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November 28, 2018

The battle for the soul of the Heart of Asia

Filed under: Indian Genetics,international relations,Tarim Basin,Xinjiang — Razib Khan @ 11:33 pm

Kumārajīva was one of the early translators of the Buddhist canon into Chinese. His father’s lineage was reputedly Indian, while his mother was from the elite of the city of Kucha, on the northern edge of the Tarim basin. It was one of the cities where a form of Tocharian was spoken. This enigmatic Indo-European language family is extinct and known from only a few examples in this region of the world (the different forms of Tocharian seem to have been mutually unintelligible, suggesting a long history in this region of the world for these languages). But Tocharian was not the only Indo-European language group that was represented in the Tarmin. Along the southern and western edge of the Taklamakan Iranian dialects were more common, such as in the city of Khotan.

Over the last 1,000 years, the Tarim Basin has undergone major changes. First, the collapse of the ancient Uyghur Turk Empire resulted in their retrenchment to the Tarim Basin. A previously pastoralist people, they became settled city-dwellers. By the time Genghis Khan rose to power, the Uyghurs had become a predominantly Buddhist people, with a focus around Turpan. They seem to have absorbed the predominantly Tocharian city-states of the eastern portion of the Tarim Basin.

But after 1000 AD a second change began to occur. A group of Turks, who spoke a Karluk dialect, converted to Islam and conquered Kashgar in the west of the Tarim Basin, and began to push eastward, conquering and converting the Buddhist city-states in turn. By 1400 the cultural expansion and military conquest reached the eastern fringe of the Tarim Basin, as Turpan and Hami were absorbed into the Islamic cultural sphere. With this, a new identity unified the city-states of the Tarim Basin. In language they spoke Karluk dialects, and in religion they were Muslim. In the 20th century the Uyghur ethnonym was resurrected in what was known as East Turkestan, but the cultural descendents of the ancient Uyghurs are actually the Yugurs (whose traditional language descends from that of Old Uyghur).

Click to Enlarge

This narrative will be familiar to anyone who reads a book such as Valerie Hansen’s excellent Silk Road. Hansen in particular focuses on the period when the Tarim Basin was at some equipoise between the west, east, and the south, with Sogdians, Turks, Chinese and some Indians, all being part of the dramatis personae of the cities of the Silk Road during the heyday of the Tang dynasty. And none of this should be surprising. Though this region of the world is divided by the highest mountains on earth, the geographic distance between Northern India, Transoxiana, and the Tarim Basin is quite minimal. As the crow flies, New Delhi is less than half the distance from Hotan as Lanzhou, in the far western province of China proper, Gansu.

9th century cave painting from Turpan

The past doesn’t always map easily onto our contemporary topographies. Some of the earliest Chinese contacts with Buddhism was through the devotions of an often blue-eyed people whose physical type was European if anything, who had no doubt learned of the religion ultimately through a chain of transmitters that went back to brown-skinned South Asians. This world did not match the demarcations which we take for granted today. It was a thing different.

Normally when I’m enjoining people to think outside of the boxes that they’re used to thinking in, I’m talking to people of white European descent, around whom the world has revolved for several centuries, and around whom they assume the world will revolve until the last day of universe. But today I’ll point to another group, and that is Indians.

A friend forwarded me this erudite post on Medium, The Rāma Story and Sanskrit in Ancient Xinjiang. It received 324 claps, which in my experience means that tens of thousands of people at minimum have read this piece.

Here is the first paragraph:

Most people do not know that until about a thousand years ago, the Tarim Basin (northwest of Tibet, which is the part of Xinjiang below the Tian Shin Mountains) was Indic in culture and it was a thriving part of the Sanskritic world; its people spoke the Gāndhārī language which many see as descended from Vedic Sanskrit, and Khotanese Saka, which is also closely related to Sanskrit. Perhaps the region to compare it most is Kashmir, to whose north it lay. There was also much interaction between the two regions with many scholars traveling from Kashmir to Khotan, and silk culture is believed to have passed from Khotan to Kashmir and then into India.

The bolded sections are misleading. The italicized section is correct. There was a great deal of Indian-Tarim Basin interaction. Sometimes directly. Sometimes through intermediaries (Sogdians). But it is simply wrong to imply that this is “Indic culture” in a way that communicates to the audience reading it the proper state of the facts.

First, the author makes some statements about the genetic connections of modern people in the Tarim Basin and Indians which are false. He does link to some papers, but they are old, and lack the power to really get at the questions that would allow us to accept or reject the hypothesis of affinity.

Since the HGDP has some Uyghurs in the dataset it’s easy to pull them, and compare them to various South Asians, Iranians, and Han Chinese.

Let’s look at the PCA:

You see a bit of an admixture cline here from the Han Chinese samples, to something more West and South Eurasian. If you run the cline outward toward the West and South Eurasians, it lands somewhere between Pathans and Iranians.

Let’s run Treemix with 4 migration edges. You see the results….

I believe most of the Iranians in this data are sampled from the west of the country. This explains the contrast, where Pathans are more South Asian, and more like Europeans, than the Iranians (at least when not taking into account the migration edge). The steppe genetic impact seems to have stronger in Turan and Khorasan, than the classical heart of Persian civilization in the Fars. The gene flow from the base of the Lithuanian-Pathan clade to the Uyghurs is indicative to me of the steppe genetic influence in this region, perhaps starting with the Afanasievo culture, and later the expansion of the Andronovo complex.

Finally, the requisite admixture analysis:

Menander I, Indo-Greek Buddhist king

These data don’t reject the thesis that the Tarim Basin in the years before 1000 AD were dominated by “Indic culture.” That is because Indic culture is separate from the predominant element that characterizes Indic genes. There was almost certainly some gene flow from northwest India into the Tarim Basin. But it was likely relatively modest. Nevertheless, it is quite possible to characterize someone as having been substantially Indic in their cultural orientation no matter their genetic provenance. The great Greco-Bactrian king, Menander, seems to have been a patron of Buddhism, which was then still perceived as a fundamentally Indian religion.

In the centuries around 400 AD the Chinese still described Buddhism as a foreign “Western religion,” in particular, from India. Indian translators of Buddhist texts are a common presence in China and elsewhere in East Asia during this period, because the original works were in Indian languages. Meanwhile, Chinese Buddhists made pilgrimage to India, in part to retrieve texts from the great ancient monasteries.

But by the end of the Tang dynasty Buddhism was no longer thought of as simply an Indian religion. Though Confucian and Daoist critics never failed to point out its foreign origins, it was clearly indigenized. By the Song dynasty no more Indian translators are mentioned. And, by this period Buddhism in South Asia itself was in serious decline, first in the face of a newly vigorous set of religious practices which we call Hinduism, but also due to the predations of Turkic Muslim invaders, who destroyed many of the great monasteries.

The primary takeaway here though is that the semantic pointers we provide to the audience often give them implications which are not warranted. For example, when scholars describe Classical Greeks as ethnocentric Europeans, that misleads many modern people into thinking that the concept of European as we understand it today entailed the same things then that it does today. The Classical Greeks were part of a broader Mediterranean civilization, and culturally at least as distinct from the peoples of Northern Europe as they were those of the Levant. Their ethnocentrism was of a very different kind than that that developed in Europe in the 19th century, after the Congress of Vienna with the synthesis between resurgent Christian chauvinism and biological essentialism.

A similar issue crops up in discussion of ancient India and Indians. In Sanjeev Sanyal’s The Ocean of Churn he assumes that the Indo-Aryans who clearly were part of the military elite of the Bronze Age Syria state of Mitanni were Indian. First, the reality is that in the Bronze Age “Indians” as we understand them today did not exist. While Mitanni flourished in the Upper Euphrates region, the great cultural complex that was the Indus Valley Civilization was unwinding, to be succeeded by a simpler society. The biological and cultural synthesis that we think of as Indian today had not come into being in the totality. Second, the Indo-Aryan elite of the Mitanni (who had quickly switched their language to the Hurrian of their subjects) likely never had any experience of India. Rather, in the coalitions of steppe agro-pastoralists the Indo-Aryans were distinct from the Iranians, and one branch of the former seems to have pushed westward into the Near East, and another gone eastward to India.

Warriors from Bronze Age Pylos

Ultimately, what is in a label? The Greeks of the Mycenaean period spoke Greek. They worshipped some Greek gods that persisted down to the Classical period. But their descendants had only the vaguest of ideas about these people. When archaeologists of the 19th and 20th century excavated Bronze Age sites in Greece they assumed that people were not Greek. The assumption was that the Greeks of the Classical period descended from people who had come down from the Balkans during the Dark Age (the Dorians). The decipherment of Linear B shocked the world. These people spoke Greek. But culturally they were very different from the Classical Greeks.

To understand the world we must reassemble and filter it in categories what are comprehensible to us, that give us meaning. But we should never confuse the categories and concepts that are our tools for the reality that is out there. Our words always collapse distinctions, and erase subtleties. The further we go back into the past, the greater the disjunction between our categories and the details that they propose to bracket.

In the specific context of Indian history and the controversies and co-options I see bubbling to the surface due to the disruptive impact of genetics, is the fact that for many of the most motivated protagonists history began with Mahmud of Ghazni. For some, the Indo-Aryans are seen as precursors to the Turkic Muslims. And so the alien becomes the indigene, and the indigene becomes the alien. For others, the Indo-Aryans are the root and basis of the Hindu Rashtra. Due to this they must by necessity be grounded in Bharat Matā everlasting. The truth from where I stand does not suggest that either narrative is correct. The Indians of today, whether from the southern tip of the subcontinent, or the high fastness of Kashmir, are not comprehensible without the Aryans of the Vedas. But the Aryans are of the Vedas are not comprehensible without the the Punjab, without their residence and immersion in the Indian subcontinent. They came from elsewhere, but they became who they were because of their emulsification in the matrix of South Asian people and environments.

Similarly, Central Asia, from Xinjiang to the Caspian, from the fringe of Siberia to the edge of India, occupies a central pivot on the World Island. Both receiving and transmitting, over the past 2,000 years it has transformed itself many times, and yet retained some elements of continuity. There is no reason that India, China, or Russia should claim it as a natural extension of their own civilizational development. It was, and is, part of them all and yet not all of any.

Welcome to our brave new 21st century

Filed under: Crispr,Genetic Engineering,Genetics,science — Razib Khan @ 4:44 pm

Sometimes you know something is going to happen. But you don’t know when it’s going to happen. It’s inevitable, but you don’t know when that inevitability is going to realize itself. In a way, death is like that for most of us.

And so it is with genetic engineering in the 21st century. This week MIT Technology Review broke the story that a researcher in China, He Jankui, used the CRISPR/Cas9 system to modify the genes of twin girls. His goal was to have them be were born with a deletion in the CCR5 gene, which would confer resistance to infection with HIV (about ~10% of Northern Europeans carry the deletion). These are the two first human beings born with genetic modifications that were directed by human beings.

Additionally, these are the first genetically modified human beings who will pass that modification to their children (unlike adults who might be targeted by genetic engineering, where their sex cells would not transmit the modification).

Humans have begun to direct their own evolution!

The science, or perhaps more precisely, the engineering, behind CRISPR/Cas9 is well outlined by this video:

There are many scientific and ethical details that go into the unpacking of the story of the gene edited children. But it is important to take a step back, evaluate the present, and consider prospects for the future. The CRISPR/Cas9 system for gene editing has been in use since 2012. In contrast, genetic engineering more broadly has been part of the scientific toolkit for nearly 50 years.

Asilomar, CA

In 1975 140 individuals from a range of disciplines came together in Asilomar, California, and agreed on rough guidelines for the use of the then-nascent technology of recombinant DNA.

This was the technology which brought the idea of genetic engineering to the public, with its first big success being the development of synthetic insulin, which has transformed the lives of millions of people who suffer from diabetes. The private sector biotechnology industry was birthed by the revolution triggered by recombinant DNA techniques in the second half of the 20th century.

For decades after 1975 genetic engineering occupied a prominent spot in science and popular culture. From genetically modified corn to transgenic mice, genetic engineering had widespread uses in both industrial and academic science.

So why is CRISPR/Cas9 such a big deal? In 2012 researchers realized that it was an efficient, cheap, and simple way to do genetic engineering (it had been known earlier as a peculiarity of bacterial defenses against viruses). In less than a decade, it has become even more effective as an editing tool.

In short, CRISPR/Cas9 democratized genetic engineering, so that small labs with few resources could perform experiments and trials. Previously, only laboratories with extensive experience and funding, or industrial scale corporations, could enter into genetic engineering projects. Within a few months, innumerable laboratories switched from other techniques of genetic engineering, which they had spent decades honing, to CRISPR/Cas9.

The nature of the transformation is obvious when you think about what has surfaced in the media in previous decades. One reason that you have heard about genetic engineering in the context of maize, “corn”, is that this is a crop with enormous economic implications. With older and more expensive technologies, genetic engineering could only be justified by a huge economic upside. Because of its cheapness and effectiveness, CRISPR/Cas9 methods have been applied to stem cells, plant and animal breeding, as well as public health. It may help in curing the most common form of muscular dystrophy, ushering in the era of curing of most Mendelian diseases.

Within the last six years, CRISPR/Cas9 has transformed whole sciences, opening up avenues of basic research which were previously not practical. Experimentation has taken over in the realm of experimentation! The plain truth of it is is that what happened in China may appeal to the love of the sensational, but it absolutely marginal to what CRISPR/Cas9 means to most scientists in their working life today. But, it reflects the fact that genetics is now an international discipline with hundreds of thousands of practitioners.

The times when 140 individuals could come together and agree on rules which industry and academia should follow, will follow, are likely long behind us. When scientists would talk about an “international consensus” in 1975, they meant North America, Western Europe, and Japan. Today that consensus has to extend to China, which is now the home to a great deal of cutting-edge biological science. But the cultural and social chasm between China and the developed world is large. And CRISPR/Cas9 is so simple and cheap that its use will likely spread to less developed countries, even less integrated into the community of science than China.

Though He, the researcher behind the “CRISPR babies”, may get the entry in Wikipedia he mentioned offhand to the media, the reality is that the scientific impact of his work is murky at best. Rather, his brazen contravention of the norms of international science presages the new era of the genetic engineering democracy, as the tools to modify the very stuff of life are now accessible to the many, rather than restricted to the few.

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


Welcome to our brave new 21st century was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Why There Will Not Be a Beige Future: Skin Color, Genetics, Race and Racism

Filed under: Evolutionary Biology,Genetics,race,Science & Tech — Razib Khan @ 2:05 pm
There is more in heaven and earth than can be dreamt of in any human philosophy. This is why science is not philosophy. Those who map the skies, observe the…
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November 27, 2018

Going being WEIRD dichotomies-cultural anthropology with a genetical lens

Filed under: Cultural Evolution — Razib Khan @ 8:35 pm

From my 10 questions for Luigi Luca Cavalli-Sforza I asked him about the reaction of anthropologists to Cultural Evolution and Transmission, a book written in the late 1970s with Marcus Feldman:

I entirely agree that the average quality of anthropological research, especially of the cultural type, is kept extremely low by lack of statistical knowledge and of hypothetical deductive methodology. At the moment there is no indication that the majority of cultural anthropologists accept science – the most vocal of them still choose to deny that anthropology is science. They are certainly correct for what regards most of their work.

He judged that Cultural Evolution and Transmission had little influence. But Peter Richerson and Robert Boyd learned the application of population and quantitative genetic modeling to cultural dynamics from Feldman in the 1980s. In their own turn, they trained researchers such as Joe Henrich.

Henrich in his turn helped train scholars such as Michael Muthukrishna. Here’s a preprint that has me really excited, Beyond WEIRD Psychology – Measuring and Mapping Scales of Cultural and Psychological Distance:

We present a new tool that provides a means to measure the psychological and cultural distance between two societies and create a distance scale with any population as the point of comparison. Since psychological data is dominated by samples drawn from the United States or other WEIRD nations, this tool provides a “WEIRD scale” to assist researchers in systematically extending the existing database of psychological phenomena to more diverse and globally representative samples. As the extreme WEIRDness of the literature begins to dissolve, the tool will become more useful for designing, planning, and justifying a wide range of comparative psychological projects. We have made our code available and developed an online application for creating other scales (including the “Sino scale” also presented in this paper). We discuss regional diversity within nations showing the relative homogeneity of the United States. Finally, we use these scales to predict various psychological outcomes.

For the people who know genetics, they have created a cultural analogy of Fst!!!. From the preprint:

Cultural FST (CFST) is calculated in the same manner as Genetic FST, but instead of a genome, we use a large survey of cultural values as a “culturome”, with questions treated as loci and answers treated as alleles.

I’m going to just present two figures without comment:

u mean english. the scottish are british as . are the welsh

Filed under: Uncategorized — Razib Khan @ 5:02 pm

u mean english. the scottish are british as . are the welsh

November 26, 2018

Open Thread, 11/26/2018

Filed under: Open Thread — Razib Khan @ 9:35 pm

So Spencer and I talked to Antonio Regalado today for the podcast (Apple and Stitcher, should be live soon as I just pushed it). We talked way more about Brave New World than I was expecting. The engineering is moved further than I had realized.

Here are the show notes for the episode.

NASA Probe Lands Safely On Martian Surface.

The Siberian unicorn lived at the same time as modern humans.

Robust estimation of recent effective population size from number of independent origins in soft sweeps.

Fire and Fire & Blood: 300 Years Before A Game of Thrones is a quick read.

Historical contingency shapes adaptive radiation in Antarctic fishes.

The Trouble With White Women: An Interview With Kyla Schuller.

Meet Denny, the ancient mixed-heritage mystery girl.

A vast 4,000-year-old spatial pattern of termite mounds.

On the Nature of Patriarchy.

Alice Dreger’s Middle Finger: Sex, Gender and Unhelpful Hair-Splitting.

What the Cult of Ruth Bader Ginsburg Got Wrong. The Right loves Ginsburg.

Woman who inherited fatal illness to sue doctors in groundbreaking case.

I was raised as a Native American. Then a DNA test rocked my identity. Dad “passed” as Native American. He was black American and Chinese American.

Regular Exercise May Keep Your Body 30 Years ‘Younger’.

Worldwide phylogeography and history of wheat genetic diversity.

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:43 pm

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

November 25, 2018

When myth becomes reality

Filed under: History — Razib Khan @ 9:40 pm


Netflix now has Arjun: The Warrior Prince on its stream. I watched most of it to get a feel for some of the details of the story. I know the general outline of the Mahabharata, but I know the Bible or the Iliad far better (in case you can’t be bothered to follow the link, it’s only a small part of Arjun’s early life).

Depending on the sources you trust, the events of the Mahabharata date to around ~1000 BC. They were probably refined at a later date, perhaps around 500 years later.

I watched a fair amount of Arjun: The Warrior Prince. In some ways, it reminded me a lot of the Iliad and the Odyssey. These two works are a melange of influences and time periods, synthesizing true recollections of the large polities with highly stratified social systems and literacy of the Bronze Age, with the simple chiefdoms of the Dark Age Greece. The issue is disentangling the different periods.

One assumes the same is true of the Mahabharata and Ramayana.

The “wild card” here is that the most recent work has now likely confirmed the arrival of agro-pastoralists from the steppe in the period between 1500 and 1000 BC. By the time the historical analogs of the Pandavas were settled in the Gangetic plain, they’d likely been there for many centuries.

The human CRISPR revolution will probably be written in Chinese

Filed under: Crispr — Razib Khan @ 5:32 pm

I am probably biased because of my professional focus, but this may be the biggest story of 2018, Chinese scientists are creating CRISPR babies:

According to Chinese medical documents posted online this month (here and here), a team at the Southern University of Science and Technology, in Shenzhen, has been recruiting couples in an effort to create the first gene-edited babies. They planned to eliminate a gene called CCR5 in order to render the offspring resistant to HIV, smallpox, and cholera.

We knew this was coming. Soon. But now we can confirm it. It confirms my assumption that gene editing in the human context is going to mostly focus on preventing disease in the near future. In a world of low fertility, every expectant parent prays (literally or metaphorically) for a healthy child. After the child is born they can think about other things like how tall they are going to be or how smart they are. But health, that is always the number one concern.

From what I know the United States still has the largest number of top-flight researchers in the basic and applied sciences. American scientific culture, for all its faults, is second to none. But for various reasons, I can’t see America trying to keep up with the Chinese when it comes to gene editing of humans. CRISPR technology will probably be applied to other things, such as in applied plant and animal sciences.

The future is here. We’re just along for the ride….

Questions for the genetics of India podcast….

Filed under: Podcast — Razib Khan @ 1:53 am

Zach, Omar, and myself will do a podcast on Indian genetics next week. I already did one on this topic for my main podcast, so I’m curious what readers of this weblog want to hear about. We can’t guarantee we’ll use the questions, but it’s possible. I think the format will mostly involve Zach and Omar leading the conversation and I’ll try to talk as fast and concisely as possible.

Also, we got our first review on iTunes. Would still like to get some on Stitcher. And in case people want to hear more from me, I was a guest on the Two for Tea podcast. My episode should drop in the next day or so.

November 24, 2018

On the anniversary of the publication of the On The Origin of Species

Filed under: Evolution — Razib Khan @ 3:25 pm

Today on this date Charles Darwin’s On The Origin of Species was published. If you haven’t, you should read it. I’m not sure if it’s the most influential book of the last few centuries, but it’s definitely up there.

That being said, sometimes people want to read something different that’s more recent. I would highly recommend Evolution: The First Four Billion Years. It’s an anthology of different thinkers from evolutionary biology, from paleontology, to genetics, and even to philosophy.

November 23, 2018

A film of the Jarawa people

Filed under: Culture,Jarawa — Razib Khan @ 9:23 pm

When ferocity is a feature, not a bug

Filed under: Cultural Anthropology,John All Chau,Sentinelese — Razib Khan @ 7:57 pm

The sad story of John Allen Chau, the young self-styled missionary who was killed on North Sentinel Island, has some really strange elements that are coming to the surface. The New York Times has published a piece which reports on extracts of a letter he wrote to his parents describing his motivations and observations when it came to proselytizing among the Sentinelese.

The people Mr. Chau chose for his mission are among the most impenetrable communities in the world, known for their intense hostility to outsiders. They have killed or tried to kill many outsiders who attempted to step on their rugged island 700 miles off India’s mainland, where they are one of the last undiluted hunter and gatherer societies.

The man yelled, and Mr. Chau tried to respond, singing some worship songs and yelling back something in Xhosa, a language he apparently knew a few words of from when he coached soccer in South Africa a few years ago.

In one passage, he asked God if North Sentinel was “Satan’s last stronghold.” In another: “What makes them become this defensive and hostile?”

The article mentions that “Anthropologists say the islanders’ ancestors possibly migrated from Africa more than a thousand years ago.” This really doesn’t make any sense, but it jumped out at me because of the weird fact that Chau tried to speak to them in Xhosa, a Bantu language with influences from Khoesan dialects. Perhaps the reason he did this inexplicable thing is he’s read too much the pap that the people of North Sentinel are some pristine population descended from early Africans?

A more interesting aspect of the article is the questioning of why these last isolated island hunter-gatherers are so hostile. The fact is if they weren’t so hostile, they would almost certainly be extinct by now. The record of hunter-gatherer populations interacting with agriculturalists is one of absorption, assimilation, extermination or subordination.

The hostility of the peoples of the Andaman Islanders to outsiders has long been attested:

Situated in the bay of Bengal, the Andaman islands have been known to outsiders since ancient times. Andaman islanders respond with intense hostility at any attempt of outside contact, hurling arrows and stones at any unlucky visitor approaching their shores.

Early Arab and Persian documents report that Andaman islands were inhabited by cannibals – an exaggeration probably originating from the ferocity of attacks with which these travelers were greeted. Later Indian and European explorers steered clear off these islands to avoid the hostile inhabitants.

And this is why the Andaman Islanders remained relatively distinct ethnographically down to the early modern period. The Negrito people of Malaysia and the Philippines no longer speak their ancestral languages, while the Andamanese did until recently.

This incident reminds me of a dark passage from Jared Diamond’s The Third Chimpanzee. Contrary to the optimism of Carl Sagan, Diamond asserted that if there were aliens out there, we should work very hard not to have them know we exist. His reasoning was that less culturally advanced peoples never had a good interaction more culturally advanced people.

November 21, 2018

The people of the Andaman Islands are not genetic fossils

Filed under: Andamanese,Population genetics,Sentinelese — Razib Khan @ 5:06 pm

So this is in the news, Police: American adventurer John Allen Chau killed by isolated Sentinelese tribe on Indian island. There is some talk about whether the guy was a Christian missionary or not, but that’s not really too relevant. Whether he believes in evolution or not (he was a graduate of a very conservative Christian college), he definitely won a Darwin award before he expired.

North Sentinel is totally isolated, and the people who live there, the Sentinelese, are out of contact with the rest of the world. They are hostile to the outside world. And this is probably why the Sentinelese are still around, as the outside world does not have a good track record with hunter-gatherers. The Andamanese as a whole had a reputation for being very hostile to outsiders, as traders new not to stop too long for water.

Because the Sentinelese are back in the news, lots of stuff is being said about them in terms of their ancestry.

First, they are not that genetically unique. A recent paper on the genetics of Southeast Asia using ancient samples makes their affinities clear.  The Onge, an Andamanese tribe, are positioned close to the two ancient samples from Laos and Malaysia. They emerge out of the same milieu as Paleolithic Southeast Asians (whose  Hoabinhian culture persisted deep into the Holocene).

The Andamanese themselves are probably from mainland Southeast Asia. The gap between the islands and the mainland was smaller ~20,000 years ago when the sea levels were lower. They could have come up from the south or the north.

Second, they are not the most “ancient” people. That doesn’t make any sense. We are all people who are equally ancient. We all descend by and large outside of Africa from a migratory wave that expanded ~60,000 years ago. Andamanese, Chinese, and Europeans. What is “ancient” about them is that they are hunter-gatherers who have continued to practice that mode of production down to the present. But that’s a matter of culture and not genetics.

Third, in alignment with the above two points, they are not uniquely and distinctly isolated from all other human populations. They are not descendants of an early wave out of Africa preserved on these islands. They are not distinct from all other non-Africans. Rather, they seem to be closer to the peoples of Oceania, Papuans, and Australian Aboriginals, than Northeast Asians. And closer to Northeast Asians than they are to West Eurasians. The latest evidence is that the Andamanese were part of a broader diversification of lineages ~40-50,000 years ago to the east of India that gave rise to the peoples of the western Pacific Rim. Within this broader set of groups, some form a distinct clade that is not with Northeast Asians (often these are like “Australasian”).

Finally, the census size for the Sentinelese is in the range of 100 individuals. This seems on the edge of viability over the long term.

The Insight Show Notes — Season 2, Episode 8: the genetics of taste

Filed under: Genetics — Razib Khan @ 3:44 pm

The Insight Show Notes — Season 2, Episode 8: the genetics of taste

This week on The Insight (Apple Podcasts and Stitcher) Razib Khan and Spencer Wells discuss the genetics of taste. Sweet, sour, salty, bitter, and of course, umami!

We talked about PTC paper test for bitter quite a bit. Here are two papers on the underlying genetics:

Though there was some discussion of other tastes, there was less exploration of the genetics. So, for salt: Genetic variation in putative salt taste receptors and salt taste perception in humans. Umami: Nonsynonymous single nucleotide polymorphisms in human tas1r1, tas1r3, and mGluR1 and individual taste sensitivity to glutamate. Here’s a paper with sweet: The Relationship between Single Nucleotide Polymorphisms in Taste Receptor Genes, Taste Function and Dietary Intake in Preschool-Aged Children and Adults in the Guelph Family Health Study.

Finally, here is a very recent overview, The Genetics of Taste.

We mentioned offhand the reason why birds can’t taste hot peppers. Here is a newspaper article on the topic.

Check out Metabolism by Insitome and our other Insights!


The Insight Show Notes — Season 2, Episode 8: the genetics of taste was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

The diverse tastes of the season

Filed under: Food,Genetics,science,thanksgiving — Razib Khan @ 1:31 pm

The holiday season is upon us. This means food, family, and fun. And when it comes to food and drink it often means excess. People gain weight during the holidays, and that’s a function of our calorie budget. There are some surpluses you don’t want.

But the process all starts with the senses. The visual allure of bright sweets and the enticing golden richness of meats. The tactile textures as we munch on foods with their own complex physical “form factor.” And of course there is smell and taste, two senses which are intimately connected, as anyone who has a severe cold can tell you.

For decades, one particular element of taste has been associated with the illustration of genetics for high school students: the strong bitter that some people experience when tasting paper soaked in phenylthiocarbamide (PTC). About ~75% of the population experiences a strong reaction when they put this paper to their tongue, and ~25% do not.

Recessive inheritance of the trait defined by shaded individuals

People who are “non-tasters” for bitter for PTC paper are recessive to those who are “tasters.” For genes, humans have two copies, and to be a non-taster individuals have to have two copies of the non-taster variant. For the ability to taste, you need only one copy.

The implication of the frequencies of the trait above and the inheritance pattern is that the underlying frequency of the genetic variants was similar. About half the gene copies in the population were non-taster, and half taster.

This was the theory. But until modern genomics, this could only be inferred. But today we know the gene and the marker within that gene that is responsible for this classical Mendelian trait. It is TAS2R38.

Here is a plot of three different genetic variations from a recent paper:

PAV = “taster” variant

One thing that is immediately evident from this map is that the ability to taste PTC is widely distributed, as is the ability to not taste PTC. There are some characteristics, such as light hair, which is found in only a few populations. In contrast, dark hair is found in most populations. What you see with PTC tasting is that variation is found across all populations.

What researchers have found is that these genetic variations are ancient, going back ~1,000,000 years, well before the emergence of modern humanity. The maintenance of this variation so long tells evolutionary biologists that both variants are useful in some fashion, and diversity is maintained within the human species.

Brussel Sprouts

It turns out that variation on TAS2R38 correlates with variation in bitter taste more generally, and that one’s sensitivity to bitter predicts phenomenon such as how much alcohol people drink, or how many vegetables children eat. What is happening is that people who are non-taster for PTC have reduced bitter sensitivity overall, and also have a lower aversion to bitter food and drink.

Because of the high genetic variation on this gene, there is going to be differences within families in terms of perception. Some research has suggested that mothers who are non-tasters who have children who are tasters report more conflict around food and that their children are particularly “picky.”

And so goes bitter, so with salt, sweet, sour, and even umami. All of these tastes that we take for granted have a biological basis that is genetically mediated. They are functionally important. In our evolutionary history bitters were often unpalatable or even toxic. This is primal, going back to the roots of the tetrapod lineages, as plants and animals have long engaged in an evolutionary arms race. Sour keys us into the acidity of foods around us. Salt is an important nutrient which was often in deficit in the ancestral environment, as were very sweet foods. Finally, umami signals that the foods we eat are rich in protein.

Lutefisk

But as omnivores, our environments are protean, as our species migrated across the face of the earth. Over the past ten years, as the complex genetic molecular genetic underpinning of variation in taste have been uncovered, a theme of diversity has been reiterated. The genes underlying variation in taste also impact other traits, and one can conceive of a model where human populations expand and must face dynamic trade-offs in particular characteristics. It’s not just about taste. One can imagine scenarios such that populations where a mix of individuals differ in taste perception are more fit than those populations which are genetically homogeneous.

However that diversity came about, it’s a fact of our life. On a social and cultural level, it results in the wide array of foods and cuisines that we as humans can enjoy. Our palette’s flexibility means that people from different cultures can and do enjoy each other’s cuisine.

The diversity even manifests within families. So this Thanksgiving while you’re observing someone wolfing down something that you’d never think of putting in your mouth, remember that we’re all different, and that’s because of our evolutionary history.

Check out Metabolism by Insitome and our other Insights!


The diverse tastes of the season was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

November 19, 2018

The dingo ate our domestication

Filed under: Dingo,Dog domestication — Razib Khan @ 11:57 pm

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.

Have we seen the face of Rama?

Filed under: Population genetics,science — Razib Khan @ 11:29 pm


One of the problems with looking up pictures of the Kalash people of Pakistan is that photographers have a bias toward highlighting the most European-looking villagers. Let’s call this “Rudyard Kipling Lost White Races” syndrome. Therefore for your edification, I post the YouTube above which is probably more representative of what the Kalash look like.

The reason I post a link to what the Kalash look like is that it is germane to the answer to the question: what did the Indo-Aryans look like? The past tense is key since “Indo-Aryans” today means a lot of people in South Asia, in a literal sense.

In the post below Zach L. made a passing comment:

(1.) The AASI’s, which are sort of co-equivalent to the Negritos and Anadamese Islanders (one of the first coastal waves out of Africa that somehow also ended up in the Amazon). It’s interesting that they are substrate to every South Asian population (I think there are trace amounts in Central Asia, Afghanistan and even Iran).

(2.) the “Dravidian” farmers out of Iran. They are probably related to the J1/J2 types and might be an olive skinned population. Prominent in Sindh and Southern Pakistan through to South India (high % in Gujarat – must have been a locus of some sort).

(3.) our beloved Aryans who are especially prevalent among Brahmins, the Punjab and Haryana (though arguably the Haryanvis and East Punjab descend from Scythians to some extent). These look “European” but it’s a very different look to #2.

The Aryans are conventional European (light eyes, light hair, white skin) the ancient Dravidians would have (probably) looked like Middle Easterners (olive skin, dark hair dark eyes) and the AASI, ” looks like Papua New Guineans.

I can’t see any disagreement with point number two.

As for the AASI (“Ancient Ancestral South Indians”), we need to be careful here. They diverged from the ancestors of the people of Papua New Guinea ~40-50 thousand years ago. The divergence from the Andamanese, who probably migrated from mainland Southeast Asia, was not too much later. Aside from being very dark-skinned, the various extant “Australasian” people can be quite distinctive in appearance. The people of Papua, and native Australians, are quite robust. A substantial minority have blonde hair color due to a mutation common among Oceanians. The “Negrito” people of Southeast Asia and India all seem to be have adapted to a narrow relic niche, and may not be representative of their ancestors.

That being said, there is a particular non-West Eurasian look that many South Asians have which we can presume is the heritage of the AASI.

The comment about Aryans looking like Europeans raised my eyebrows a bit. This is a touchy subject, and to be honest my initial reaction was to be skeptical. But the more I read the primary literature to check up on Zach, the more reasonable this seemed to be. The dominant steppe signal into South Asia does resemble the people who were pushing into Central and Western Europe 1,000 years earlier than the Indo-Aryans, who were moving southward probably ~3,500 years ago. This is clear in rather simple statistical genetic analyses-populations such as the Kalash and Pathans for example show strong evidence of “European-like” gene flow.

Current work out of David Reich’s lab suggests that the Kalash are the best modern proxies we have for the “Ancestral North Indians,” the ANI. This population is modeled as:

– ~30% “steppe”, which is very similar to the ancestry which expaned westward into Europe between 3000 and 2500 BCE
– ~70% “Indus Periphery”, which seems the likely ancestral contribution of the people of the IVC, and is a heterogenous mix of Iranian-farmer and AASI

The mid-range estimate for the emergence of the Kalash mix is ~2,500 years before the present, but these usually have some downward bias, so it is reasonable that it would be greater than ~3,000 years. The samples from the Swat Valley dating to this period show gradual increase of “steppe” ancestry over time.

So one reason to be skeptical that the Indo-Aryans were “European-like” in appearance is that by the time they were flourishing in the lands previous inhabited by the IVC they may already have been more than 50% genetically like the people of the IVC. In which case, a minority would be very European-looking, but most would look vaguely West Asia, with some looking more stereotypically South Asian. If you look at the video above I think you do see the Kalash look this way.

One reason I’ve always been skeptical of the idea that the Indo-Aryans looked European, or, that their demographic impact was large, is that it seemed unlike both could be true. The expression of blue eyes among Indians was too low of a percentage.

Here is the frequency at a major SNP which predicts a lot of the blue vs. brown eye color.

What you see here is that the Kalash have the derived (“light”) variant at 25-30%. Notice that some Northern European populations are >75%.

Here are the frequencies from the 1000 Genomes:

I was a little surprise of the lack of variation from Punjabis (PJL), to Gujaratis (GIH), and Bangladeshis (BEB). Using the above logic the ~10% result would imply that a bit more than 10% European-like Indo-Aryan ancestry. This is reasonable.

But there are more SNPs than that that impact pigmentation. SLC24A5 is derived and fixed in Europeans, but pretty high frequency in South Asians (I have two homozygote derived copies and I’m rather brown). But some SNPs in SNP SLC45A2 are much more European specific in derived allele frequencies. So the 1000 Genomes surprised me somewhat:

Here you notice that the derived variant is nearly fixed in Northern Europe.  But in South Asian populations it’s not as high as you would expect. The frequency of OCA2 derived variant is higher than SLC45A2 in South Asia, while in Northern Europe it’s the opposite.

One explanation could be in situ selection in Northern Europe or in South Asia (or Central Asia). So these two markers suggest to me we can’t draw a straight line between physical affinity and total genetic ancestry/affinity.

 

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 6:42 pm

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

Open Thread, 11/19/2018

Filed under: Open Thread — Razib Khan @ 2:25 pm

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” on 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.

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