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.

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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.

The visual world economy

The depiction of the change in the top 10 economies over the last 60 years in the above graph is pretty mesmerizing. It tells you so much without the recourse to narrative description.

Below is a Google chart I generated of the top 10 economies in 2017 going back to the 1960s and plotting GDP per capita, log-transformed, vs. GDP, log-transformed.

Rice culture reduces individualism

The above map comes from a 2014 paper, Large-scale psychological differences within China explained by rice versus wheat agriculture. From the abstract:

Cross-cultural psychologists have mostly contrasted East Asia with the West. However, this study shows that there are major psychological differences within China. We propose that a history of farming rice makes cultures more interdependent, whereas farming wheat makes cultures more independent, and these agricultural legacies continue to affect people in the modern world. We tested 1162 Han Chinese participants in six sites and found that rice-growing southern China is more interdependent and holistic-thinking than the wheat-growing north. To control for confounds like climate, we tested people from neighboring counties along the rice-wheat border and found differences that were just as large. We also find that modernization and pathogen prevalence theories do not fit the data.

Basically, rice has a higher per unit yield than wheat, but requires a lot more coordinated labor input. To grow paddy rice it takes a village.

This insight was not surprising to me, and introduced in David Sloan Wilson’s Darwin’s Cathedral: Evolution, Religion, and the Nature of Society. In this book Wilson argued for a rehabilitation of the tradition of evolutionary functionalism in the social sciences. Basically, viewing human societies as adaptive functional units. One of his examples to illustrate the necessity of examining group-level function was wet-rice paddy agriculture in Bali, which was only feasible through coordination and collective action between interdependent farms.

The 2014 results made total sense to me in light of what little I knew. Southern Chinese are stereotypically more patriarchal and clannish than Northern Chinese. My inference here being that the collectivist nature of rice agriculture meant that paternal clan units of social organization were more important in the South than the North.

I haven’t followed up on this work at all in all these years. Then I saw this on my Twitter feed: Teens in Rice County Are More Interdependent and Think More Holistically Than Nearby Wheat County.

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Sequence the thousands and your eyes shall be open

Charles Darwin’s The Origin of Species as an audacious work that birthed a whole discipline. But it had its failings. In particular, Darwin famously lacked the Mendelian model of genetic inheritance which easily maintained variation from generation to generation. The reason that variation is important is that it is one of the major raw materials which is required from biological diversification through adaptation (natural selection and the heritability of that variation being other important components). Mendelian genetics is defined by a rearrangement of discrete units of heredity, alleles of various genes, and so solves the problem of the maintenance of genetic variation.

Genes are quite convenient as instruments of evolutionary bookkeeping, and one reason that John Maynard Smith believed that biologists had an advantage over economists in their deployment of game theory. He believed that genes were superior to various attempts by economists to measure “utility.”

Obviously, evolution is not just genes. But, if you are an evolutionary geneticist, then evolution for all practical purposes is defined by changes in frequencies of genetic variants over time.

Until very recently the genetic currency fed into the theoretical machine of evolutionary genetics was precious. There was a great deal of scarcity. A few model organisms, and a few loci. The birth of genomics meant that many common and “important” organisms were sequenced en masse. But the revolution left most of the tree of life untouched.

That is going to change very soon, as geonomicists begin to churn out sequences of a huge number of species. More importantly, they will begin to have population-scale datasets of many species.

This is a step forward from comparing single genomes of various species in a comparative sense. With population genomics researchers can inspect dynamics within numerous species across their whole genomes. This is a big deal. A lot of old questions regarding the generality and specificity, the inevitability and contingency, could be answered within a generation.

Open Thread, 11/4/2018

So in a few days everyone can stop pretending to be cut-rate Nate Silvers.

My prediction: Dems will take the House. But Republicans will make a gain of +1 in the Senate.

Pakistan’s Hybrid Government and the Aasia Bibi Fiasco.. Basically, reasonable people in Pakistan are terrified about being openly reasonable, lest the crazy minority kill them. Another thing is that the details of what this woman did is irrelevant now, she’s a symbol. We’ve seen this in the United States: feelings don’t care about your facts.

DNA Sequencing Giant Illumina Will Buy Pacific Biosciences For $1.2 Billion – Exclusive CEO Interview. I think this is precautionary.

Half of Americans believe in ghosts…

Least-cost pathway models indicate northern human dispersal from Sunda to Sahul.

Inferring the ancestry of everyone. “We introduce an algorithm to infer whole-genome history which has comparable accuracy to the state-of-the-art but can process around four orders of magnitude more sequences.”

Largest genome-wide association study for PTSD identifies genetic risk loci in European and African ancestries and implicates novel biological pathways.

Many options, few solutions: over 60 million years snakes converged on a few optimal venom formulations.

Genetic Consequences of Social Stratification in Great Britain. This is obviously triggering discussion. But please note this preprint is the beginning of a conversation, not the closure on anything.

Species limits in butterflies (Lepidoptera: Nymphalidae): Reconciling classical taxonomy with the multispecies coalescent.

Again, Tim Blanning’s Frederick The Great is interesting as both biography and history of 18th century Prussia. The book has the subtitle “King of Prussia,” but if Blanning was in it for the clicks, it would be “The Gay Atheist Autocrat.”

It’s raining selective sweeps

A week ago a very cool new preprint came out, Identifying loci under positive selection in complex population histories. It’s something that you can’t even imagine just ten years ago. The authors basically figure out ways to identify deviations of markers from expected allele frequency given a null neutral evolutionary model. The method is put first, which I really like, before getting to results or discussion. Additionally, they did a lot of simulation ahead of time. The sort of simulation that is really not possible before the sort of computational resources we have now.

Here’s the abstract:

Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method – called Graph-aware Retrieval of Selective Sweeps (GRoSS) – has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish and human population genomic data containing multiple population panels related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in under-studied human populations, as well as muscle mass, milk production and tameness in particular bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation due to inversions in the history of Atlantic codfish.

On a related note in regards to selection, On the well-founded enthusiasm for soft sweeps in humans: a reply to Harris, Sackman, and Jensen. The authors are responding to a recent preprint criticizing their earlier work. The reason that it’s fascinating to me is that these sorts of arguments today are really concrete and not so theoretical. There’s a lot of data for analytic techinques to chew through, and computation has really transformed the possibilities.

A generation ago these sorts of debates would be a sequence of “you’re wrong!” vs. “no, you’re wrong!” Today the disputes involve a lot of data, and so have a reasonable chance of resolution.

The first preprint identifies the usual candidates in humans that you normally see, and expected targets in cattle and cod. Sure, that will given biologists more interested in mechanisms and pathways things to chew upon, but imagine once researchers have large numbers of genomes for thousands and thousands of species. Then they’ll be testing deviations from neutral allele frequencies across many trees, and getting a more general and abstract sense of the parameter that selection explores, conditional on particularities o evolutionary history.

This is why I’m excited about plans to sequence lots and lots of species.

The rise of printing and the populist republic

The media needs clicks and people are rather myopic. This explains patently false pieces such as this in Buzzfeed, This Is How We Radicalized The World. It is a rather unorganized list of facts, but they are assembled in a way to convince and persuade the reading audience that modern information technology has facilitated the rise of political radicalism, as if it is something new and notable. So wrong it hurts.

Anyone who knows history will realize this is patently false. Anyone who is aware of the Taiping Rebellion, the October Revolution, or the unrest of 1848. Of course, that “anyone” is a small set of individuals because most people don’t know history. Their minds are devoid of most facts not having to do with the Khardashians. And journalists are not much better. Many of them are in the game of creating stories rather than interpreting the world. If public relations operatives are well paid propagandists on a short leash, many journalists are poorly paid propagandists compensated with the freedom to be fabulists.

A piece like the above could convince, but only with a scatterplot. Social science can convince whether history says otherwise, because it is systematic and clear. But most people are not fluent and competent enough to do such data analysis, so they create a conclusion that is congenial to their audience, and marshal evidence in a biased manner (wittingly or unwittingly) to support their conclusion.

To get a sense of what we’re seeing today in the world, we need to go back centuries.

In the early 16th century, the unity of Western Christianity shattered. The standard story you see in the movies is that a German Augustinian monk named Martin Luther led a rebellion against the Roman Church, what became the Roman Catholic Church after it was clear that the Protestants were going to go their own way.

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