Egypt and the Levant, and not to that in southern Arabia (in particular, Yemen). Their method broke down “tracts” of Eurasian ancestry, and compared affinities segment-by-segment. This is curious because genome-wide methods (e.g., Admixture, Treemix) always indicate that the Eurasian affinity of Ethiopians are with Yemenis. Seeing as how Yemen is literally across the Red Sea, this is reasonable. Pagani et al. suggest that the Yemeni affinity is due to Ethiopian gene-flow into Yemen (the two regions are historically bound together through conquests, etc.).

To make a long story short, I’m not totally convinced by this analysis. Over the past few years, we have more information on the genesis of the East African genetic landscape. First, an ancient genome from Mota in the Ethiopian highlands dated to 4,500 years ago did not have Eurasian admixture. This confirms Pagani et al.’s supposition of a relatively recent admixture event in the Ethiopian highlands. Skoglund et al. 2017 reported on ancient DNA from a Tanzanian pastoralist dating to 3,100 years before the present. This individual’s Eurasian ancestry (~40 percent) is similar to that of pre-pottery Neolithic Levantines. In other words, they lack genetic affinity with farmers from the eastern regions of the Near East. In contrast, Skoglund et al. report that modern Somalis have about ~15 percent of their ancestry from these eastern (“Iranian”) farmers, as well as the Levantine ancestry.

The data seem to be pointing to the fact that the emergence of the genetic patterns in the “Horn of Africa” were likely complex, and occurred through multiple waves of interaction and migration. As the map above makes clears there are two major branches of the Afro-Asiatic language families present in Ethiopia and Somalia, Semitic and Cushitic. The presence of Arabic to the north and west is a relatively recent phenomenon. The Nubian languages were Nilo-Saharan, while the language of ancient Egypt was a separate branch of Afro-Asiatic from Cushitic and Semitic.

The ancient languages of Yemen are part of the same “South Semitic” family as the Ethiopian Semitic languages. Though this may have been cultural diffusion, it does suggest that the genetic signal of connection points to a real phenomenon in terms of migration. Yemenite Jews and many Yemeni non-Jews do not have very much Sub-Saharan African ancestry, suggesting to me that before the rise of Islam most of the gene-flow was from southern Arabia to Ethiopia. A dynamic which reversed with Islam, as a substantial minority of the ancestry of most Yemenis is now Sub-Saharan African.

This does not account for the Cushitic languages. It seems that the Savanna Pastoral Neolithic cultures, of whom the Tanzanian pastoralist in Skoglund et al. was a representative, spoke Cushitic languages. This would mean that the languages of the largest number of Ethiopians, and that of Somalia, is that of the earliest Eurasian migrants into much of Sub-Saharan East Africa. The “Iranian farmer” ancestry in modern Somalis indicates long-term contacts with later migrants, possibly Semitic-speaking populations. Only in the highlands of northern Ethiopia did Semitic languages overtake Cushitic ones. Meanwhile in much of East Africa Cushitic gave way to other languages, often from the Nilo-Saharan family.

There is the broader question of where Afro-Asiatic languages come from. The diversity of languages in Ethiopia have suggested to some that one should look in Africa. I think that Ethiopia’s diversity is like that of the Caucasus: an artifact of rugged mountainous terrain. Rather, the existence of a very distinct Egyptian language 5,000 years ago quite different from contemporaneous Semitic Akkadian, suggests that the roots of this language family are quite old. I suspect that Semitic was intrusive to Ethiopia from Yemen, and that Cushitic became dominant in the period after the Mota individual flourished, and probably arrived from the north. Both the affinities with Levant populations and Yemenis make sense in this light. Much stronger genome-wide affinities with Yemenis could be because of the Ethiopian admixture into Yemen at some basal level quite early in history.

Update: The always well informed “Lank” leaves this comment:

Several problems with this. The Somali model you are referring to models them as a mixture of the 3100 ybp Tanzanian pastoralist, modern Sudanese Dinka, and Iranian farmers. This is unrealistic for several reasons, which could explain the strange 15% Iran-related ancestry that would imply very significant Semitic ancestry in Somalis, since early Semites themselves were mostly not of Iran-related ancestry as far as we know.

Analyses of the 3100 YBP Tanzanian pastoralist’s raw data, e.g. using David’s G25, reveal her to be very similar to Somalis. She can actually be modeled as ~90% Somali, with admixture related to East/South African hunter-gatherers. This is plausible as hunter-gatherers were the natives of the Rift Valley, and mixed with the proto-South Cushites of the Savannah Pastoralist culture represented by this sample. We see this in modern South Cushitic Tanzanian Iraqw (and ‘Nilo-Hamites’ like the Datog, of mostly Cushitic ancestry and cultural affinity) as well, who have very significant mtDNA related to the native hunter-gatherers of the Rift Valley. Much more than the currently more numerous Bantus, who have arrived more recently, South Cushites have mixed with hunter-gatherers. So using admixed early South Cushites like the Tanzanian to model Somalis, who despite being a modern population are actually fairly similar to pre-proto-South Cushites, may be what results in the strange model. Other analyses show that Iran/CHG-related ancestry in Somalis, if present, is very low. The raw data is out there if you want to try the models yourself.

Mota is a highly interesting sample, but not relevant for dating the admixture in early Cushites. He was found in remote southwestern Ethiopia, not really a stronghold of Cushites even today. The African component in Somalis (and most of the SSA in Cushitic/Semitic Ethiopians) is more closely related to the Sudanese, not the Omotic-speaking groups, who we now know tend to have high levels of ancestry related to Mota (other than Omotic groups like the Wolayta living closer to Cushitic/Semitic groups).

The recent 3 kya admixture model for the majority of the Eurasian admixture in Cushitic/Semitic populations does not hold up to scrutiny. The predominant overall ancestry as well as Eurasian admixture levels of the Tanzanian 3100 YBP sample is actually very similar to Somalis, with some local admixture. Finding this sample resembling modern Cushites all the way in Tanzania supports that its admixture traces back to the very earliest Cushites, who are certainly older than 3000 years.

Open Thread, 01/07/2019

Because of BookBub I get notified of a lot of book deals. For example, The Roman Empire and the Silk Routes: The Ancient World Economy and the Empires of Parthia, Central Asia and Han China is now $1.30 on Kindle. This is like when The Shape of Ancient Thought was steeply discounted a few years ago. The prices go up and down. But definitely a boon to any nerd.

It is highly likely I’ll try a leaky gated model for this weblog next month as a trial. I’ll try and set it up so a few extended entry posts are free so links from high-traffic sites aren’t impacted (I don’t see gating posts which aren’t extended entry). If it doesn’t work, perhaps I’ll try something else, or, just sunset the blog. There are enough posts that there is still value even if this becomes an archive website.

Twitter is toxic to discussions with any subtlety or depth are pretty. People are polarized. It’s a great place to get links to papers. But not a great place to have a discussion except on a subset of very narrowly delimited topics.

China Targets Prominent Uighur Intellectuals to Erase an Ethnic Identity. Looks like China wants all its citizens to become Han.

One of the major biases of the “chattering” classes is that they are drawn from the upper socioeconomic strata. And those that aren’t, tend to be conscientious and studious in relation to the average American.

The Myth of Drug Expiration Dates. “News you can use.” This is usually on a list of “things doctors know that you don’t.”

The scientist who tried to be as selfless as possible, until it killed him. Props to Vox for putting a form of the Price Equation in the text! Oren Harman’s book The Price of Altruism: George Price and the Search for the Origins of Kindness is highly recommended. I had drinks with Harman and George Price’s daughters in Berkeley about eight years ago. Unfortunately, it is clear Price’s personal life was a total mess in ways that aren’t totally communicable in books. It’s particularly interesting comparing Harman’s fuller picture with the George Price that you get to know in Defenders of the Truth, which was refracted through William D. Hamilton’s recollections.

Apple’s Biggest Problem? My Mom. Smartphones are utilities now. When was the last time you upgraded your microwave? There are lots of things in computing which are like this now. Until it breaks, why get a new computer, tablet, or smartphone?

Can Sexual Selection Cause Divergence In Mating System-Related Floral Traits?

Genetic legacy of state centralization in the Kuba Kingdom of the Democratic Republic of the Congo.

Ecological causes of uneven diversification and richness in the mammal tree of life.

Must Writers Be Moral? Their Contracts May Require It.

Hidden ‘risk’ in polygenic scores: clinical use today could exacerbate health disparities.

Effects of phenotypic robustness on adaptive evolutionary dynamics.

Highly Heritable and Functionally Relevant Breed Differences in Dog Behavior.

Whole-genome sequencing of rare disease patients in a national healthcare system.

Locally Fixed Alleles: A method to localize gene drive to island populations.

The One Issue the Left and Right Can Agree On.

The variation in religion and our evolutionary history

As my post on intelligence was quite successful, I thought perhaps I would offer up something similar on religion, since that’s a topic where I have been giving opinions based on fragments of my own views for some time. The point in this post is to unpack the general set of ideas and frameworks that I take for granted and are tacitly operating with as background priors.

If you have been reading me back more than ten years ago, you know that there was a period between 2005 and 2008 when I wrote a fair amount about religion. This was the several years when Richard Dawkins’ The God Delusion was at the center of the culture, and near enough after 9/11 that there remained a fresh interest in Islamic radicalism and religious fundamentalism (e.g., The End of Faith). I wrote enough about the topic that I even got invited to a conference about religion and evolution, and received books from publishers on religion and evolution.

But that period cooled off because at a certain point my views were changing only on the margin, and stabilized into a form which conditions my ideas in a stable state. The distance between me in 2018 and me in 2008 on this topic is one to two orders of magnitude smaller than the distance between me in 2008 and me in 2004.

Instead of defining religion a priori, I will describe my perception of the dynamics and phenomena in terms of scale and history (small to large, earlier to later).

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How is Austin getting less diverse? Not racially

Lawrence Wright has a new book out, God Save Texas: A Journey into the Soul of the Lone Star State. One thing I see him saying is that Austin is less diverse. Since he’s lived there for many decades, he has some personal data to bring to the table. And yet I wasn’t sure that that was right.

The Census shows that Austin is much more racially diverse than a generation ago. So what’s going on? I think Wright is talking about socioeconomic diversity, in particular how Austin is getting priced out of the range of the musicians who bring positive externalities to the city.

Why Indian forms dominated Chinese forms in mainland Southeast Asia

On Twitter Peter Turchin had a question in response to me tweeting a new preprint on bioRxiv:

This was my impression too until a few years ago, but the genetic evidence does point to gene-flow. Here are two recent posts from me, Likely Male-Mediated Indianization In Southeast Asia and Indic Civilization Came To Southeast Asia Because Indian People Came To Southeast Asia. Lots Of Them.

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How the English abolished their British (Celtic) ancestors

Reading both Bryan Ward-Perkins’ 2000 paper Why did the Anglo-Saxons not become more British? and The fine scale genetic structure of the British population, published in 2015, is interesting. To date, this second paper is probably the “best of breed” when it comes to estimating Anglo-Saxon admixture into the British population in the 5th to 7th centuries (confirmed with a smaller sample ancient DNA publication). The authors conclude that:

Two separate analyses (ancestry profiles and GLOBETROTTER) show clear evidence in modern England of the Saxon migration, but each limits the proportion of Saxon ancestry, clearly excluding the possibility of long-term Saxon replacement. We estimate the proportion of Saxon ancestry in C./S England as very likely to be under 50%, and most likely in the range 10%-40%.

The ancient DNA paper gives an estimate of ~38% Anglo-Saxon (German) for the “East English.” So the two seem roughly in line. The C./S. England cluster refers to the genealogical network of the lowlands of central and eastern England.

There are several ways we can look at this. First, the majority of the ancestors of the modern English were British. That is, Brythonic people of various levels of Romanization. They became Anglo-Saxon. Even on the “Saxon Shore” in the far east of England it is likely that the majority of the ancestors of the natives derive from post-Roman Britons (if barely).

A second way to look at it this that this validates Peter Heather’s model in Empires and Barbarians: The Fall of Rome and the Birth of Europe. The model being that the post-Roman barbarian migrations were coherent “folk wanderings,” and large numbers of Germans moved into the collapsing Roman Empire. In post-Roman Britain, a large number of Germans clearly arrived and demographically marginalized many Britons. To be sure, it is unlikely that in the year 550 AD the census size of Germans to Britons in East Anglia was ever 38 to 62 in ratio. Rather, I suspect that in the centuries after the rise of the Anglo-Saxon kingdoms German elites had higher reproductive rates than the Britons due to their superior access to resources. Over time this resulted in their contribution being more prominent in the genealogies of people alive today.

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