The dingo ate our domestication

Below I mentioned the preprint, Genomic analysis of dingoes identifies genomic regions under reversible selection during domestication and feralization. I do think that readers will be quite interested in reading it, and it’s not too technical. As the authors note, the dingo is interesting because of the longest lasting “feral” lineage that is known. Additionally, unlike other feral lineages hybridization with other populations has been pretty minimal until recently (though they detected some in two of their dingo samples).

The phylogenetics isn’t that surprising. Dingos are closest to New Guinea Singing Dogs (NGSD). And this clade is most similar to Indonesian dogs. Basically, as you’d expect dingos are the product of a serial founder event from Southeast Asia into Australia. Their ancestral population is really, really, small.

The authors quote a time of arrival of the dingos to ~3,500 years ago, and their phylogenetic inferences seem to indicate divergence from Indonesian lineages ~5,000 years ago. That divergence is probably sensitive to some parameter estimates. But, it does make me wonder who the domestic dogs came with. Since they seem to be descended from Eurasian wolves, the most likely candidate is the first Austro-Asiatic farmers. From them, dogs could spread rapidly through feralization to neighboring populations of hunter-gatherers.*

But here’s the interesting part from the abstract:

Selection analysis identified 99 positively selected genes enriched in starch and fat metabolism pathways, indicating a diet change during feralization of dingoes. Interestingly, we found that 14 genes have shifted allele frequencies compared to dogs but not compared to wolves. This suggests that the selection affecting these genes during domestication of the wolf was reversed in the feralization process. One of these genes, ARHGEF7, may promote the formation of neural spine and synapses in hippocampal neurons. Functional assays showed that an A to G mutation in ARHGEF7, located in a transcription factor-binding site, decreases the endogenous expression. This suggests that ARHGEF7 may have been under selection for behavioral adaptations related to the transitions in environment both from wild to domestic and from domestic back to wild. Our results indicate that adaptation to domestication and feralization primarily affected different genomic regions, but that some genes, related to neurodevelopment, metabolism and reproduction, may have been reversibly affected in the two processes.

There are lots of arguments about how the dog got domesticated. One thing to remember is there is a distinction between population divergence of the ancestors of dogs from the ancestors of Eurasian wolves and the domestication of the dog in various steps and stages. One can imagine, for example, a close association between some groups of wolves and humans, with the former existing in a symbiotic relationship with nomadic bands. This state could persist for thousands of years (in fact, I have heard that this may resemble the relationship of the dingo to Aboriginal people, whose landscaping through fires may have been helpful to dingo predation).

Eventually, though humans settled down into sedentary villages. It is hard not to imagine that the village garbage pile dogs didn’t evolve to be even more human accommodating at this stage, with some of them being helpmates to human populations as work dogs (watch-dogs, hunting-dogs, and even war-dogs).

The dingo may illustrate a shift back toward more detachment from humans. The Aboriginal people never lived in large agricultural villages, so the opportunities for extremely close coexistence did not present themselves. But it is interesting that the dingo did not revert to becoming an Australian wolf, but remained distinctively dog-like. This may be a function of loss of genetic diversity through the bottleneck, a different ecological niche than the wolves of Eurasia, or, irreversible evolutionary genetic changes in the morphology and physiology of the canid lineage.

* Australians on the north coast have a legend of a dog arriving in a boat. Most likely they arrived from Sulawesi in Indonesia.

Open Thread, 11/19/2018

I figure I should post the “Open Thread” sooner than later since people are using last week’s “Open Thread” to post stuff.

So I’m getting a copy of Fire & Blood: 300 Years Before A Game of Thrones tomorrow according to Amazon. But I have a legitimate reason to get this book: we’ll be talking about the “genetics of Game of Thrones” soon on The Insight, my podcast with Spencer Wells.

Finally recorded a second episode of the Brown Pundits podcast, where we talk about the woman imprisoned for blasphemy in Pakistan and colorism. Mostly it’s Zach talking to be honest since he has a lot more passion about these topics, especially the former one.

This guy is a legitimate University of Chicago biologist. What have you done with your life?


Demographic histories and genetic diversity acrosspinnipeds are shaped by human exploitation,ecology and life-history. Pinnipeds.

Genomic analysis of dingoes identifies genomic regions under reversible selection during domestication and feralization. An interesting thing is that dogs almost certainly descend from a wolf/wolf-like population, but when they go feral they don’t quite become wolves. Perhaps it would be different if they went feral in northern Eurasia. But the ones in tropical/mid-latitude zones that “de-domesticate” don’t become Eurasian wolves. Perhaps something to do with genetic variation lost, but I think some of it is different selection pressures.

Sigrid Johnson Was Black. A DNA Test Said She Wasn’t. The title comes from an early forensic test that probably used hundreds of ancestrally informative markers. If you read the whole thing you see that the results kept getting closer and closer to reality.

Psychology’s Replication Crisis Is Running Out of Excuses.

Middle Palaeolithic occupations in central Saudi Arabia during MIS 5 and MIS 7: new insights on the origins of the peopling of Arabia and Late Middle Pleistocene Levallois stone-tool technology in southwest China. The spread of non-Africans around ~60,000 was responsible for most of the non-African ancestry. But there were probably some “false dawns.”

In relation to Robert Plomin’s Blueprint: How DNA Makes Us Who We Are probably worth it if you haven’t ever read behavior genetics. But really a lot of it is reemphasizing/reintroducing results from the field over the past generation. Hopefully will write review soon.

Super-smart designer babies could be on offer soon. But is that ethical? I suspect that the vast majority of the customers for many years will be focused on diseases. The best way to have tall and smart children is to select a tall and smart spouse. We might be talking about something different in the 2030s. I’m struck by how little discussion there is from bioethicists and geneticists about NIPT tests for stuff like Down Syndrome. They’re ubiquitous, but talk is limited generally to pro-life circles.

A friend told me that Conquerors: How Portugal Forged The First Global Empire is pretty good. I might quibble with the subtitle, but he confirms that the Portuguese were indeed huge dicks. The Iberians as a whole were brutal and nasty. Though not as nasty as the Anglo-Protestant “Black Legend” would imply. Mostly they didn’t follow the norms and rules which were present in parts of Asia and the New World between states and peoples.

Is anyone still getting 500 errors very often?

Happy Thanksgiving to Americans.

Trader Joe’s Yuzu and Habanero Hot Sauce

Normally I get hot sauces from specialty shops. But now and then I buy brands at supermarkets. So I saw two hot sauces at Trader Joe’s, yuzu sauce, and a habanero sauce.

I don’t buy habanero sauces that have carrot juice, and this one did not. In general, I’d say it’s a pretty generic product, not bad, not good. The simplicity of the ingredient list seems to have resulted in something pretty bland, though spicy enough if you are a weakling.

The yuzu sauce is something different. In some ways it reminds me of a Louisana hot sauce, there’s a tang to it. But the difference is a citrus flavor that outlasts and pervades the very mild spice. Its refined delicacy is something that I’ve put good use to: I have been using the yuzu sauce as salad dressing!

Unless you are hard up for a kick, I’d pass on Trader Joe’s habanero sauce. But the yuzu is worth it.

The creation of Islam in Late Antiquity

Periodically people ask me my opinion of Tom Holland’s In the Shadow of the Sword: The Birth of Islam and the Rise of the Global Arab Empire. I don’t have an opinion because I haven’t read it. Many years ago I took an interest in the topic of Islamic revisionism, and from what I can tell the field hasn’t moved that much in terms of clarity. Rather, Holland’s project in the book has been to repackage it for lay audiences.

Basically, it seems Holland wants to do to Islam what has happened to Christianity over the past few centuries in the West: turn it into a natural phenomenon and not part of the numen of the cosmos. Though a fair number of traditionalist Christian believers exist, many people who say they are Christians are often quite aware of revisionist theories about their religion. It’s not taboo or shocking. It’s just the norm.

Consider Candida Moss’s book, The Myth of Persecution: How Early Christians Invented a Story of Martyrdom. Moss is a Roman Catholic, who published The Myth of Persecution while a professor of the New Testament at Roman Catholic Notre Dame University. As the title indicates Moss challenges one of the foundational beliefs about the rise of early Christianity: “the blood of the martyrs is the seed  of the Church.” And yet she remains identified as a Christian, a professor of the New Testament.

Most educated Christians are probably vaguely aware that the four gospels were written between 70 AD and 100 AD. And, because of the Dan Brown’s The Da Vinci Code many people are aware that the development of early Christianity was to some extent a cumulative process (even though Brown’s description is totally off base).

Before the 19th century, most Christians did not even comprehend that their religion could be viewed in such a critical-rationalist manner. They were not necessarily “fundamentalists” as we would understand them. Some apologists for Catholicism arguing against early scripturalist Reformers even pointed out inconsistencies within the Bible to illustrate the futility of sola scriptura. But, Christians accepted their traditions and beliefs in a relatively innocent manner (though the debunking of the Donation of Constantine occurred rather early).

The vast majority of Muslims today are where Christians were several centuries ago. Even liberal Muslims, or atheists from a Muslim background, tend to accept the traditional view as the view which they reject piecemeal or in totality. As for as the origins and rise of Islam and the Arab empires, Hugh Kennedy’s The Great Arab Conquests lays out the traditional received model.

Kennedy’s book focuses on the Umayyads, the first hereditary dynasty of the Islamic world (an earlier book was on the Abbasids-When Baghdad Ruled the Muslim World).  Kennedy does not write from the perspective of a Muslim historian, but a Western historian who takes the Muslim sources at face value (he acknowledges in the introduction that there is a revisionist view, though that is not his book).

The story is a simple one. Muhammad founds a new monotheistic religion in pagan Arabia, and after his death in 632 the tribes united in the faith explode out of their desolate peninsula. In 636 these forces defeat both the Romans and the Persians. Within a few decades the Muslims rule a vast swath of territory, and in 661 the Umayyad dynasty is inaugurated with the reign of Muawiya I, who reputation and fame would likely be greater if history had not been written by the enemies of his dynasty. One of the reasons that the Umayyads have a low reputation is that their interpretation of Islam was closely tied to their Arab tribal identity. Their religion was not quite the trans-ethnic one that would flourish under the Abbasids. Some Islamic scholars even called the Umayyads the “Arab Kingdom” (the title “king” is considered un-Islamic).

What is the revisionist story that Holland wants to tell?  The outline is simple: in the first two generations after the Arab conquest, the Arabs were not Muslims as we, or they, would understand it. Holland specifically seems to believe that Islam as a religious ideology that bounds together the Arab ruling class of the Umayyad domains crystallized during the reign of Abd al-Malik in the 680s AD. This is fifty years after the death of Muhammed, and nearly four decades after the conquest of the Near East and Persia.

There are is a lot more to what Holland believes went down. To get a good sense, watch his 2012 documentary on Youtube.

Do I believe it? Obviously, I don’t believe that Muhammad is a prophet of God, since I don’t believe in God. But, that doesn’t mean that Muhammad didn’t think he was a prophet of God and that his followers were insincere. The rise of Islam is a fundamentally material affair. There is no magic. That would come later with Sufi saints with miraculous powers.

One reason we can have this debate is that the sources are sparse and vague. This may sound strange to say, but as an example, we have very little written records that come down from pre-Islamic Persia. For our knowledge of the ancient and early medieval world we are faced with three major periods of massive literary production: in Baghdad in the 9th century, under Charlemagne in the 9th, in Constantinople in the 10th. The 7th century was a period of stress and deprivation in the East Roman Empire, as it lost massive territory to the Arabs. But one thing that seems clear is that these East Romans did not have a clear sense of the Arabs as practitioners of a new world religion that was not Christian. They were clear that they were ethnic Arabs, but not clear that they were anything but heretics or some sort.

The sparsity of “non-traditional” sources means that revisionists have to engage in deep philological analysis of the extant sources, an enterprise which is beyond the ken of non-specialists to evaluate. I have no strong opinions on whether Muhammad existed or not. Nor am I sure that Mecca and Medina as holy sites were later additions to the history of Islam (revisionists tend to believe that the Arabs emerged out of the Syrian desert, not from further south). I suspect in a lot of the details Holland is incorrect. But I do not think that the orthodox view is correct in the details either.

The Late Antique world was not as neatly sectarian as we might imagine. It was messily sectarian. The advance of Islam in the domains under the rule of the Arab Caliphates was uneven. Substantial regions of Iran proper remained under the rule of Zoroastrian kings as late as the 9th century, and Muslims were probably not a majority in Iran until the 10th century.

The Levant and Mesopotamia had a Christian majority for centuries under the rule of the Umayyads and Abbasids. In The Rise of Western Christendom Peter Brown claims that Islamicization in the Near East was associated with Arabicization. That is, once Christian populations switched to Arabic as their everyday language, conversion to Islam became much more feasible.

But knowing what we know about other religions it seems implausible to me that Islamic emerged out of the desert in the fully formed manner that Muslim tradition implies. The rise of Christianity is a clear case of debates, arguments, and gradual rough consensus over a period of decades and later centuries. When it comes to younger religions such as that of the Bahai or Mormonism, we can see in “real time” how religions can evolve after the death of their founders. The Bahai religion has its roots in Shia revivalism, but eventually, it transformed itself into a post-Muslim world religion. Though Mormons retain a Christian identity, their theology is extremely exotic in comparison to the Christian mainstream.

The Umayyad positive attitudes toward Late Antique Hellenism and their total co-option of the East Roman system is suggestive of a barbarian conquest elite, not an ideologically motivated one. The Rashidun period and the life of Muhammad may always be mysteries to us, but they almost certainly do point to unlikely events in the Arabian Peninsula (or its liminal zone) which resulted in the military mobilization of Arabs bent on conquest. Islam’s emergence in a form more recognizable to us in the late 7th century may have been an inevitable result of declining cohesion of the Arab conquest elite, and the necessity of an ideology to bind them together, along with notables from conquered populations.

And of course, we know that the 8th and 9th centuries saw the transformation of Islam in a deeper and more thoroughgoing manner, with the shift to the east of the Abbassids and the emergence of the ulema class and the marginalizations of philosophy. But that needed the ideology of empire, and that ideology did not emerge de novo from the desert. Islam did not create an empire, the empire necessitated the precipitation of Islam.

Random and inevitable forces in world history: the 6th century

In Science Anne Gibbons reports on new ice-core evidence for why the middle of the 6th century A.D. was so difficult in much of Europe:

Historians have long known that the middle of the sixth century was a dark hour in what used to be called the Dark Ages, but the source of the mysterious clouds has long been a puzzle. Now, an ultraprecise analysis of ice from a Swiss glacier by a team led by McCormick and glaciologist Paul Mayewski at the Climate Change Institute of The University of Maine (UM) in Orono has fingered a culprit. At a workshop at Harvard this week, the team reported that a cataclysmic volcanic eruption in Iceland spewed ash across the Northern Hemisphere early in 536. Two other massive eruptions followed, in 540 and 547. The repeated blows, followed by plague, plunged Europe into economic stagnation that lasted until 640, when another signal in the ice—a spike in airborne lead—marks a resurgence of silver mining, as the team reports in Antiquity this week.

Kyle Harper, author of the excellent The Fate of Rome: Climate, Disease, and the End of an Empire, is quoted in the piece. It’s curious to me to observe the stochastic and correlated events in this particular story.

I assume that volcanic mega-eruptions occur in a pattern defined by a Poisson distribution. That is, they are rare and random events. One thing about the Poisson distribution is that the events tend to cluster together more than human intuition would predict based on what we think might occur when we hear “random events.” Those with more paleoclimate knowledge that I can evaluate this, but it seems that massive eruptions that occurring so close in time are going to be rare indeed, but, they will happen now and then.

That’s the random part. The outbreak of plague is probably less random. In Europe, the plague faded in the early modern period. Though people disagree about the reasons, modern developed societies where people are more well-fed are probably less susceptible to it (as well as low-density hunter-gatherer or pastoralist populations). As Peter Turchin has pointed out only one sitting European monarch died during the Black Death of the bubonic plague, even as 30-60% of the local population succumbed. It seems likely that extremely difficult conditions for agriculture, and the consequent malnutrition, made the spread of plague through vulnerable populations much more likely.

A major consequence of the calamities of the mid-6th century is the reconquest of the West Roman Empire under the push from Justinian and his heirs lost steam. Unlike in China, the Roman system was never recreated in full. Many explanations have to do with the violence of the Gothic Wars, or the inability of East Roman power to expand west while dealing with a more vigorous Persia to the east. We can’t rerun the experiment, but the above volcanic eruptions suggest that the likelihood of total reconquest took a major hit because of an event that was not inevitable.

Remember that the Roman state recovered by near total unwinding in the middle of the 3rd century.

Though we will never resolve the issue of whether the fall and collapse of the Roman Empire was inevitable and its reassembly impossible, by looking in totality at volcanic events and seeing how it correlates with state-formation or collapse, and social complexity, we may get a sense of the nature of the balance of endogenous cyclical forces and exogenous random shocks in the rise and fall of polities. By endogenous cyclical forces, I’m referring here to social cohesion and elite unity, which over time degrades and decays. As states and societies fracture and a new cycle of integration begins anew. I suspect that the exogenous shocks occur periodically, but that if they slam a society at its peak, then the social structure may be able to absorb the shock. In contrast, societies under stress collapse due to unexpected perturbations.

Patterns of genetic diversity within Africa

The violin-plot above is from a new preprint, Runs of Homozygosity in sub-Saharan African populations provide insights into a complex demographic and health history. Here’s the abstract:

The study of runs of homozygosity (ROH), contiguous regions in the genome where an individual is homozygous across all sites, can shed light on the demographic history and cultural practices. We present a fine-scale ROH analysis of 1679 individuals from 28 sub-Saharan African (SSA) populations along with 1384 individuals from 17 world-wide populations. Using high-density SNP coverage, we could accurately obtain ROH as low as 300Kb using PLINK software. The analyses showed a heterogeneous distribution of autozygosity across SSA, revealing a complex demographic history. They highlight differences between African groups and can differentiate between the impact of consanguineous practices (e.g. among the Somali) and endogamy (e.g. among several Khoe-San groups). The genomic distribution of ROH was analysed through the identification of ROH islands and regions of heterozygosity (RHZ). These homozygosity cold and hotspots harbour multiple protein coding genes. Studying ROH therefore not only sheds light on population history, but can also be used to study genetic variation related to the health of extant populations.

This sort of run-of-homozygosity analysis is enabled by high-density genotyping or whole-genome sequencing. After quality control, the authors had 1 to 1.5 million SNPs for all populations.

The interesting thing about this preprint is that by looking at the violin-plots can you can see exactly all the things that population geneticists have learned about the demography, structure, and history of humans in the past generation or so.

  • The rightmost panel shows the average total length of short ROH. Partly the pattern fits into the older serial bottleneck model of the settlement of the world. The pattern of Amerindian > East Asian > European > African. But what about the lower fractions for mixed Latin Americans and Gujuratis? This is a consequence of admixture, as these populations are mixtures in a sense of other groups.
  • The length of the long ROH segments, the second to last panel on the right, is indicative of recent patterns of marriage. Within Africa, you see some groups have many individuals with lots of long ROH segments. This is because of consanguinity. As the authors observe, the Oromo and Somali are both Cushitic speaking groups from the Horn of Africa, but the latter are universally Muslim, while only a minority of the former are. Islamic cultures have traditionally encouraged consanguineous marriages, and you can see the difference between these groups (whose total length of short segments is similar).
  • The pattern of ROH here can be predicted by simple genetic models: the extent of random mating within populations, recombination rates across the genome, and total population size. What modern genomic technology does is provide data to test the models.

 

The golden age of pigmentation is yet to come

Skin color is important and interesting. It is important because people think it is important. Humans often classify each other by complexion, and it has a high social importance in many cultures.

This tendency starts at a very young age. When my children are toddlers they’ve all misidentified photographs of black American males with a medium brown complexion as their father (for example, my son recently misidentified a photograph of me that was actually the singer Pharrell). In terms of my background though, I’m 100% Eurasian in ancestry. On a PCA plot, I’m about halfway between Europeans & Near Easterners and East Asians (I have 15% East Asian ancestry so I’m more shifted to East Asians than the typical South Asian).

Skin is the largest human organ, and we are a visual species. It is an incredibly salient canvas. So it’s no surprise that we use complexion as a diagnostic marker for taxonomic purposes. The ancient Greeks correctly observed that the peoples of southern India have dark skin like Sub-Saharan Africans (“Ethiopians”), but that their hair is not woolly. Islamic commenters regularly referred to South Asians as “black crows”, while European observers of the 17th century noted that the ruling class of Indian Muslims tended to be white (i.e., mostly Turkic and Iranian in provenance) while the non-elites were black (descendants of Indian converts).*

Luckily, for a characteristic that we’re fascinated by, pigmentation has been reasonably tractable to genetics. As early as the 1950s human geneticists using classical methods of pedigree analysis predicted that pigmentation was polygenic, but that most of the variation was due to a small number of loci (see The Genetics of Human Populations). In particular, they focused on families of mixed European and African ancestry in British ports with known pedigrees.

When genomic methods came on the scene in the 2000s, pigmentation was one of the first traits that yielded positive GWAS hits as well as population genetic findings related to natural selection. In Mutants, written in the middle aughts, the author observed that there wasn’t much known about the basis of normal human variation in pigmentation. This all changed literally a year after the publication of this book. By the middle of 2006, a review paper came out with the title, A golden age of human pigmentation genetics. The reason this paper was written is that a host of studies on European populations had identified several loci which explained a substantial proportion of the intercontinental difference in pigmentation between Africans and Europeans.

Read More

Open Thread, 11/12/2018

Fatal Discord: Erasmus, Luther, and the Fight for the Western Mind is an interesting book. Very much on the side of Erasmus. Like the author, I do think Erasmus turned out to be a beautiful loser. But ideas and biographies can have second acts.

How the GOP Gave Up on Porn. Basically, the war was lost. The curious thing about the pervasiveness of porn today is that arguably in many ways our modern society is more prudish than that of the 1970s and 1980s when the political activity around obscenity was very active.

Population genomics of grey wolves and wolf-like canids in North America.

The Summer’s Most Unread Book Is… From 2014. People don’t seem to finish non-fiction. Though for a lot of nonfiction books you don’t have to read every chapter, and they are very loose in a narrative sense.

Outlaw King Is a Lot Better Than You’ve Heard.

Estimates of the Heritability of Human Longevity Are Substantially Inflated due to Assortative Mating.

If you need a paper, Sci-Hub.

Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference.

Shades of complexity: New perspectives on the evolution andgenetic architecture of human skin.

A Two-Player Iterated Survival Game.

Cultural Selection Shapes Network Structure.

A new blog, Academic Parents. Two of my kids were born during graduate school. I was not the primary caregiver at all, and obviously did not give birth to them. But it was somewhat difficult still. Can’t imagine if I was the one taking care of the newborn.

It’s also nice to see people starting blogs. Both Twitter and YouTube streaming have replaced the “voice” that blogging gave random people, but both media are relatively vapid and shallow compared to having to write down your thoughts.

Bob Trivers’ Natural Selection and Social Theory is now a free PDF. Highly recommend this book. Trivers is an engaging writer.

Last week I made a bet with a friend that Republicans would gain one seat in the Senate, and Democrats would gain the House. Looks like I won that bet.

 

A Kimura Age to the Kern-Hahn Era: neutrality & selection

I’m pretty jaded about a lot of journalism, mostly due to the incentives in the industry driven by consumers and clicks. But Quanta Magazine has a really good piece out, Theorists Debate How ‘Neutral’ Evolution Really Is. It hits all the right notes (you can listen to one of the researchers quoted, Matt Hahn, on an episode of my podcast from last spring).

As someone who is old enough to remember reading about the ‘controversy’ more than 20 years ago, it’s interesting to see how things have changed and how they haven’t. We have so much more data today, so the arguments are really concrete and substantive, instead of shadow-boxing with strawmen. And yet still so much of the disagreement seems to hinge on semantic shadings and understandings even now.

But, as Richard McElreath suggested on Twitter part of the issue is that ultimately Neutral Theory might not even be wrong. It simply tries to shoehorn too many different things into a simple and seductively elegant null model when real biology is probably more complicated than that. With more data (well, exponentially more data) and computational power biologists don’t need to collapse all the complexity of evolutionary process across the tree of life into one general model, so they aren’t.

Let me finish with a quote from Ambrose, Bishop of Milan, commenting on the suffocation of the Classical religious rites of Late Antiquity:

It is undoubtedly true that no age is too late to learn. Let that old age blush which cannot amend itself. Not the old age of years is worthy of praise but that of character. There is no shame in passing to better things.

Selection for rs3827760 at EDAR (“shovel-shaped” incisor SNP) during Holocene around the “Ring of Fire”

EDAR and East Asian hair

If you have been reading my blog will you be familiar with the SNP rs3827760
within the EDAR gene. This mutation has high derived frequencies in East Asians and is associated with a suite of physical characteristics. Most famously, the thickness of hair shaft and “shovel-shaped” incisors (a phenotype also found in Neanderthals). So the reason people of East Asian ancestry seem to have very thick straight hair is that their hair strands are actually thicker due to the new variant.

Almost all Africans, West Eurasians, and South Eurasians lack the derived variant. Those populations outside of East Asia which have it in appreciable frequencies, whether it be Munda tribal people in India or Finns in Northern Europe, always have relatively recent East Asian ancestry. The fraction of the derived allele is usually easily inferred from genome-wide East Asian ancestry and source population fraction (southern East Asians have a lower fraction than northern ones).

But there’s another modern group* of people with high frequencies of the derived variant: people of Amerindian heritage. This is reasonable because East Asians and Amerindians share common ancestry, at least in part, going back ~25,000 years ago. The ALFRED database actually has the largest coverage of the New World for this marker that I know of. One inference you can make is that many Amerindian groups were fixed or nearly fixed for the derived variant before some European admixture. For example, the Maya carry ~5% of the ancestral variant, but those samples are known to have a small but significant amount of European admixture (curiously, the derived variant hasn’t swept to fixation in many populations; that implies to me that the phenotypic target of selection has a dominant genetic expression).

So this section of a new ancient DNA paper, Reconstructing the Deep Population History of Central and South America, jumped out at me:

Our data show that a variant in EDAR that affects tooth shape, hair follicles and thickness, sweat, and mammary gland ductal branching and that occurs at nearly 100% frequency in present day Native Americans and East Asians…was not fixed in USR1Anzick-1, a Brazil_LapaDoSanto_9600BP individual and a Brazil_Laranjal_6700BP individual, all of whom carry the ancestral allele. Thus, the derived allele rose in frequency in parallel in both East Asians and in Native Americans.

These are on the older side as far as samples in the paper go. The numbers are small, but looking at modern Amerindian groups to have this much ancestral variant is surprising. The authors’ conclusion seems highly likely. The EDAR locus, and probably this particular SNP, was segregating in the ancient proto-East Asian/Amerindian metapopulation, and during the Holocene, there was selection on both sides of the Pacific.

Why? Unlike some people, I don’t think it was sexual selection for silky hair with full body. EDAR does a lot of things. From GeneCard:

The EDAR gene provides instructions for making a protein called the ectodysplasin A receptor. This protein is part of a signaling pathway that plays an important role in development before birth. Specifically, it is critical for interactions between two embryonic cell layers called the ectoderm and the mesoderm. In the early embryo, these cell layers form the basis for many of the body’s organs and tissues. Ectoderm-mesoderm interactions are essential for the formation of several structures that arise from the ectoderm, including the skin, hair, nails, teeth, and sweat glands.

This locus doesn’t seem to have been targeted elsewhere during the Holocene. Why not? Perhaps there’s another locus (or set of loci) that do similar things and were the targets of selection in other cases.

The bigger story, emphasized more in the other ancient DNA paper about South and North America that came out today in Science, Early human dispersals within the Americas, is that populations in the New World clearly seem to have been changing morphologically over the past ~10,000 years. Well, yeah….

* Ancient Mesolithic Scandinavian hunter-gatherers seem to have carried the derived variant at rs3827760. These people did not contribute much to the ancestry of later Scandinavians.