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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The end of the year as we know it

Another one is almost in the bag. Lots of interesting stuff this year, though probably the most important story in “world-historical” terms, the genome-editing of babies in China, hasn’t really ended.

Ushering in 2019 with a $20.19 Tardigrade t-shirt New Years Eve sale at DNA Geeks. And 30% off everything with code WELCOME2019.

I am playing around with Member Pass to create a leaky gated model for this website. Suggestions are welcome in the comments (I’ll say that I’m not going to gate archives).

I think 2019 will finally see the ancient India DNA. They can’t keep putting this off. My review of the new Tony Joseph book is up at India Today by the way.

I think we’ll see more “Golden State Killer” style stories. Well, actually, perhaps not…because it’s becoming so banal.

We won’t be able to predict what happens in the genomics space, because it’s moving so fast. But the stuff that David Mittelmann and I said in our Genome Biology comment will really apply.

We’ll get more ancient DNA of course…but I don’t know what, as it seems Europe is tapped out.

The plot will keep thickening in “archaic hominin” land.

What are you looking forward to?

Judith Rich Harris, 1938-2018


With hindsight, I judge Steve Pinker’s The Blank Slate: The Modern Denial of Human Nature as something of a high-tide in biologically informed realism in the psychological and behavioral sciences in the 21st century. A reread is bittersweet, knowing what has come to pass. But one of the best things about The Blank Slate is that he gave extensive publicity to Judith Rich Harris’ The Nurture Assumption. I like to think, perhaps hope, that her work influenced many “Generation X” parents.

In January of 2006 she answered 10 Questions for this weblog. Judy and her husband were always gracious and kind in their email correspondence with me. I can’t say that for many academics who are in the fullness of their health and well-being, something she struggled with for decades.

Her life made a difference. Read The Nurture Assumption and her follow-up book, No Two Alike: Human Nature and Human Individuality, to understand why.

Variation in general intelligence and our evolutionary history

In a bit of “TMI”, I’m far more intellectually promiscuous than I am in my personal life. My primary focus on this blog, if I have one, is probably historical population genetics of the sort highlighted in David Reich’s Who We Are and How We Got Here. But I have plenty of other interests, from economic history to cognitive psychology. Like religion, I have precise and clear opinions about a topic like “intelligence.” Unlike many people with an interest in evolutionary genetics I have read psychometric work, am familiar with some of the empirical results, as well as being personally acquainted with people in the field of psychometrics.

A few days ago Nassim Nicholas Taleb opined on intelligence, and I was silent. Today some individuals who I know from within the field of cultural evolution, another one of my interests, discussed intelligence, and I was silent. I’ve said all I really have to say over 15 years, and it isn’t as if I reanalyze psychometric data sets. But, a question that Taleb acolytes (and presumably Taleb) have brought up is if intelligence is such an important heritable trait, why isn’t everyone much smarter?

Think of this as the second Von Neumann paradox. What I’m alluding to is the fact that we know for a fact that human biology is capable of producing a god-made-flesh. With all due respect to another Jew who lived 2,000 years earlier than him, I speak here of John Von Neumann. We know that he is possible because he was. So why are the likes of Von Neumann bright comets amongst the dust of the stars of the common man, rather than the norm?

First, consider the case of Von Neumann himself. He had one daughter and two grandchildren. That is, within two generations genetically there was less “Von Neumann” than there had been. Though his abilities were clearly mentat-like, from the perspective of evolution Von Neumann was not a many sigma individual. He was within the normal range. Close to the median, a bit below in fecundity and fitness.

Taking a step back and focusing on aggregate populations, the fact that intelligence seems to be a quantitative trait that is at least moderately heritable and normally distributed due to polygenic variation tells us some things evolutionarily already. In Principles of Population Genetics is noted that heritable quantitative traits are often those where directional selection is not occurring due to huge consistent fitness differentials within the population.

Breaking it down, if being very smart was much, much, better than being of average smarts, then everyone would become very smart up to the physiological limit and heritable genetic variation would be removed from the population. Characteristics with huge implications for fitness tend not to be heritable because natural selection quickly expunges the deleterious alleles. The reason that fingerprints are highly heritable is that the variation genetically is not much impacted by natural selection.

The fact that being very intelligent is not evolutionarily clearly “good” seems ridiculousness to many people who think about these things. That’s because if you think about these things, you are probably very good at thinking, and no one wants to think that what they are good at is not evolutionarily very important. The thinking man cannot comprehend that thinking is not the apotheosis of what it is to be a man (similarly, the thinking religious man sometimes confuses theological rumination with the heights of spirituality; reality is that man does not know god through analysis, man experiences god).

So let’s talk about another quantitative trait which is even more heritable than intelligence, and easier to measure: height. In most societies males, in particular, seem to be more attractive to females if they are taller. As a male who is a bit shorter than the American average, it is obvious that there is some penalty to this in social and potentially reproductive contexts. And yet there is normal variation in height, and some populations seem to be genetically smaller than others, such as the Pygmy peoples of the Congo rainforest. Why?

Though being a tall male seems in most circumstances to be better in terms of physical attractiveness than being a short male, circumstances vary, and being too tall increases one’s mortality and morbidity. Being larger is calorically expensive. Large people need to eat more because they have larger muscles. Selection for smaller size in many marginalized rainforest populations is indicative of the fact that in such calorically challenging environments (humans in rainforests have to work hard to obtain enough calories in a hunter-gatherer context), the fitness gain due to intrasexual competition is balanced by reduced fitness during times of ecological stress as well as individual correlated responses (very large males die more often than smaller males).

Additionally, for height I mentioned the sexual component: there does not seem to be a necessary association with higher reproductive fitness with being a tall woman. Though this is subject to taste and fashion, there is likely some antagonistic selection across the two sexes at work, where tall men are the fathers of taller daughters, whose reproductive fitness may actually be lower than smaller women. And vice versa, as short men may produce more fit short daughters (though again, this depends on ecological context and cultural preconditions).

Being very large impacts fitness through the genetic correlation of size with other characteristics. Very large males are subject to higher risk for sudden tears in their lungs, or suboptimal cardiac function. Humans select chickens to be very large in the breast for food, but these chickens can barely walk, and may not be able to reproduce without assistance. Evolution in a quantitative genetic sense may then be all about trade-offs.

So let’s go back to intelligence. What could be the trade-offs? First, there are now results presented at conferences that very high general intelligence may exhibit a correlation with some mental pathologies. Though unpublished, this aligns with some prior intuitions. Additionally, there is the issue where on some characteristics being “species-typical” increases reproductive fitness (an average size nose), while in other characteristics being at an extreme is more attractive (very curvy women with large eyes and small chins; secondary sexual characteristics). Within intelligence, one could argue that being too deviated from the norm might make socialization and pair-bonding difficult. Here is an anecdote about the genius Von Neumann:

Neumann married twice. He married Mariette Kövesi in 1930. When he proposed to her, he was incapable of expressing anything beyond “You and I might be able to have some fun together, seeing as how we both like to drink.”

Apparently having a very fast analytic mind which can engage in abstraction and conceptual manipulation does not mean that one can come up with anything better than that when it came to procuring a mate. And procuring a mate is one of the only “good” things from an evolutionary perspective.

The human mind is neither universally plastic, nor it is a prefabricated set of specialized modules. It is a mix of both. We clearly have some “pre-loaded” code, such as the ability to recognize faces intuitively and rapidly (which a small proportion of the population lacks). But other competencies develop over time, co-opting neurological architecture that grew organically for other purposes. In Reading in the Brain Stanislas Dehaene recounts how the region which specializes in the ability to recognize letter shapes is a preexistent visual-spatial module, probably developed for ecological adaptation to environments where recognition of various organic and inorganic objects was of fitness relevance (obviously now tied in to regions of the brain geared toward verbal comprehension). Dehaene even seems to suggest there may be a trade-off between various cognitive capacities when comparing individuals from urban developed societies and individuals from non-literate small-scale societies.

As human societies have specialized over the last 10,000 years a small number of people who naturally were on the end of a particular distribution in abstraction-and-analysis ability began to preferentially fill exotic niches that had previously not existed. From all we can tell the ancient polymath Archimedes was a Von Neumann for his age. Archimedes seems likely to have been of aristocratic background, and part of the class of leisured intellectuals. The fact that he had such innate talent and disposition, combined with his life circumstances, was simple happenstance.

Today we live in a different age. Specialization, and the post-industrial economy, put a premium on competencies associated only with individuals on the “right tail” of the IQ distribution. Similarly, our genetic background predisposes many of us to obesity because the modern environment is “obesogenic.” The reality is that obesity was not an issue for almost all of human history, so genetic variation (often behavioral/cognitive) that is associated with obesity today was not so associated with it in the past. There could be no selection against obesity when it wasn’t a trait within the population.

Just as the modern environment is potentially “obesogenic,” it is also potentially “intelligenic.” Here’s what I’m talking about, The Science Behind Making Your Child Smarter:

The research also lends insight into why many apps and training programs aimed at raising IQ fail to produce lasting effects, says Elliot Tucker-Drob, an associate professor of psychology at the University of Texas at Austin, and co-author of the study.

Raising IQ may require the kind of sustained involvement that comes with attending school, with all the practice and challenges it entails. “It’s not like you just go in for an hour of treatment a week. It’s a real lifestyle change,” he says

.

To be a “nerd” is a lifestyle only possible in the modern information-rich environment. The Flynn effect is evidence that changing environments can shift the whole distribution. But just as with obesity or adult-onset diabetes risk, there is also heritable variation latent across the genome that seems to affect one’s response to the intelligenic environment.

Humans have large brains for our size. We are smarter than other primates. But evolutionary genetics today seems to be coming to the conclusion that it wasn’t a quantum jump, but gradual selection and change. Having a very low intellectual capacity was probably correlated with low fitness in the past (though small brains are calorically less greedy).

But, having a very high general intelligence does not seem to have resulted in that great of a gain in social or cultural status in comparison to being of normal intelligence. In fact, if the genetic correlation is such that it’s associated with some higher risk for mental instability, it could simply be that a form of stabilizating selection over time kept humans within the “normal range” because that was evolutionarily optimal. Be smart enough. But not too smart that you are weird.

And, as theorists from cultural evolution have observed, we are a “hive-mind” which leverages collective wisdom. Most of us don’t have to derive mathematical equations, we can use the formula provided to us. Though it’s useful to have a few people around who can invent statistics that the rest of us use…

Making Sense of Roman History: A Reading List

Inspired by Tanner Greer, I’ve decided to put together a list of books that I think will useful to understanding the Romans from the perspective of a non-specialist without a background in Latin, or Classics more broadly (I am in this category obviously).

First, I’m a big fan of Michael Grant’s History of Rome. Grant was a historian who wrote a great many books for the popular audience, and his History of Rome is a comprehensive survey. I’ve read it multiple times. Mary Beard’s SPQR: A History of Ancient Rome is a more contemporary take which covers a similar period. But I’m not sure it’s as useful if you have less background than Grant’s more traditional sequence.

Robin Lane Fox’s The Classical World: From Homer to Hadrian covers a lot more than Rome, but what it does cover that is Greek is essential to understanding Rome.

Adrian Goldsworthy’s The Fall of Carthage: The Punic Wars 265-146 BC is a good read on a classic topic. Goldsworthy is a military historian, and it shows. To be frank I haven’t read many treatments of the republican period since so much of it is back-loaded to the decades before the principate. But Goldsworthy’s Caesar: Life of a Colossus illuminates this critical juncture in Roman history well enough.

There are so many nearly novel-like treatments of figures from the Second Triumvirate and the Julio-Claudians that I’m not going with anything conventional: try Agrippina: Sex, Power, and Politics in the Early Empire. Colin Wells’ The Roman Empire focuses on the imperial apogee and the early years of the 3rd-century troubles. It’s a bit pedestrian but has interesting quantitative data like the decline in the proportion of soldiers of Italian origin over the centuries. If you’ve read the survey above then you know why Gwyn Morgan’s 69 A.D.: Year of Four Emperors is important to read.

I think biography is a pretty good way to get a sense of particular periods. With that in mind, Frank McLynn’s Marcus Aurelius: A Life and David Potter’s Constantine the Emperor are useful if a bit plodding and overmuch for the casual student.

The Fall of Rome: And the End of Civilization, The Fate of Rome: Climate, Disease, and the End of an Empire, and The Fall of the Roman Empire: A New History of Rome and the Barbarians are all critical contemporary analyses of the end the Roman polity. Written from an archaeological, environmental scientific, and narrative historical angles, they give different viewpoints on the same questions. These are all more or less responses to the sort of work written by Peter Brown a generation earlier, The Rise of Western Christendom: Triumph and Diversity, A.D. 200-1000, which argues against the idea of the fall. From a different perspective (the barbarian), The End of Empire: Attila the Hun & the Fall of Rome, though to be frank this book is as much about Aetius as it is about Attila.

Life and Leisure in Ancient Rome is one of the many books on the topic of “daily life” during this period and place. You should read at least one of these.

I’m not a humanist in Tanner’s league, so you won’t get poetry recommendations from me, but Aupelius’ The Golden Ass is the only complete surviving Latin novel. It’s rather weird. You surely know the list of eminences of the Latin poets, but Ovid’s Metamorphoses induced less labor than Virgil’s Aeneid. I recall thinking Virgil was a bit too “try hard.” Unlike The Fall of Rome: And the End of Civilization and History of Rome, both of which I’ve read more than half a dozen times front to back, with literature I usually read once, and don’t retain too much. I’m a Philistine!

Rome and China: Comparative Perspectives on Ancient World Empires and Rome and Jerusalem: The Clash of Ancient Civilizations are interesting comparative analyses. If you had to pick between the two, go with the first. But that’s because purely intellectual histories are not as interesting to me.

Historical fiction isn’t always accurate, but it really brings the dramatis personae alive. Colleen McCoullough’s First Man in Rome series is excellent, especially the first few novels. Everyone knows Robert Graves’ I, Claudius. But my teenage-self really enjoyed Allan Massie’s Let the Emperor Speak, about Augustus, and Tiberius: The Memoirs of the Emperor. Gore Vidal’s Julian: A Novel is well written and engaging, though a little light on history (not surprisingly there is a lot of editorializing by Vidal through Julian).

You have in some way read the works of Seutonius,Tacitus, and Livy because they are the foundation for so much of the narrative works written today. They are also the source material for fiction and dramatizations. If you want to “go back to the sources”, give Ammianus Marcellinus a try. He’s overlooked, and he’s excellent.

Rodney Stark wrote The Rise of Christianity: How the Obscure, Marginal Jesus Movement Became the Dominant Religious Force in the Western World in a Few Centuries back when he was a scholar and not a polemicist. I’m skeptical of some of his conclusions, but his thinking here is rigorous. It’s not the long scream that his last few books have been. Robin Lane Fox’s Pagans and Christians is complementary to The Rise of Christianity. Michelle Salzman’s The Making of a Christian Aristocracy: Social and Religious Change in the Western Roman Empire is worth a very deep read, as it synthesizes textual analysis with some quantitative work.

Some of the New Testament is interesting too. I especially think that the material attributed to St. Paul, a Roman citizen, is worth reading closely.

And finally, St. Augustine is worth a read. City of God is interminably long, but Confessions is more compact, and the beginning of a whole genre which eventually culminated in James Frey.

Open Thread, 12/28/2018

Last open thread of the year. Been busy with life obviously. Won’t be posting this on Sunday as usual, but just making up for missing the pre-Christmas weekend.

Battling the Gods: Atheism in the Ancient World is an interesting book because it’s more about the nature of religion in the ancient world than unbelief. Much of the text is preoccupied with the transition that occurred with Christianity’s dominance in the West. Probably good to pair with The Rise of Western Christendom: Triumph and Diversity, A.D. 200-1000.

No Invasion Or Migration, But Interaction: What This New Genetic Study Suggests About Prehistoric India. I heard the usage of the word “interaction” was being pushed by some Indian researchers as early as a year ago. It’s less provocative than the term “invasion” and perhaps even “migration.” But a word is a word. Science is not mathematics or religion, where terminology is substance.

The piece linked here puts an incorrect gloss on the research it’s reporting on in my opinion. It is highly likely that about 50% of the ancestral contribution to the population of the Indian subcontinent today was not resident within the Indian subcontinent before 10,000 years ago. We’ll see as more ancient DNA comes out.

The first Indians. An extract from a new book to be published in India. I have a review written for India Today (not online yet). To my surprise, it’s already selling on Amazon, Early Indians : The Story of Our Ancestors and Where We Came From. As per the subhead, it is clearly geared toward a subcontinental audience.

Polygenic risk scores: a biased prediction?

Polygenic adaptation to an environmental shift: temporal dynamics of variation under Gaussian stabilizing selection and additive effects on a single trait.

Genomic Prediction of Complex Disease Risk.

Analysis of 100 high coverage genomes from a pedigreed captive baboon colony.

Most retweeted social science in 2018.

Five Amazing Things We Learned About History From Ancient DNA In 2018.

Inside Facebook’s Secret Rulebook for Global Political Speech. This has been reported before. But it’s finally entering the mainstream because I think the mainstream realizes that there is no longer any mainstream that’s controllable by the Western establishment. In the 1990s some non-Western governments, such as Saudi Arabia, made the argument for enforcing much stricter censorship on the internet. Instead, American standards generally won out, though there were attempts to create regional gardens. Ironically (or not), it is a private American corporation which is enforcing the “lowest common denominator” non-offensive speech, albeit haphazardly and capriciously.

1) Some anti-war conservatives were observing issues with how we recruit our military back in the 2000s when neocon adventures were at high tide. These are the type of people who might know the implications of the Marian reforms in recruitment in the late Republic, and how it empowered generals. Not sure Matt Yglesias is part of that set, though perhaps I’m wrong.

2) Most “centrist” types are usually anti-“identity politics” liberals or moderates who “come from the Left.” That’s why the issues in academia loom large and those in the military don’t. They don’t know many people in the military, just like much of the intelligentsia.

3) The Left dominates the academy, while the Right is the conventional orientation of the American officer corps. Social liberals are probably somewhat more intelligent and intellectual than social conservatives. Social conservatives are probably somewhat more courageous and patriotic than social liberals. But the difference is not enough to account for the disproportionate representation across the professional groups. This is probably a matter of self-selection and sorting.

If you read one Nassim Nicholas Taleb book I would suggest Fooled by Randomness: The Hidden Role of Chance in Life and in the Markets. There was a big thing on Twitter about Taleb’s opinions on IQ. Since he blocks me I saw it through other parties. Someone close to Taleb and myself told me he seems to express himself in the most opaque and disagreeable way possible on Twitter. Sounds right.

He was probably more right than wrong in his disagreement with Mary Beard (again, he blocks me, so hard to know), but because of his online persona, few geneticists would defend him (I did after a fashion). But I knew I was going to be blocked by him because we have lots of mutual followers, and they kept asking me his opinions on GMO. When I said I thought he was wrong and didn’t really know biology as well as he thought, of course, he called me a fucking moron and blocked me. Sorry, not gonna lie!

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas.

One of the reasons that Scholars Stage is one of the few blogs I still read, Making Sense of Chinese History: A Reading List. Will second Imperial China.

In case you missed it, Tanner was a guest on this week’s BrownCast, the Brown Pundits podcast.

As for my other podcast, The Insight, very proud that we closed 2018 with 44 episodes total now! That’s not quite one a week, but it’s not that far off.

Amy Harmon of the NYT on Race & Genetics, Women in Science. If you enjoy listening to white liberals talk about racism and science. Since all white people are “racist” I guess it makes sense to have experts weigh in. They certainly are never shy about explaining racism to me.

David Frum mentioned offhand that in 2019 he is thinking about doing YouTube commentary on books, etc. My response is simple: in terms of data density, it’s written >>> audio > video (with obvious audio). But in terms of the nominal number of people you reach in a short period of time, it’s probably flipped. I have experience with all formats for what it’s worth.

Also, reflecting on my life and how I allocate time…and if whatever I’m doing here is “worth it to me,” I do want to give readers a heads up that I’m wondering about ways I can increase remuneration from this weblog beyond the trivial (e.g., some sort of gating for readers who follow me regularly).

Finally, this current domain has been active again for about a year now. Here are the top 10 posts of 2018:

Why The Chinese Don’t Buy Deodorant
Intercourse and Intelligence
Making What Harvard Is About Transparent
The Maturation Of The South Asian Genetic Landscape
Traits of men who prefer breasts, booty, or legs
Elizabeth Warren Carries Native American DNA
The Great Genetic Map And History Of China
The Origin Of The Ashkenazi Jews In Early Medieval Europe
The Genome Of “Cheddar Man” Is About To Be Published
White People Are Not Gods, They Bleed

Drivers of selection for ghosts in the genome

A new preprint on bioRxiv, Strong selective sweeps before 45,000BP displaced archaic admixture across the human X chromosome, is suggestive of an exciting new phase in human evolutionary genomics. Basically, leveraging whole-genomes in diverse populations to explore selection dynamics.

The authors looked at X chromosomes in males for reasons of technical tractability. Human males carry a single X chromosome, so it’s easy to determine the sequence of genetic variants across a physical stretch of DNA (females, with two X chromosomes, require phasing). The X is interesting for two other reasons: it is present in females about 2/3 of the time (because they have two copies), and, is subject to really strong selection in males 1/3 of the time. Basically, males exhibit no recessive dynamics on the X chromosome because we carry only one. This means that genetic variants which are “recessive” in their expression to selection in females are expressed in males.

The fact that the X is disproportionately found in females also means that all sorts of intra-genomic conflict driven by sex occur on this chromosome. You will know this if you read Matt Ridley’s excellent The Red Queen.

The specific result here is that the authors found a common family of haplotypes in males on the X chromosome outside of Africa whose homogeneity is indicative of a very strong sweep. From the text:

The identified selective sweeps are as strong or even stronger than the most dramatic sweeps previously found in humans. Ten sweeps span between 500kb and 1.8Mb in more than 50% of non-Africans (Table S2). The strongest sweep span 900kb in 91% of non-Africans and affects 53% of non-Africans across a 1.8Mb region. For comparison, the strongest sweep previously reported surrounds the lactase gene and spans 800kb in 77% of European Americans (24). The selection coefficient on the genetic variant driving this sweep was estimated to 0.15 (24) suggesting even stronger selection for several of the X chromosome sweeps we have identified.

The swept regions we identify here may be recurrent targets of strong selection during human evolution. To investigate this possibility, we intersect our findings with our previously reported evidence of selective sweeps in the human-chimpanzee ancestor (16).We find a strong overlap between the sweeps reported here and regions swept during the 2-4 my that separated the human-chimpanzee and human-gorilla speciation events (17, 25) shown as grey regions in Figure 2 (Jaccard stat.: 0.17, p-value: <1e-5) (Materials and Methods). This suggests that the identified regions of the X chromosome are continually subjected to extreme positive selection.

A selection coefficient of 0.15 is eye-popping. Selection coefficients of 0.01 are reasonable. For humans, anything in the 0.10 range is more like a weird artifact than a true result. But here it is. The fact that the regions overlap with earlier targets of selection during the speciation event that led up to our lineage is clearly of interest.

Looking more closely at the regions of the X which was subject to the selection, they found almost no archaic ancestry. That is, the ~1% Neanderthal ancestry that is expected across the X chromosome is almost absent in these segments derived from the selection event. The inference is made that perhaps then these sweeps occurred due to introgression from a sister modern human lineage, perhaps an earlier wave out of Africa which never mixed with Neanderthals. The archaeology is compelling now that these people existed, and there are tentative suggestions from genomics which attests to their presence as well (e.g., modern human admixture into the Altai Neanderthals).

Looking at the 45,000-year-old Siberian genome the authors found the same signatures that they see in other non-Africans. This means the event had to happen between 55 and 45 thousand years ago, after the Neanderthal admixture (which is found all around these zones in the genome), but before geographical diversification and expansion of the modern human lineage.

The authors conclude:

We hypothesize that our observations are due to meiotic drive in the form of an inter-chromosomal conflict between the X and the Y chromosomes for transmission to the next generation. If an averagely even transmission in meiosis is maintained by a dynamic equilibrium of antagonizing drivers on X and Y, it is possible that the main bottlenecked out-of-Africa population was invaded by drivers retained in earlier out-of-Africa populations. If this hypothesis is true, the swept regions represent the only remaining haplotypes from such early populations not admixed with Neanderthals.

Meiotic drive is a segregation distorter. A form of intra-genomic selection which is potentially very powerful. Some hypothesize that alleles normally subject to meiotic drive sweep through the population so fast that researchers underestimate the phenomenon’s ubiquity because they haven’t caught sweeps in action.

This strange evolutionary genetic process then may have preserved a genetic relic within the human genome. But on Twitter Iosif Lazaridis suggests that perhaps the donor population were “Basal Eurasians,” and all non-Africans may have some Basal Eurasian ancestry, with Near Easterners exhibiting more than baseline ancestry (presumably through later admixture).