Razib Khan One-stop-shopping for all of my content

November 21, 2020

How much “steppe” ancestry is there in South Asia? (Indian subcontinent)

Filed under: Genetics,Sintashta,steppe — Razib Khan @ 5:46 pm

Since this question always comes up at some point, I decided to do a rough back-of-the-envelope calculation of the % steppe across the Indian subcontinent. The way I did it was by taking Pakistan, Bangladesh, and India, and estimating the average percentage from the caste breakdowns (e.g., UP is 20% “upper caste” and 20% “Dalit” and 60% neither, with fractions of steppe/Sintashta about 30%, 10%, and 15%, respectively).

So the final number I came back is that 14% of the ancestry in modern-day South Asia is from the steppe in the form of people descended from Sintashta pastoralists. That is about 220 million human beings worth. You can judge whether that’s significant or not. Additionally, it looks like closer to 20-25% of the Y chromosomes are derived from these people.

I’m not “showing my work” because I think no matter how you estimate it, you’ll get a number in this range. Perhaps 12%. Perhaps 16%. But what difference does that make?

October 28, 2020

The Evolutionary History of Man’s Best Friend Revealed

Filed under: Biology,Genetics,science,Science & Tech,Spotlight — Razib Khan @ 10:28 pm

Man and dog share a long history. In much of the world, a history as old as humanity. The latest genetic evidence now tells us that the emergence of the domestic dog lineage occurred soon after the human expansion out of Africa 50,000 years ago, in the depths of the last Ice Age. We came. We saw. And we befriended. This we knew, but now we can closely examine how. A paper out today in Science uses 27 ancient dog genomes from the past 11,000 years to construct an evolutionary history nearly as rich as that produced by human population geneticists over the last decade.

The authors found five lineages of ancient dogs that were present at the end of the last Ice Age. These were the dogs that interacted with human migrations during the rise of agriculture and the fall of civilizations to produce the riotous dog diversity that we know today. Familiar breeds like the Pekingese and the St. Bernard, as well as stray Asian village mutts, they’re all the products of a deep shared history, which has left its imprint on the genetic variation of modern dogs.

The dog-human relationship has always been special in several ways. Our canine companions are well adapted to us, in that they can engage with humans socially in a manner no other animal seems equipped to, not even our closest relatives, the chimpanzees. This is thanks to tens of thousands of years of co-evolution. In a very real sense the evolutionary niche of the domestic dog is the human mind. Wolves may have higher IQs, and yet there are 1,500–3,000 times more dogs alive today. Perhaps it was smarter to be friendly than just smart.

Dogs are the only domestic species who have been with us since the Pleistocene, which ended 11,500 years ago. Crops, cattle, and cats all came later, during the Holocene, after the Ice Age. When Siberians crossed over to the New World 15,000 years ago, they also brought their dogs. These dogs served many roles. Friend, beast of burden, and yes, even food.

The New World dogs, who were present when the Spaniards landed in 1492, are one of the five great Pleistocene lineages from which all modern dogs descend. The authors of the Science paper call them the Neolithic Levant, Mesolithic Karelia, Mesolithic Baikal, ancient America, and the New Guinea singing dog. The last group includes Australian dingos and represents the ancient expansion of our species and its companions into Southeast Asia. Karelia is a region bordering Finland and Russia, while the Baikal dogs come from the lake of that name in east-central Siberia. These samples are termed Mesolithic because they are more recent than the Ice Age (7–11,000 years ago), but the peoples in Karelia and Baikal were still hunter-gatherers at that time. In contrast, the Neolithic Levant dogs date to 7,000 years ago, and were companions to agricultural populations.

All modern dogs can be thought of as a mixture between these five early Holocene lineages. Despite their highly specific names, the Karelian and Baikal lineages represent huge geographic distributions, not just the sample sites. In this regard, they are analogous to modern humans. As David Reich has shown in his magisterial work, Who We Are and How We Got Here, the past 10,000 years have witnessed the merging of disparate hunter-gatherer tribes to form the peoples we see today, threaded together from distinct strands. This naturally leads us to the question: did human populations bring their particular dogs everywhere they went?

Comparing the relatedness of humans and relatedness of dogs, the authors of the Science paper found that there was a definite correlation. Phylogenetic trees of both dogs and humans exhibited strikingly similar shapes, indicating common underlying histories of separation and diversification. Analyses comparing the genetic data of dogs and humans revealed that they were tightly correlated. In fact, the relationship between the evolutionary trees for dogs and for humans is close enough that the tree for humans explains much of the pattern we see for dogs. There is an underlying structure which spans the two species, but also novel and curious deviations that alert us to particular stories.

Some of the stories are straightforward and to be expected. The dogs of ancient Europe are a mix of the Karelian and Neolithic Levant lineages. The latter clearly tagged along with the early farmers expanding out of the Near East. Further south in Europe, the dogs were more like those of the Neolithic Levant, while further north they were more like the Mesolithic Karelian dogs. American dogs were genetically closest to the Siberian dogs from Lake Baikal. Additionally, both these groups were closer to the dogs of Southeast Asia than they were to those of the Levant. This recapitulates the pattern for Eurasian peoples; East Asians are more closely related to Europeans than they are to Middle Eastern people.

But a few surprising findings confound our expectations. Four thousand years ago on the Volga steppe of Russia, on the cusp between Europe and Asia, the Srubna people flourished as part of a broad continuum of Indo-European peoples that stretched far to the west. While the Indo-European relatives of the Srubna came to dominate much of Europe, their dogs did not. The burials of early Indo-Europeans in Europe yield dogs whose heritage connected them to the Eurasian steppe and the Srubna, but this was a fleeting affair. The dogs of Northern Europe were not replaced by the dogs of the steppe, though the people largely were.

Instead, the heritage of the Srubna dog persists far to the east. Chinese dogs are mostly a mixture of ancient Southeast Asian dogs, related to the New Guinea singing dog and the dingo, plus the Srubna steppe dogs. While half the ancestry of modern Europeans comes from people related to the Srubna, very little of that ancestry is to be found in modern Chinese. And yet dogs are not the only evidence of the influence of steppe people in ancient China. In 1200 BC, chariots became prominent during the Bronze Age Shang dynasty, chariots whose design indicates borrowing from the Iranian peoples of Central Asia, direct descendants of the Srubna. It seems entirely likely that if chariots were brought to China during the Bronze Age, then so were dogs. While the dogs of the steppe found no welcome in Europe, the Chinese adopted them as their own.

It also sometimes happens that the migration of dogs runs counter to the migration of peoples. While humanity evolved in Africa and spread to the rest of the world through the Middle East, the origin of African domestic dogs reflects the reverse. Indigenous African breeds such as the Basenji descend from dogs of the Neolithic Levant. These dogs were likely brought south and west by the Near Eastern pastoralists who also brought cattle to the continent. Meanwhile, the ancient canine populations of the prehistoric Levant have been totally replaced by groups from Iran and Europe, so the primary legacy of the dogs that were associated with the first human cities is to be found today in Africa.

But perhaps the biggest twist of the great canine diasporas is that their recent history is obscured and dominated by the phenomenon which has overshadowed our own species’ history: the rise, expansion, and domination of the world by Europe.

Modern European dogs do not descend from the full diversity of the continent. Rather, almost all European breeds today derive from a population best represented by a 5,000-year-old sample discovered in southern Sweden, an individual who was equally descended from Karelian and Levantine populations. The authors could not pinpoint the time or place that this replacement of the ancient lineages occurred, but by the time of the rise of European colonialism this single population had swept aside all the other ancient populations of the continent.

Today the majority of the ancestry of dogs across the world is from this single European population that flourished 5,000 years ago. In the New World almost all the ancestry is now European, with the exception of the Arctic dogs. The venerable chihuahua has less than five percent of its ancestry from the dogs of the Aztecs. In Africa and the Middle East, most canine ancestry is now European, while European ancestry is often the majority in many Asian dog populations, and is substantial even in the dingo. Decolonization may have occurred politically, but the evolutionary history and genetic variation of dogs illustrate how powerful the hand of history can be and how long its shadow persists.

Ancient DNA is like a genetic time capsule. We’ve spent these first decades honing our extraordinary new tools as we examine our own ancient human ancestry. But ours is hardly the only species with a history worth unpacking in such fascinatingly granular detail. Rather, we can look forward to the recent history of life on Earth being thoroughly illuminated via the evidence left behind by hardy fragments of DNA from creatures long gone.

The past 40,000 years has seen the transformation of our planet’s ecosystems due to humans. We live in the “Anthropocene” because our species has reshaped the planet to our ends. The evolutionary history of the domestic dog reflects humanity’s first, and longest, bioengineering experiment. We took a pack of wolves and transmuted it into a new species to walk alongside us. We bred dogs to be useful tools, but eventually they became our most loyal allies. We owe it to them to understand how they came to be as they are. And in the process we’ll inevitably continue to learn about ourselves.


Razib Khan is a geneticist and director of science at the Insitome Institute. He has written for the New York Times, India Today, National Review Online, and runs two weblogs, Gene Expression and Brown Pundits. You can follow him on Twitter @razibkhan or visit his website here.


October 21, 2020

Tibeto-Burmans, Munda, and Bengalis

Filed under: Genetics — Razib Khan @ 10:58 am

I’m pretty sure I posted this Chaubey lab work as a preprint, but it’s now a published paper. For those who can’t understand the table, it illustrates a big difference between Tibeto-Burmans and Munda. The samples from Bangladesh look to be generic Bangladeshis, the 10% frequency for O2a seems to match the other data I’ve seen for East Bengalis.

This confirms that the East Asian admixture into Bengalis was not Munda. And, the Tibeto-Burmans of the nTibeortheast have no assimilated Munda ancestry. I think it does lend more credence to the idea that the Munda arrived in the Indian subcontinent across the Bay of Bengal, landing in Odisha, rather than from the northeast.

October 16, 2020

The rise of Indicus!

Filed under: Genetics — Razib Khan @ 12:00 am

A few years ago an ancient DNA paper on cattle was published, Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. It’s a pretty good paper with interesting results. The paper confirmed pretty strikingly that there was a punctuated and massive expansion of indicus ancestry across the Near East between 3,500 and 4,000 years ago.

The interesting aspect of cattle is that there are really two species that intermix. Using mtDNA researchers estimate indicus and taurus diverged 300,000 to 2,000,000 years ago. But the main thing you have to remember is cattle generations are about 20% as long as human generations. So 300,000 cattle years are equivalent to 1.5 million human years. And, for technical reasons (smaller effective population size) one should probably assume mtDNA underestimates the divergence.

Ancient cattle from the Near East are all taurus. The PCA plot shows that most of the variance is on PC 1 which separates indicus and taurus (a secondary dimension is PC 2, between African and Near Eastern/European lineages). The figure at the top of this post shows that there is a massive jump in genome-wide indicus ancestry across the Near East between 2000 and 1500 BC. As the authors note this can’t be diffusion; the jump is too sudden and sweeping.

So what happened during this period? As noted in the paper: Bronze Age civilization almost collapsed around ~2000 BC. More concretely, after 2000 BC is when we see evidence of Indo-Europeans in the Near East. The Indo-Aryan Mittani show up in Mesopotamia in ~1600 BC. The Indo-European Hittites, the Nesa, are known from Anatolia a bit earlier.

This is also the period that small, but detectable, levels of “steppe” ancestry show up in some ancient samples.

Before this paper, I would have leaned to the position that the Mittani Indo-Aryans migrated directly from the Sintashta homeland without much contact with Indian Indo-Aryans. These data are too suggestive of a widespread zone of expanding agro-pastoralists that existed between western South Asia and the Near East between 2000 BC and 1500 BC.

One of the things we know from the barbarian period during the Fall of Rome is that barbarian groups had strong channels of information flow. For example, a group of Saxons arrived with the Lombards in Italy in the second half of the 6th century. But, through various channels, these Saxon warriors learned that their co-ethnics had established dominance in what was to become England, and there are texts which allude to the reality that they decamped and crossed the Alps, presumably on the way to what was going to be England. The point here is that there was a “Saxon international.”

Aside from the Mittani the evidence of Indo-Aryans in the Near East is tenuous, though some of the Kassites of Babylonia may have had Indo-European affinities. There is not nearly as strong a genetic imprint of steppe in the Fertile Crescent as in Northwest India. The Hittites were very different from Indo-Aryans, who seem to have the closest relationship to the Slavic language family.

The indicus breed is adapted to tropical dry climates. It seems plausible that the Indo-Aryan international facilitated the spread of this breed in the centuries before 1500 BC.

October 7, 2020

Armenia, Azerbaijan, Turkey, and genetics

Filed under: Armenia,Genetics,Turkey — Razib Khan @ 12:18 am

Recently a few people have been asking me about Armenian, Turks, and genetics. Mostly because I’ve written about this topic before. Unless you’ve been asleep you know that there is a war going on in the Caucasus. Armenia and Azeribaijan are renewing their decades-long conflict, and bringing other nations into as the local powers choose sides. Unpleasant all around.

Who are the Armenians? The Turks? Azeris?

Azeris in particular are not well known in the West, but they’re kind of a big deal. The Iranian province of Azerbaijan has nearly as many people as the Republic of Azerbaijan, and there are more Azeris in Iran than in independent Azerbaijan itself. The leader of Iran has an ethnic Azeri father. Azeris are Turkic and have traditionally been dominant in Iran’s military. Before the Turkification of the region over the last 500 years, Azerbaijan was called Albania. The native language was Iranian and related to Persian.

Living in close proximity to each other, it is no surprise that the peoples of the region are genetically rather similar. That being said, there are notable differences.

While a few Armenians in my datasets have Russian admixture (they are likely F1 individuals who identify as Armenian), what is notable about Azeris is like Turks they exhibit a small but notable shift toward East Asians. This is almost certainly the consequence of Turkic ancestry. Though most of the ancestry of Azeri is pre-Turkic, Turkification occurred through assimilation of nomads with some East Asian ancestry.

The sample applies to Turks to the west of Armenia. In previous posts, I’ve had discussions about the nature of Turkish ancestry, but in general, I am convinced by those who argue that the non-Turkic component (which would include East Asian and Turanian) reflects the earlier pattern of variation; Greek in the west, Armenian and Kurdish in the east.

Conflicts, like we are seeing today, illustrates the power of ideas over relatedness. Armenians are Christians, albeit peculiar Oriental Orthodox Christians. Additionally, they continue to speak an ancient Indo-European language. This sets them against Turkic speaking Muslims to the west, and Turkic speaking Muslims to the east, though all the groups share deep common ancestry.

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