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November 16, 2018

Patterns of genetic diversity within Africa

Filed under: Human Population Genetics — Razib Khan @ 12:02 am

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.

 

November 15, 2018

The 20,000 year adventur eof the

Filed under: Genetics,History,science — Razib Khan @ 1:28 am

The great adventure of the Native Americans

Comanche warriors in 19th century Texas

In 1492 Christopher Columbus made definitive and lasting contact between Europe and the New World. This was not the first contact. We know for a fact that Greenland Norse knew of the New World as “Vineland.” They visited Labrador and Newfoundland to obtain resources, and in one instance, at L’Anse aux Meadows, attempted to settle permanently. But aside from sagas, nothing came of this.

It was for Columbus and the Europeans who came after to grapple with the fact that across the Atlantic there was a whole world unknown to them. Not Asia, but something fundamentally new. Peoples beyond their ken. In the five centuries since that contact, the engagement between these two worlds has defined much of the history of the world, as the displacement of the native peoples tracked the ascension of European peoples and their eventual conquest of the globe.

But in geological history, five hundred years is but a blink of an eye. The story of the native peoples of the New World, called Native Americans in the United States of America, First Nations, Aboriginal or indigenous elsewhere, begins over 30,000 years ago at the “top of the world.” The Asian landmass adjacent to the Arctic.

Citation: The population history of northeastern Siberia since the Pleistocene

Rather soon after modern humans break out of Africa ~50,000 years they began to expand all across Eurasia rapidly, absorbing groups like Neanderthals and Denisovans. One wave pushed north through the Caucasus and Central Asia and veered west, eventually giving rise to the various European hunter-gatherers of the Paleolithic and Mesolithic. Another group moved north and east, and gave rise a Siberian population, sometimes called “Ancient North Eurasians”, whose genetic shadow today spans Patagonia to Portugal.

But by ~25,000 years ago the appropriately named “Last Glacial Maximum” had commenced, and the habitable zones in Siberia shrank. These first Siberian populations retreated to the clement pockets available, and human habitation disappeared from much of the northern swaths of Eurasia.

A world of ice ~20,000 years ago
“This climatic change had major demographic consequences.”
Yakuts

Today most of the ancestry of people in Siberia does not descend from these Ancestral North Eurasians but from peoples related to the Han Chinese further to the south and east. While one group of African humans moved north rapidly ~50,000 years ago, another pushed eastward, through southern Asia, and onward toward the Pacific. Coming up from the south up through Manchuria as the climate warmed, these new Siberians eventually came to overwhelm the older populations. They contribute most of the ancestry of the Siberians of today.

But the genetic ghost of Ancient North Eurasians persisted as they were absorbed by other groups. This is how some of their ancestry can be found in many peoples to the west due to migrations out of the heart of Asia in the last 10,000 years. And yet another fragment of this people found itself far to the east, beyond the edge of modern Siberia, in a land now under the ocean in what is the Bering Sea. This was Beringia. A vast open tundra occupied by megafauna.

Further to the east were the vast ice sheets of North America, while to the west the rugged mountains of eastern Siberia, which were more frigid than they are today. But Beringia was not totally isolated. Sometime between 20,000 and 25,000 years ago, during the very heart of the Last Glacial Maximum, a group of hunter-gatherers migrated from the south and merged with a group of the older Siberian peoples.

Fused together, these became what we term “Beringians,” inhabitants of a lost subcontinent. About ~40% of the ancestry of the Beringians derived from the Ancient North Eurasians, and so connects them with people all across Eurasia, from Europe to India. No people in the world is predominantly Ancient North Eurasian today, but many people in the world are partly Ancient North Eurasian. The remaining ~60% of the ancestry of Beringians comes from a group of people who split from the ancestors of modern Chinese ~25,000 years ago. This is likely one reason that many anthropologists have long observed an affinity between Native Americans and the people of eastern Eurasia.

Modern Native Americans are overwhelmingly descendants of these ancient Beringians. Modern Native Americans are therefore ~40% Ancient North Eurasian, and 60% descended from a group of ancient East Asians.

This fusion likely occurred by ~20,000 years ago. But the archaeology seems to indicate that the native people of the New World did not begin to spread across the landscape of North and South America until ~15,000 years ago. The reason is simple: ice sheets blocked migration south and west. But by ~15,000 years ago we see evidence of humans as far as south as Chile! The movement seems to have been rapid and immediate.

One of the consequences of the period of isolation in Beringia is that the ancestral population of the Native Americans was relatively homogeneous, and went through what population geneticists term a “bottleneck.” When isolated populations remain small for many generations they lose much of their genetic variation by chance. And so it is that anyone who looks at the genetics of the peoples of the Americas notices that from north to south they are relatively similar to each other.

The rapid expansion from such a small population means that ancient DNA suggests that much of the genetic structure we see, differences between groups, have emerged only in the last 15,000 years. The thousands and thousands of languages of the indigenous peoples of these two continents are also the consequence of human cultural evolution over the last 15,000 years.

The native language families of North America

As these tribes diverged and separated, they began to develop their own distinctiveness through isolation. In some cases, population replacements and admixtures occurred. The latest evidence suggests that waves of people moved both north and south out of modern-day Mesoamerica in the last 10,000 years. Meanwhile, far to the north, populations continued to move out of northeastern Siberia well after the initial expansion phase and added to the palimpsest of peoples. The Na-Dene speaking groups of the western half of the United States and Canada seem distantly related to various Siberian tribes, and their linguistic unity and more noticeable East Asian appearance suggest a more recent history in the New World than those of the peoples to their south and east.

Surui elders of the Amazon

From the original unity has come a wide diversity. And yet there is one curious lacuna and perplexity: both ancient DNA and analyses of modern samples indicate that some tribes in the Amazon have a deep affinity with the hunter-gatherer tribes of Southeast Asia and the peoples of Papua New Guinea and Australia! And yet there is no signal of this ancestry in peoples to the north, ancient or modern.

Fundamentally, this is a deep mystery which no researchers have a good explanation for. And that goes to show that science can still present us with surprises that defy our expectations and to which we can present no good response.

The future will be filled with surprises, but the last 15,000 years of humans in the Americas have already been a great adventure.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


The 20,000 year adventur eof the was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

November 14, 2018

The Insight Show Notes — Season 2, Episode 7: the genetics of Native Americans

Filed under: Genetics,History,Native Americans,science — Razib Khan @ 7:34 pm

The Insight Show Notes — Season 2, Episode 7: the genetics of Native Americans

Ancient Beringians

This week on The Insight (Apple Podcasts and Stitcher) Razib Khan and Spencer Wells discuss the genetics and history of Native Americans, from the icy shores of the Arctic and to the frigid windswept plains of Patagonia, and all places in between. A 15,000 years story of migration and settlement.

Beringia

There was a lot of talk about Beringia. This is a region between Alaska and Siberia which is now under the ocean. But during the Last Glacial Maximum ~20,000 years ago when sea levels were lower it likely served as a refuge for Paleo-Siberians who retreated from other zones of northeast Asia. Once the climate warmed and the ice sheets opened up, about 15,000 years ago it seems that humans began to migrate southward.

A new preprint, The population history of northeastern Siberia since the Pleistocene, outlines the context of the emergence of the Beringian ancestors of modern Native Americans about 20,000 years ago. They were the fusion of two populations. One group was related to the people of modern East Asia, such as the Han Chinese. This group contributed about 60–70% of the ancestry to the Beringian population.

But the second population, sometimes termed “Ancient North Eurasians”, are very distantly related to the peoples of Europe. This group contributed to 30–40% of the ancestry to modern Native Americans, as well as 10–20% of the ancestry of Northern Europeans, and substantial fractions in parts of West and South Asia. See, 24,000-Year-Old Body Shows Kinship to Europeans and American Indians.

We alluded to the Beringian standstill hypothesis, that the Berengians were bottled up within their small corner of the world for many thousands of years. This is also connected to the small founding population of the New World.

Spencer discussed that haplogroup Q, the paternal lineage common in the New World, has a wide distribution in Eurasia. This could be the impact of the Ancient North Eurasians:

There was an extensive survey of the archaeology of the New World, and the Clovis First hypothesis. The Monte Verde site was mentioned as one of the primary ways in which Clovis First was refuted. Finally, we mentioned a paper in Nature that might push the occupation as far back as 130,000 years! (though most archaeologists dismiss it).

There was some reference to the Greenberg model of the classification of Amerind languages, as well as the Dené–Yeniseian family.

Much of the middle of the podcast focused on two papers that came out this week that filled in many details of the populating of the New World, one in Cell, and another in Science.

We talked about a 2015 result that indicated an Australasian population contributed some ancestry to people in the Amazon.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


The Insight Show Notes — Season 2, Episode 7: the genetics of Native Americans was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

November 13, 2018

Indian culture started when the British arrived: tales of shadology

Filed under: Culture,Shadology — Razib Khan @ 11:27 pm

When looking at Google Scholar after reading the paper on South Asian pigmentation, I came across this work, The Unfair Selection: A Study on Skin Color Bias in Arranged Indian Marriages:

Underlying the growing popularity of skin-lightening or fairness cosmetics in India is one of the most baseless biases experienced and practiced. Yet, the overriding importance of skin-color especially in context of marriage has been largely unaddressed. This exploratory study examined the influence of skin-color on preference for potential marriage partner. A 2 × 2 (gender × skin-color) between-group experimental design was used. Mothers (N = 108) of individuals of marriageable age group were presented with an option of five marital profiles containing education and work information only. The participants were shown profiles of either males or females depending on whether they had a son or a daughter. Once a profile was chosen, the participant was either shown a photograph of highly attractive fair girl/boy or a highly attractive dark girl/boy. The light-skinned and dark-skinned photograph was of the same person, except their skin tones were manipulated with the use of computer software. Participants were asked to rate how strongly would they recommend the girl/boy as potential bride/groom for their children. As expected, fair-skinned highly attractive people received higher ratings than dark-skinned highly attractive people. However, contrary to our expectations, ratings received for dark-skinned woman were not significantly lower than the ratings received for dark-skinned man. This study shows that the color of skin has the potential to even overpower traits such as general competency and physical attractiveness in both men and women.

The subjects are from the Indian capital. The surprising result is no sex difference. I’m not too interested in the paper’s primary result, but the introduction and discussion, which frames the preference for light skin historically, is of interest.

From the introduction:

While Black scholars in the Unites States have thoroughly examined the link between racism and colorism, there is paucity of information tracing the historical roots of skin-color discrimination in India (Parameswaran & Cardoza, 2009a). Internalization of superiority of fair/white skin has been related to the combined influences of colonialism, caste system,
and globalization. Many South-Asian countries like India, Pakistan, Sri Lanka, Nepal, and so on were ruled by the British for around 200 years; “white” race was the ruler and the “dark” native were the ruled. This led to internalization of superiority and power of the “white” skin and inferiority and powerlessness of the “dark skin” (Speight, 2007). Internalized racism reveals itself in a variety of situations from work environment to social situations where people of color reject or denigrate those with dark-skin. The caste system in India is likely to have given impetus to the notion of superiority of fair skin-color brought by colonial rule (Parameswaran & Cardoza, 2009b; Shankar & Subish, 2016). Higher castes have been perceived to be “fairer” and superior while lower castes have been perceived to be “darker” and inferior. Today, in postcolonial world, globalization has led to increased spread and acceptance of Western beauty ideals in Asian and African cultures (Hunter, 2011; Peltzer, Pengpid, & James, 2016).

First, the Muslim West and Central Asians who arrived in South Asia, described it as a pattern where white people conquered black people. These people were quite aware that South Asians were not black in the way Sub-Saharan Africans were. There were black Africans in the armies of the Muslims, as the Siddi community demonstrates. Nor did the Iranians, let alone the Turks, consider themselves to be of the same people as the Europeans.

But when it came to the metric of skin color, the Muslim ruling class of South Asia was disproportionately very light in complexion and described themselves often as white. The natives were described often, though not always, as black (though more often obviously as “Hindus” or whatnot). When Europeans arrived they did not come as conquerors, but as supplicants to the great Mughal and the other powers. They perceived themselves to be white, just like the elite Muslims, as opposed to the dark-skinned native Indian population, which was mostly, though not exclusively, non-Muslim.

As the 19th century proceeded Europeans, and in particular the British, developed a refined, narrow, and simultaneously biological and cultural conception of whiteness which excluded West and Central Asian Muslims. But this was a process and does not negate the fact that the ruling elite of South Asia was disproportionate of the Muslim religion and very light-skinned in comparison to the populace as a whole for many more centuries than British rule occurred.

Second, “higher castes” are not perceived to be lighter in complexion. The data is clear: higher castes are on the whole on average lighter in complexion. Just as people from the north, and west, of the subcontinent, are lighter in complexion than people from the south and east. This is not a perception dictated by ideology, but biology.

As for whether Brahmins have become “higher” castes recently, my understanding is that they have always been a high caste, and that the British did not give them their high casteness. To be frank, Indian social heirarchies do not need the imprimateur of white Europeans to come into existence, ex nihlo.

And genetics makes it clear that castes seem to have been separated and distinct for around ~2,000 years or so in South Asia. Even before the Muslims!

Now, I don’t know enough about South Asian history and culture to comment on this part:

Thus, skin-color is related to social hierarchy in India; fair skin is often considered to be a mark of higher social standing. However, it is important to note that historically and culturally, dark not white skin was considered to be ideal and desirable in India. Some notable examples are the popularity of God Krishna (literally black) and Draupadi (also called Krishnaa), a character from the epic Mahabharata. Krishna is worshipped in many parts of India whereas Draupadi was considered to be one of the most desirable women in the world. The transformation of ideal skin-color from dark to fair can be traced to the influence of caste system, British imperialism, and global hegemony of whiteness. The caste system also called varna (literally color) accounts for the perceived superiority of fair skin over dark. Owing to the association of fairer skin with upper caste and darker skin with lower castes, skin-color came to signify the social position of an individual in our society. In addition, the racist construction of “dark native” by the British seems to have become a part of our unconscious and is often projected as strong dislike for the “dark other” (Parameswaran & Cardoza, 2009b).

I would be curious about the idea that dark skin was preferred to light skin. The historical genetics makes it clear that lighter invasive populations seem to have arrived and placed themselves on top of darker populations, with some mixing before caste crystallization.

Finally:

The popularity of some dark-skin colored Bollywood actresses like Bipasha Basu, Kajol, Deepika Padukone, and so on suggests that masses are likely to accept a dark-skinned woman if she is perceived as highly attractive.

I do understand that Indian actresses use make-up (or lightening cream) to make their complexion seem fairer than it would otherwise be…but it is clear none of these actresses are actually dark-skinned in the broader South Asian context. They are at best of average complexion.

Now, perhaps you will tell me that I spend time only with kala-batchas or something, I really don’t know. But this whole paper is soaked in postcolonial anti-Western delusional discourse…and then it ends in the shadological delusion that these average complexioned actresses are actually dark skinned! Average South Asians are not light brown, they are medium brown. Medium brown actresses are not dark-skinned, they are dark-skinned for actresses (which is fine, but a different thing than being representative of the population).

Go to Google Images and type “dark-skinned Indian actress” and then “dark-skinned black actress.” In the latter case, the actresses are genuinely dark-skinned. In the former case, only a minority are actresses with the complexion of Sharon Muthu.

Skin color of South Asian groups

Filed under: race,Skin Color — Razib Khan @ 1:38 am

A massive new review, Shades of complexity: New perspectives on the evolution and genetic architecture of human skin, pointed me to another paper on South Asian skin color, The influences of genes, the environment, and social factors on the evolution of skin color diversity in India. I was very interested because South Asians have been telling me about complexion my whole life. Usually, it is to suggest that their group is lighter than some other group. So I thought it would be interesting to post some data.

Solomon Islanders

The figure at the top shows melanin indexes for a host of populations. The lower the value, the lighter the skin. So you see that Irish samples above have a melanin index of 26.5, while Italians have one of 31. East Asians in Canada have a melanin index of 38. Predominantly African ancestry populations have melanin indices >50, while the very dark Melanesian people of the Solomon Islands have a melanin index of about 90.

I’ve collected the Indian data from the paper:

Group N Mean Melanin Index Range stdev
AP Brahmin 88 40.52 30.9-54.8 4.7
Kapu 272 43.41 30.1-63.5 4.8
Naidu 111 43.57 32.3-54.9 4.9
Reddy 585 43.34 32.4-57 4.7
Vysya 75 44.5 34-59 5.5
TN Brahmin 22 41.4 34.4-59.8 5.4
Saurashtrian 36 41.9 33.3-51.8 4.7
Yadava 30 57.8 42.9-72.8 7.7
UP Brahmin 65 44.6 34.2-63 5.1
Bihar Scheduled Castes 80 59.9 46.2-78.9 7.8
TN Kurumba 39 56.1    
TN Bagada 47 44.7    
Korku Maharashtra 64 53.2    
TN Kota 46 44.6    
Nihali Maharashtra 63 56.9    
Ror Haryana 56 41.7    
TN Toda 43 43.3    
Brahmin Maharashtra 97 43    
Maratha 67 49.8    
Kokana 89 53.9    
Warli 101 58.9    
Bhil 105 53.8    
Pawara 96 54.7  

And here’s a figure for Andhra Pradesh:

Finally, 42% of the skin color variation in the data can be explained by caste.

The golden age of pigmentation is yet to come

Filed under: Human Population Genetics,Pigmentation — Razib Khan @ 12:45 am

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.

But note the qualification in terms of the populations. As you can see from the figure at the top of this post the vast majority of the study of pigmentation genetics has been performed on Europeans. The figure is from a very comprehensive review, Shades of complexity: New perspectives on the evolution andgenetic architecture of human skin. I recommend all readers of this blog to check it out (the link is not paywalled), because it does a great job of covering all the bases.

First, it turns out that there are probably as many as 50 loci implicated in skin color variation. Focusing on Europeans, and admixtures between Europeans and West Africans, resulted in a major ascertainment bias and a fixation on a few loci and a few variants within these loci. This was probably the reason that the original pedigree analysis inferred such a small number of loci as well.

Second, one of the major issues with pigmentation is that a core set of genes implicated in variation in melanogenesis seem to have been targeted by selection or been subject to drift again and again, but the mutations within those genes may differ. For example, the locus implicated in blue vs. brown eye-color variation in Europeans is also associated with skin color difference in East Asians, but it is at a different SNP.

Third, African variation is a big part of the story, and it looks as if a lot of the variation in pigmentation in modern populations that have been the targets of selection in northern Eurasia may have been segregating in the ancestral African populations. In other words, some African populations may have carried “light” allele variants at low frequencies, and the difference in phenotypes of some Eurasians may simply be the concerted shift in allele frequencies across many loci. Additionally, there is also selection for darker variants in some African groups, such as the Nilotic people, as well as lighter variants in others, such as the indigenous people of southern Africa.

Fourth, there’s still no comprehensive selection story (not much definitive beyond what I reviewed eight years ago). The authors point out that new work shows in India only 12% of the pigmentation variation is due to differences in radiation exposure, but 42% is due to caste. It is suspicious to me that all of these pigmentation loci often show up as positive hits on selection tests…it is hard for me to think that pigmentation is not being targeted. But, it is not implausible that there could be secondary selection targets due to pleiotropy on these genes. The authors point out that there is no evidence for a universal cross-cultural sexual dimorphism, but there is some local evidence. Please note that sexually dimorphic characteristics take about an order of magnitude more time to evolve, because the sexes have to express the trait differentially despite having the same basic genetic character, so the recent selection events are unlikely to be able to drive such a change.

Young boy with typical blond hair of Lajamanu, at the edge of the Tanami.

It’s clear from this review that a lot of the work in the next decade, the real golden age of pigmentation genetics, is going to involve non-European populations. In particular, I have long been fascinated by the fact that among non-Europeans, blondism seems to be a feature of some Oceanian populations. The genetic basis of this trait has already been established in Solomon Islanders, but I am curious if it is the same among the Aboriginal people of Australia. Some of the populations in central Australia have long been well known to exhibit this trait, especially in children and women. If it’s the same mutation and haplotype as in the Solomons, then it is a characteristic ancestral to the original Oceanian meta-population.

The yield of this research is relatively straightforward. In forensics, the methods will continue to get better as we have more results from non-European populations. And the evolutionary patterns yielded by tests for selection will be very informative in understanding the adaptive pressures faced by our ancestors. For whatever reason, pigmentation genes get targeted over and over.

* Immunaeul Kant observed correctly that the Parsis of Bombay were white, not brown, in his attempt at racial anthropology.

November 12, 2018

Open Thread, 11/12/2018

Filed under: Open Thread — Razib Khan @ 7:03 pm

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.

 

November 9, 2018

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

Filed under: Evolutionary Genetics — Razib Khan @ 12:48 am

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 seducingly 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”

Filed under: Edar,Natural Selection — Razib Khan @ 12:01 am

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.

November 8, 2018

The visual world economy

Filed under: Economic History — Razib Khan @ 2:06 am

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

Filed under: Cultural Evolution — Razib Khan @ 12:34 am


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.

The authors utilize a natural experiment, a district in the northern province of Ningxia which through a peculiar geological quirk allows for wet-rice agriculture, unlike the rest of the province and the broader region. This is a natural “control” for many variables, as the people of this district are not demographically very different other areas of Ningxia (at least in comparison to North vs. South China).

Their results are clear and seem to confirm the 2014 study:

China’s smallest province Ningxia sits in North Central China. Surrounded by herding cultures to the north and wheat farmers to the south, Qingtongxia is a small outpost of rice farming fed by the Yellow River. We test the hypothesis that rice-farming cultures are more interdependent by comparing high school students from Qingtongxia (N = 190) to students in a nearby wheat district, Yuanzhou (N = 223). Comparing two nearby counties provides a natural test case that controls for third variables. Students in the rice county thought more holistically, treated a close friend better than a stranger, and showed lower implicit individualism. Students in the rice area showed more relative perception than students from the wheat areas on the practice trials of the framed line task, but differences were nonsignificant on the main trials. Differences between teenagers—born after the year 2000—suggest that rice–wheat differences continue among China’s next generation.

One can make a Marxist interpretation of these results: the material conditions determined aspects of economic and social organization which had cultural and psychological consequences. But, the authors also suggest that younger generations which do not engage in farming continue to exhibit the same differences as their agriculturalist parents, suggesting that an element of cultural transmission from prior generations maintained particular folkways and dispositions.

A final note: a few people reading this know that 15 years ago I read The Geography of Thought: How Asians and Westerners Think Differently…and why. The title is a little deceptive, as the author focused on three basic groups in regards to cognition. First, Anglo-Nordic people, who were highly individualistic. Second, Continental Europeans, who were somewhat less individualistic than Anglo-Nordics. And finally, the whole rest of the world, which was less individualistic still.

But a lot of the data to construct the contrast was drawn from East Asia. And, I specifically remembered results from Hong Kong. If the above results are correct, it could be that biased sampling in Hong Kong, as well as South Korea and Japan, may have amplified our perception of the importance of “rice psychology”, if that makes any sense….

November 7, 2018

Hasan Minhaj’s Patriot Act on Affirmative Action

Filed under: Hassan Minahj,Politics — Razib Khan @ 10:23 pm

Three comments

1 – He was relatively fair. I mean you knew what talking points he was going to deploy and what his conclusion was going to be.

2 – Minhaj is very American. A particular sort of American. Though the episode focuses on “Asian Americans”, Minhaj sounds like he was birthed out of The Daily Show comedy-clone factory.

3 – I don’t think it was that funny. And I don’t think the audience found it particularly funny either.

November 5, 2018

Sequence the thousands and your eyes shall be open

Filed under: Evolutionary Biology — Razib Khan @ 11:15 pm

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 – Brown Pundits

Filed under: Uncategorized — Razib Khan @ 6:26 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

November 4, 2018

Open Thread, 11/4/2018

Filed under: Open Thread — Razib Khan @ 12:46 am

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.”

November 3, 2018

It’s raining selective sweeps

Filed under: Population genetics,Population genomics,Selection — Razib Khan @ 11:44 pm

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.

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