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

March 31, 2018

The Ugly Delicious of food

Filed under: Television,Ugly Delicious — Razib Khan @ 10:31 pm

If you have Netflix I highly recommend Ugly Delicious.

I watched it over the past week, as opposed to binging, and that probably made it easier, because the visuals and display of gustatory prowess can be a bit much.

Many viewers will roll their eyes at the excessive seriousness and constant attempt to hook food into politics or culture. But that’s what makes it attractive and interesting to many people as television.

I’m probably biased though because a whole episode was devoted to shellfish (shrimp is my favorite food), and much time was given to Asian cuisines which I’m partial to, Chinese and Korean.

South Asian genetics, the penultimate chapter

Filed under: Genetics — Razib Khan @ 10:01 pm

A long post at my other blog, The Maturation Of The South Asian Genetic Landscape, a reflection on the important preprint The Genomic Formation of South and Central Asia. Shorter:

  1. The original inhabitants of the Indian subcontinent who descent from the “out of Africa” migration separated very quickly, ~50,000 years ago, from other eastern populations (East Asians, Andaman Islanders, Papuans, etc.). These are the “Ancient Ancestral South Indians” (AASI).
  2. Agriculturalists from what is today Iran seem to have entered and mixed with the AASI in the Indus Valley earlier than 5,000 years ago, and possibly as early as 9,000 years ago. The only samples they have are from extra-Indian sites, in Central Asia and eastern Iran, as outlier individuals. They call these “Indus_Periphery” (I call then InPe).
  3. The “Ancestral South Indians” (ASI) were created from a mixing of InPe with AASI still extant in much of South Asia ~4,000 years ago.
  4. Between ~4,000 and ~3,200 years ago populations from the steppe arrive, carrying admixture from Iranian farmers, as well as people from the steppe (Andronovo-Sintashta?). They mix with the ASI population, though a few groups, such as the Kalash, mix directly with InPe, and create unmixed “Ancestral North Indian” (ANI).
  5. Subsequent mixing between ASI and ANI populations in various fractions accounts for most of the variation in South Asia.
  6. Some groups are enriched for “steppe” as opposed to the Iranian agriculturalist that first came with InPe. In particular, Brahmins. The hypothesis then is differential ancestry of Indo-Aryan heritage persists to this day.
  7. The Munda of northeast India have a somewhat different origin, mixing Southeast Asian ancestry with ASI and further AASI. The fact that unmixed AASI were present in South Asia indicates that the Munda arrived before the full mixture was complete. Though Austro-Asiatic expansion into northern Vietnam dates to ~4,000 BC, so I think it can’t be that early.

Things I now think are unlikely:

  • Indo-Aryan interpenetration with non-Indo-Aryans in the IVC before 4,000 years ago (I was somewhat agnostic on this). The date for migration now seem very close to the “Classical Model” of arrival around 1500 BC.
  • The AASI is very diverged from the Onge, who form a clade with mainland Southeast Asian Negritos. I now think it is likely that the AASI were primal, and not migrants from Southeast Asia.

It would be nice if the results were published from the Rakhigarhi site, which dates to 4,600 years ago. But it seems less and less necessary. Perhaps at some point we’ll get enough samples from Pakistan to generate a reasonable model….

The maturation of the South Asian genetic landscape

Filed under: Dravidian,Human Population Genetics,India,Indo-Aryan — Razib Khan @ 9:39 pm


The above is a stylized map from the preprint, The Genomic Formation of South and Central Asia. In broad strokes, it says some things that are very expected, and some things that are not so expected.

The abstract is long, but I’ll reproduce it in full:

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

First Turk Empire

Though the abstract is focused on South Asia, the preprint actually has quite a bit about Inner Asia, because of the provenance of the samples. We often view the typical person in the past as a peasant in an agricultural society, and therefore relatively immobile over their lifetime. The story we like to tell ourselves is that non-elites in premodern societies, on the whole, had narrow horizons, delimited by their home village, or the neighboring network of villages.

But results from this work and others show that mobile populations where individuals spanned vast areas of Eurasia across their lifetimes, were not that uncommon for pastoralists. We know this historically, as empires such as that of the Turks and Mongols were defined by a ruling elite whose writ extended from eastern to western Eurasia. The Sintashta samples, which exhibit genetic heterogeneity, with some individuals very different from the norm in their settlement, is exactly what you’d expect from a social and political culture which was united in some fashion over huge distances.

As the sample sizes for ancient DNA have increased it seems rather clear that demographic dynamics that we see in later historical expansions of Inner Asian polities extends back to the Bronze Age. With expanding populations across the ecologically friendly landscape, the ancient proto-Indo-Europeans seem to have mixed with the local substrate wherever they went, just as Turks did later. As they moved west, they mixed with late Neolithic Europeans, as they went east, they mixed with Siberian populations, and as they conquered south they mixed with descendants of West Asian farmers.

One of the primary aspects that I think one needs to keep in mind is that one can’t just imagine that this was defined by simple diffusion dynamics. Historically the boundary between pastoralists and peasants could be fluid, but when political resistance collapses pastoralists have been able to use their military prowess to swarm across the lands of agriculturalists. In other words, centuries of gradual inter-demic gene flow might be interrupted by a rapid “pulse” admixture. There’s no reason that pre-literate polities couldn’t exist. The Inca were one such example, the homogeneity of the Uruk civilization in the 4th millennium BC is strongly suggestive of an imperial hegemony or paramountcy.

Another dynamic is that pastoralists are highly mobile, and so may leapfrog over territory which is unsuitable. Or, they may move so rapidly that there isn’t much mixing with populations in between point A and point B.

This is apparently the case with the Bactria–Margiana Archaeological Complex. These people were mostly descended from people related to the eastern farmers of West Asia, those in modern day Iran. Some of their ancestry had affinities with Anatolian farmers, and there is some evidence even of Siberian admixture in this region. But there are three important takehomes of this preprint in relation to this area 1) the BMAC did not contribute much genetically to South Asia at all, 2) steppe ancestry, related to that of the Yamna culture of the Pontic region, only shows up in BMAC ~2000 3)  there is actually evidence of South Asian (Indus valley?) migration into the BMAC.

The fact that Yamna-like ancestry shows up in the BMAC region so late is a strong reason to suspect that Indo-Iranian peoples did not move to Iran and India until after 2000 BC. In earlier comments on this issue, I was rather vague about timing, because the Corded-Ware people show up in Europe before 2500 BC, and I was going along with the parsimonious idea that this was part of one single cultural and social revolution.

I was wrong. Going back to the Turkic analogy, there were multiple waves of migration and folk wandering by Turkic pastoralists. By different Turkic groups. One of the major ones occurred due to the rise of the Mongols, and the Mongols were not even Turks. The same seems to be true of Inner Eurasian Indo-European groups.

Moving on to South Asia, there are two primary constructs which come out of this preprint. “Indus Periphery” and “Ancient Ancestral South Indians.” I’ll call the former InPe and the latter is termed AASI. To some extent these complement and replace the earlier terms “Ancestral North Indian” and “Ancestral South Indian” (ANI and ASI). The AASI are the ancient hunter-gatherers of the Indian subcontinent. The authors suggested that divergence of this group from other eastern Eurasians occurred very early, that the division between the ancestors of the Papuans, Onge, and AASI was even polytomic (that basically separated very quickly without discernible structure).

The InPe samples are from eastern Iran and the BMAC. They’re unique in having AASI ancestry, at variable fractions (indicating contemporaneous admixture). They also resemble samples from Swat Valley which date to 1200 BC and later, with one major difference: the Swat Valley samples have steppe ancestry.

There are no samples from the Indus Valley proper, so the authors suggest that the InPe are reasonable proxies. Additionally, they assert that ASI can best be modeled as a mixture between InPe and AASI. In other words, there were two admixture events. Their Pulliyar samples are actually pretty good proxies for the resultant ASI, while the Kalash of Pakistan are good proxies for the ANI, who are presumably now modeled as a mixture of steppe populations with the InPe.

This resolves the enigmatic result that Priya Moorjani reported to me last year: less than 4,000 years ago “pure” ANI and ASI people existed. She was presumably going off admixture timing estimates. These results suggest that in some form ANI and ASI still exist, and the first admixture occurred with the creation of InPe.

Using a new method the authors contend that InPe emerged 4700-3000 BC. If this is true then the Indus Valley Civilization (IVC) was a compound of AASI and Iranian agriculturalists (sampled from the eastern end of the cline of admixture with Anatolians, that is, they had none of that ancestry). They also post the first arrival of agriculture to Mehrgarh by 2,000 years at the least. I suspect that it will turn out there were earlier admixtures, which are not being detected. For various ecological reasons the West Asian cultural complex was portable only to the northwest fringe of South Asia, and there it persisted for ~4,000 years. This served as a natural eastern limit for cultures which were migrating out of the West Asian zone, and a point where AASI hunter-gatherers constantly mixed into the local population.

As the IVC sites begin to get sampled in the future I predict that instead of a homogeneous transect of admixture over time and space we’ll see a lot of heterogeneity.

In the Swat samples, the authors see two correlated trends, an increase in steppe ancestry, and an increase in AASI ancestry. No doubt this dates to the “great admixture” which occurred between 2000 BC, and some time before 1000 AD (the Bengali admixture with East Asians dates to between 0 and 1000 AD, as does that of Brahmins who left the North Indian plain and mixed with local populations elsewhere).

Finally, the authors detect a skew toward steppe ancestry among some populations, in particular, Brahmins. The skew is in relation to Iranian farmer ancestry, the two being the primary constituents of ANI ancestry. In Who We Are and How We Got Here David Reich says some of the ANI admixture is much more recent than the rest, judging by tract length. And also going by the BMAC and Swat samples it seems that the time period for when Indo-Aryans arrived in South Asia has to be in the interval between 2000 BC and 1200 BC.

There’s another aspect of the preprint which allows for dating. The arrival of Austro-Asiatic people in South Asia probably has to postdate the expansion of the same group in Vietnam about 4,000 years ago (though not necessarily obviously). But the Munda Austro-Asiatic people of northeast India exhibit curious genetic patterns. They clearly have East Asian ancestry related to other Austro-Asiatic populations in Southeast Asia, but they have a lot less “West Eurasian” in their ANI/ASI mix. The authors resolve this by suggesting that the Munda arrived in South Asia when there was still heterogeneity among the ASI, and unadmixed AASI.

After 2000 BC the IVC went into decline. Various groups of Indo-Aryans were expanding and admixing. From the other end of the subcontinent arrived rice cultivators from Southeast Asia. At some point, they ran into an ASI population that had some Iranian admixture, but not as much as typical. All of this probably occurred in the period between 2000 BC and 1000 BC. I know that some researchers have argued that the Gangetic plain was inhabited by Munda speaking peoples before it was inhabited by Indo-Aryans. The main issue I’ve had with this is that modern Munda peoples are very genetically distinctive, and there’s no evidence of East Asian ancestry in most populations of the Gangetic plain (the main exceptions are those which have experienced Tibetan influence/contact).

So here is my interpretation of the genetic and historical evidence:

1) IVC emerges out of a matrix that was a synthesis of West Asian farmers and indigenous hunter-gatherers. I would not be surprised if later genetic work recapitulates the findings in Europe of an initial period of separation, and then a “resurgence” of indigenous ancestry as the barriers between the two groups break.

2) The period between 2000 BC and 1000 BC is the beginning of the transformation of the South Asian genetic and ethnolinguistic landscape, with the intrusion of two different groups from different directions, Indo-Aryans to the west and Austro-Asiatics from the east. Austro-Asiatic rice culture was superior to western wheat culture because rice is more delicious than wheat, but the Indo-Aryans ultimately established cultural supremacy across South Asia by the Iron Age.

3) The situation in South India is more complicated and confused. The admixture of groups like Pulliyar from InPe and AASI into the classic ASI configuration seems to be more recent than 2000 BC (their low bound dates go as late as 400 BC). The admixture may have occurred in various places, not just in South India. The evidence from this paper suggests that the Andronovo/Sintashta cultural zone was characterized by some genetic heterogeneity due to variation in admixture with neighboring peoples, and the same could be said for the IVC then. I would not be surprised if northern IVC locations had more AASI than southern IVC, as the latter were more insulated from the east due to the Thar desert (the results are consistent with earlier work that suggest modern populations in the lower Indus basis have less Indo-Aryan and more Iranian, with less AASI).

4) We need to be careful about assuming that everything here is a linear combination of distinct and separable atomic units of cultural integrity and wholeness. What I mean is that though Brahmins and some other North Indian groups are enriched for steppe ancestry, it is not only their purview. Rather, it may be that these upper caste groups simply mixed less with the other populations with Iranian and AASI ancestry. The statistics in this paper do not detect enrichment of steppe ancestry in South Indian Brahmins. I believe this is simply an artifact of the reality that South Indian Brahmins mixed with Iranian-enriched elites, like Reddys, when they emigrated to the south.

Though the model outlined in the preprint is much more complicated than a simple ANI/ASI mix, it still simplifies the demographic histories of many populations. For example, own survey of the data suggests that Brahmins who left the Indo-Gangetic plain mixed with local elites wherever they went (Bengali Brahmins have East Asian ancestry, just as South Indian Brahmins have more Iranian-like ancestry).

5) Language is important but is not determinative. R1a1a-Z93 arrived in South Asia relatively late with groups from the steppe. Its frequency is highest in the northwest, and among upper castes. That is, it is correlated in a coarse manner to steppe ancestry. But R1a1a-Z93 is pervasive throughout South Asia irrespective of caste and region. Even in Dravidian speaking southern populations, some groups have quite a bit of R1a1a-Z93.

The analogy that presents itself here is Southern Europe, where some groups with high frequencies of R1b, such as the Basques and Sardinians, are clearly descended in the main from pre-steppe populations. What this suggests is that a broad social-culture prestige network mediated by males extended itself into regions where its cultural hegemony was not assured. Additionally, the autosomal genetic impact was modest, even if privileges given to particular male lineages allowed them to sweep other groups out of the gene pool.

Tamil history precipitates out only a little later than that of North Indian Indo-Aryan civilization. I suspect that this is not a coincidence, that South Asia after the collapse of the IVC and the arrival of the Indo-Aryans and Mundas, could be thought of as a brought mixing cauldron genetically and culturally. In many regions, Dravidian languages persisted in the face of the expansive Indo-Aryan, but there was a cultural influence, likely reciprocal. This is why once Indian civilization reemerged its coherent unity set against peoples to the west and east was not strange despite the linguistic gap between the north and the south.

The only exception here might be the Munda. As I have said, R1a1a-Z93 is pervasive. But it is nearly unfound among the Munda, who tend to carry relatively exotic Southeast Asian Y lineages such as O. I believe that the Munda were in some way losers in a cultural conflict, but they maintained themselves in the hills above the Gangetic plain.

Finally, two reflections, one navel-gazing, one big picture. Genome bloggers in the years around 2010 actually anticipated many of these results. There’s some hindsight bias here because you remember the times you are right and not the times you were wrong. We were right that there was more than one ANI pulse. Additionally, we were looking at the ratio between “Eastern European” and “West Asian” ancestry years ago and noticing the skewed patterns, with North Indian Brahmins biased toward the former and South Indian elite non-Brahmins skewed toward the latter. Chaubey 2010 suggested to us that something was different about the Munda not only in their East Asian ancestry but in their ANI/ASI ancestry. They just didn’t seem to have any Indo-European ancestry (steppe), and a lot of ASI. Over the past few years I’ve been suggesting that Dravidian languages were not primal to South India, but the product of a recent expansion (though part of this is due to scientific publications).

The truth was out there. It just took ancient DNA and the analytic chops of the Reich group and their collaborators to prune the tree of possibilities so that we could zero in on a few precise and likely models.

In the general, I wonder about the role of clines, diffusions, and pulses. The models that the foremost practitioners of the science of ancient DNA utilize tend to assume pulse admixtures, rather than isolation-by-distance gene flow. This isn’t always a crazy assumption. But there was a discussion in the paper of a west-east admixture cline between Anatolian farmers and Iranian farmers. Is this cline due to admixture, or was it always there? A paper from a few years ago implied that early farmers were highly structured, structure that broke down later.

Also, the polytomy at the base of the eastern Eurasian human family tree, where all the major lineages diverge rapidly from each other, makes me wonder about gene flow vs. admixture. It seems possible that the polytomy may mask a phylogenetic tree topology which had gradually bifurcating nodes, if periodically a single daughter population replaced all its sister lineages in a local geographic zone. Much of history in human meta-populations may be characterized by isolation-by-distance and gene flow, erased by the extinction of most lineages and expansion of a favored lineage.

March 30, 2018

Administrative note on this weblog

Filed under: Uncategorized — Razib Khan @ 9:28 pm

I don’t know most of the people who contribute to this weblog anymore. So I don’t know how to contact you. Can you please update your profile with an image icon so that it’s easy to see who is who?

Thanks.

March 29, 2018

The Indian chapter of Who We Are and How We Got Here

Filed under: Genetics,Indo-Aryans — Razib Khan @ 10:33 pm

Since Who We Are and How We Got Here is out I thought I would spoil the “India chapter” (though you should buy the book!).

– The “Ancestral North Indians” are best modeled as a 50/50 ratio of Yamna-type people from the steppes & “Iranian farmers.” The implication is that the Indo-Aryans mixed with agriculturalists in the BMC on the way into South Asia.

– The “Ancestral South Indians” have about ~25% “Iranian farmer”, along with the indigenous component more like the Andaman Islanders.

Bow before me Dasa!

David Reich clearly believes in a model of the ethnogenesis of South Asian populations detailed in A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. Also, I think I can now say in public when I had lunch with him he indicated that he thinks this is the most likely model. Also, the West Eurasian admixture into South Asian populations is “male-mediated.” R1a1a-z93 for the win!

He also believes there were several admixtures. He notes that his group’s 2013 paper, Genetic Evidence for Recent Population Mixture in India, reported two admixture events in North India, but one in South India. And the North Indian populations had the most recent event. This makes more sense if you consider that much of the admixture probably happened in the Northwest, as a mixed population spread across the subcontinent.

Reich contends that long tracts of ANI ancestry in some North Indians indicate that later people arrived from the first ANI wave. Also, several populations have an atypical Yamna-Iranian ratio in their ANI ancestry, being enriched for Yamna, and not so enriched for Iranian. These are all Brahmin groups.

Finally, he unmasks some of the backstories of difficulties collaborating with researchers in India, who have to be sensitive to cultural and political pressures. 2009’s Reconstructing Indian Population History was hailed in India as refuting the “Aryan invasion theory,” but the evidence was on the contrary, and I said so at the time.

In Who We Are and How We Got Here David Reich makes an explicit analogy between the Indian subcontinent and Europe. Both protrusions from Eurasia are characterized by a synthesis of indigenous hunter-gatherers, intrusive pastoralists from the Eurasian steppe, and migrating West Asian farmers.

Ancestry does not always match up with appearance

Filed under: Human Genetic Variation,megan bowen — Razib Khan @ 9:04 pm

A few years ago I watched a bunch of Megan Bowen’s YouTubes about living in Korea as an expat. In one episode she had explained that the reason she had a black American accent (she’s from Georgia I think) is that she is a black American. Just a very light-skinned one.

In other videos, you can see that her skin is a little darker without typical Korean makeup, though she is still very light-skinned. And her natural hair is quite curly. But it would not be implausible to assume that she is one of the 10% or so of African Americans who are more than 50% white.

I didn’t think much about this until today. As part of my job, I watch ancestry-related YouTube videos to get a sense of how people interpret their results, and Megan Bowen showed up!

So I watched her video. There are some photos of her parents, and both look darker in complexion and more typically African American in their appearance. She also admitted that she was so light at birth that her father took a paternity test, and she was his.

The results for her ancestry came back…and she’s 65% Sub-Saharan African! This is curious because arguably Megan Bowen looks more “white” than the actress Megalyn Echikunwoke, who is 50% European (American) and 50% Nigerian (or half-Shona half-English Thandie Newton, the list could go on).

We have the genome-wide data. Megan is 65% Sub-Saharan African. And ~32% European.

Ultimately this is a pretty clear issue of the fact that only a subset of genes are responsible for the features which we deem ancestrally informative in a naive manner. Skin color, hair form, and facial features.

To the right is a plot from a paper which looked for variants affecting skin color in a Cape Vedre sample. They used ~900,000 SNPs to assess ancestry, so you know that that’s right. They also used a melanin index generated with a spectrophotometer. You see that 44% of the variation in skin color can be predicted by ancestry in this admixed population.

There’s a clear correlation between ancestry and complexion, but because the number of loci affecting the variation of complexion in humans is relatively small for a polygenic trait, the relationship can get decoupled rather easily (a few large effect genetic loci explain a lot of the rest of the variation).

If you looked at pigmentation loci in Megan Bowen and did local ancestry analysis, you’d see a strong enrichment for European segments. Far greater than the genome-wide 32%. It happens. It’s probability, not magic.

Abraham on the shoulders of Zoroaster (and others)

Filed under: History,Zoroastrianism — Razib Khan @ 7:54 pm

Yesterday on Twitter I made a quip about “linear Western models of time.” A friend pointed out that that was actually “Judeo-Christian.” I was going to agree…but then I realized something: I vaguely recalled that eschatology and millenarianism were things that some have hypothesized came into Judaism from Zoroastrianism.

The historical context is straightforward. The Babylonians took the Jews to Mesopotamia, where they were strongly influenced by the local cultures. Mesopotamia for most of the period before the Islamic conquest was dominated by Iranian polities, the Achaemenids, Parthians, and Sassanids. Though the non-Iranian populace of Mesopotamia never took to Zoroastrianism, which was considered somewhat the ethnic religion of Iranian peoples,* it has hard to imagine they were not influenced by the religion.

Early Islamic chronicles describe a religious culture in Mesopotamia in the early centuries after Muhammad that would be both familiar and alien. The familiar aspect would be the dominance of various forms of Christianity and Judaism among the Semitic speaking population. The form of Judaism which came to be dominant by the medieval period was strongly influenced by Jewish thinkers in late antique Mesopotamia, who operated with a certain freedom that Jews under Christian rule did not have. Though Christians in Mesopotamia tended to be Oriental Orthodox, whether it be what we would today term Jacobite or the Church of the East, they were Christian.

But the exotic aspect is that many other religious groups, inflected with Zoroastrian and pagan beliefs, were also present. The pagans of Harran persisted down to the Islamic period because of the protection that they had received from the Persian emperors during the Byzantine period. Though groups like Mandeans and Yazidis seems exotic to us today, they were probably part of the bubbling matrix of beliefs which produced novel religious movements rather regularly (ghulat Shia sects like the Alawites probably have laundered some of these old beliefs into modern outwardly Muslim groups).

Manicheanism, for example, seems to have emerged at this intersection of religions. The prophet himself was from a heterodox (from our perspective) Christian background, but his new religion integrated aspects of Christianity, Zoroastrianism, and Buddhism, as well as agnosticism which seems to have channeled Neoplatonic conceptions of the corruption of this world.

The important point here is that this was not a unique confluence of events. Centuries before the Roman Empire, exiled Judaeans were in contact with Zoroastrians in Mesopotamia. The dislocation probably helped force their shift away from belief in a geographically delimited tribal god, local to Palestine, toward a more mature monotheism. But they were also introduced to new ideas which seem to be derived from Zoroastrianism: angels, the prominent role of Satan as God’s foil, an elaborated heaven, and eschatology, seem to be derived from the milieu of Zoroastrian influenced culture.

But were they? One of the major themes, perhaps the most interesting one, in The Shape of Ancient Thought: Comparative Studies in Greek and Indian Philosophies, are the common Mesopotamian motifs which seem to pervade the West Eurasian oikoumene, from Europe to South Asia.

Perhaps the Zoroastrian influence on the Abrahamic religions is less about the creative genius of the Iranian peoples as they impinged upon the older civilizations of West Asia, as it is about their absorption and synthesis of far older motifs?

Again, this sort of synthesis, cooption, and appropriation should be unsurprising. The more and more I’ve dug into the early history of Islam, the more I’ve come to the conclusion that subjugated Iran & Turan held captive the uncouth Arab and brought the arts to the rustic desert nomads! Actually, that appropriation of a classicist jibe misleads as to my view of the early Arab conquerors of Persia. I suspect they were primarily civilized peoples on the margins of the Persian and Roman world, not raw Bedouins. But, many of the aspects of Islam that we think of as constitutive to the religion probably only dates to the Abbasid period and later, when Iranians of Zoroastrian, Christian, and Buddhist background dominated the culture (e.g, the emphasis messianism in Shia Islam probably is accentuated by Zoroastrian influences, while Sunni Islam’s focus on learning of the ulema in a formal sense may be modeled on Central Asian Buddhist monastic forms).

Ultimately the reason I’ve brought this up is that many things that we in the modern world find beautiful or good are said to be contingent on the nature of Christianity, and Christianity is contingent on Jewish thought. Quite often this is false. I used to watch Bible documentaries where David Wolpe was a frequent guest. Wolpe was wont to say that the genius of the Jews was the invention of ethical monotheism. If I had to bet I think this is just wrong. My own suspicion is that on the probability the Jewish shift toward ethical monotheism in their conception of their tribal religion was given a strong push sufficiently, if not necessarily, by the widespread currency of proto-Zoroastrian ideas in Persian Babylon (and later Ctesiphon).

The idea of linear time is often connected liberal individualism and the possibility of progress. The caricature is that the “Judeo-Christian tradition invented progress,” ergo, liberalism, science, etc. This sort of reductive causal model has always struck me as implausible, in part because most of the people (thought not all!) who make this assertion know very little outside of our their own tradition, so they are easily impressed by its uniqueness due to its singular hold on their imagination.

I’m not presupposing here that Zoroastrianism was a necessary condition for the emergence of many traits unique to Judaism. It seems likely that something like ethical monotheism was going to be “invented” somewhere (note that millenarianism seems to have developed in China independently before the first “Western” influences, such as Buddhism and Manichaeanism).

This speaks to the thesis of whether history is driven by unique ideas, or structural forces. They aren’t exclusive, nor are they unrelated. Peter Turchin and others have suggested that ethical metaphysical/religious systems were nearly inevitable with the maturing of large multi-ethnic imperial polities. I believe that evolutionary psychology allows us to understand why those ethical systems were broadly similar in the generalities. The human quest for cosmic justice is just an elaboration of our intuitions about fair-play in a Paleolithic tribal band.

* Zoroastrianism was more successful in the Caucasus, probably because Caucasian elites were integrated into the military elite of the Iranian states.

We’re descended from Lilith and Eve

Filed under: Human Population Genetics — Razib Khan @ 5:13 pm

From the comments:

Something that confused me very early on in the book- the San are shown branching off from the rest of humanity prior to Mitochondrial Eve. How can Eve be a common ancestor in this case? Admixture?

The commenter is talking about an early portion of Who We Are and How We Got Here. Someone who reads a book like that is “in the know,” and this is a reasonable question. But it points to a bigger issue that’s going to crop up with the complexificaiton of the origin of anatomically modern humanity over the last few years, and proceeding forward.

An upside of the very-recent-out-of-Africa model, where all modern humans descended exclusively from a group of East Africans who lived ~50,000 years ago, is that it was very simple. So simple that you could write the model out on a postcard.

The new model benefits from being correct and making humans less sui generis (though perhaps that is a bug rather than a feature to some?), but it also forces more thought and complexity on the lay audience.

Calibration on the coalescence of the last common ancestor of all mitochondrial DNA lineages for humans has changed several times, the last estimates are for a time to last common ancestor for all mtDNA lineages being around 100 to 200 thousand years ago. This is curious in light of the fact that both fossils and genomics are starting to suggest that anatomically modern humans emerged in their current form 200 to 400 thousand years ago.

The shallower coalescence isn’t that surprising. Y and mtDNA both have lower effective population sizes and so higher turnover rates. These high turnover rates mean the extinction of other lineages. As most of you know, the extinction of these mtDNA lineages does not mean that the genetic material of other women alive at the same time as “mtDNA Eve” is not present in modern humans (though who knows what it means to say there’s distinctive genetic material left after all these generations with recombination). Eve was always simply a personification of the coalescence of the mtDNA genealogy. Both the Y and mtDNA phylogenies and coalescence were useful in their time. They pointed to the likely important role of Africa in the origin of modern humans, and the relatively recent time depth of our species. But their coalescence at a specific time was somewhat random around a certain expected value. This is why it was not surprising at all that “Y chromosomal Adam” and “mtDNA Eve” lived at different times (there is some evidence that the Y chromosome has had a lower long-term effective population size).

The above question is inspired by the fact that San Bushmen seem to diverge earlier in their total genome than in their mtDNA. There’s always been a distinction in the literature between demographic divergence between two populations, and the divergence of their genetic genealogies. Oftentimes daughter populations share genetic variation that dates back to before their separation. But sometimes, you have this situation where it seems that the starting point of genetic variation post-dates the divergence between population.

What’s the explanation? I think the simplest one is admixture and reciprocal gene flow, as implied by the commenter. In fact, Pontus Skoglund’s latest African ancient DNA paper implies that there was some sort of isolation-by-distance cline in the eastern part of the continent, from modern Ethiopia far to the south.

And, it may also turn out that the San Bushmen themselves are an admixture between two very different populations, one more like other eastern Africans, and one basal to this clade. If so, then it may be that their divergence estimate is a compound, and the most divergent mtDNA lineages come from the eastern African population that mixed with the more basal population.

The bigger answer is that we really need to move beyond the “mitochondrial Eve” story as being central. It had its time and played its role, but we can move beyond it. Otherwise, the public will be in for a big surprise as ancient DNA starts to uncover the story of a whole antediluvian world within Africa of anatomically modern humans that flourished for hundreds of thousands of years before a small branch left to populate the rest of the world ~50,000 years ago.

March 28, 2018

Complex traits to individual predictions

Filed under: Genetics — Razib Khan @ 12:52 pm

The classical model of genetic inheritance, which dates back to the 19th century, involves discrete traits that are transmitted across generations in easily detectable patterns. These patterns follow what is known as a “Mendelian” model of inheritance: first adopted by the Austrian monk Gregor Mendel, based on his work with pea breeding in the mid-19th century. Largely unrecognized during his lifetime, Mendel’s work was rediscovered in the early 20th century, when biologists adopted it to explain patterns of genetic inheritance. These were the first professional geneticists.

Punnet square for pea pod color

The Mendelian framework is simple. Most complex organisms have two copies of a given gene. These are alleles. The alleles can come in particular varieties. In the example to the left, you see that pea pods come in two colors, and there are two alleles, yellow Y and green y. Because the expression of y is recessive, plants with green pea pods can only produce other plants with green pea pods. In contrast, since Y expresses dominantly, meaning you only need a single copy for the trait to be expressed, two plants with yellow pea pods can potentially give rise to both colors.

This elegant simplicity of Mendelian genetics did two things. First, it replaced the prescientific “blending” model of inheritance, where the physical characteristics of parents “mix” together to produce offspring. For example, they thought cross pollination of a red and a white flower would produce a pink one. This model, which makes intuitive sense, could never explain how populations retained all their variation — as opposed to being blended away. Second, the theoretical basis of modern population and medical genetics derives from Mendelian principles.

Malia, 6'1" (left) is taller than her mother Michelle, 5'11"

Diseases like Cystic Fibrosis and Tay-Sachs express in individuals who carry two copies of the malfunctioning gene. They’re recessive Mendelian diseases, and diseases like these are the basis of much of modern medical genetics.

Not all traits and diseases, however, are like this. Neither height nor risk of developing schizophrenia have a simple inheritance pattern. You probably know tall offspring of short parents, and vice versa. Many people with schizophrenia do not have parents with schizophrenia, and many people who develop schizophrenia don’t have children who later develop it. You can’t just look at a pedigree and figure out simple probabilities, like you can with many simple traits and Mendelian diseases.

We also know that these characteristics are heritable within the population. That is, if you look at the characteristic in parents and offspring, they tend to be positively correlated. It’s not a perfect correlation, but the relationship is strong enough to suggest that there is a genetic disposition within individuals.

The heritability of height and schizophrenia is about 80% or more. That means 80% or more of the variation of the trait in the population is due to variation of genes in the population. This is a statistical inference.

How does this relate to Mendelism?

In the early 20th century, population geneticists realized that if you assume that there are alleles at many different genes, the combined action of those alleles could result in a distribution of outcomes. Instead of two flavors at one gene, there could be different variants across hundreds or thousands of genes. This results in an increase in a wide range of outcomes, as opposed to just two outcomes (as with recessive diseases) — potentially thousands of positions along a spectrum.

There aren’t two categories, tall or short, but a value of how tall you are. It’s a quantitative trait.
Correlation between height prediction and true height

Before modern genomics, which gave us access to the fine-grained variation across the DNA sequence, and computing, which allows for powerful analysis of large quantities of data, we couldn’t relate quantitative traits to individual genes. Luckily, we live in a world where modern genomics and computing do exist. Researchers can look at patterns of variation across the whole genome of many individuals in populations and how that relates to variation in characteristics. A new method can predict 40% of the variation in height simply from the genetic sequence!

Like height, schizophrenia is a highly heritable trait whose variation is controlled by many genes. But unlike height, for schizophrenia we are more interested in the likelihood of developing the disease rather than any quantitative value. Therefore, researchers will construct a “polygenic risk score,” which takes all your “risk” alleles across your genome, and combines them to produce and overall risk against the population norm.

Researchers do this by looking at associations between schizophrenia and particular markers. They assemble a list of markers that are associated with schizophrenia to a level of statistical significance. Then they look at another dataset, and test their markers to see if it predicts the variation of risk within that dataset across individuals. In this way researchers can construct a list of valid markers from the genome and use them to give individually tailored risks.

All of this is state-of-the-art and in its early phase. Most individuals haven’t been genotyped, much less had their genomes sequenced. You can’t construct a risk score on an individual who doesn’t have their genetic data. Additionally, many of these predictions are sensitive to the populations that they were tested in: there is still much medical research that needs to be done in people of non-European origin. Finally, unlike many Mendelian diseases, polygenic risk prediction may not be definitive enough for anyone to act on the results in any concrete manner. If you are told you have a two times greater risk of developing a disease where the average person has a 5% risk, does knowing you are at 10% change your behavior at all?

But knowing who is, and isn’t, as risk within the population is useful for public health and prevention, and probably saves money and lives if you add up all of the individuals. In the end, this is the “big data” direction our society is heading.

Learn more about where your traits for food tolerance fall on the spectrum and explore your Metabolism story today.


Complex traits to individual predictions was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

One the eons of salutary neglect

Filed under: Human Population Genetics — Razib Khan @ 12:35 am


New preprint, Something old, something borrowed: Admixture and adaptation in human evolution. This part jumped out at me:

…Indeed, for most traits, the contribution of archaic human alleles to present-day human phenotypic variation is not significantly larger than those of randomly drawn non-introgressed alleles occurring at the same frequency in modern humans. Interestingly, in both studies, neurological and behavioral phenotypes are an exception, with Neanderthal alleles contributing more to variation in these traits than frequency-matched modern human alleles.

I joked that perhaps we can talk about people “acting like a Neanderthal” again?

But seriously, I was thinking today about one particular stage of human evolutionary history, the long sojourn outside of Africa for the ancestors of non-Africans (including “Basal Eurasians”) which produced a sustained bottleneck. In David Reich’s new book he alludes to it, and I’ve seen other mentions of it (this is an old idea).

How long was the bottleneck? What was the normal census size? What were the cultural implications of having a small isolated population?

The PSMC and MSMC diagrams I’ve seen don’t really answer my questions.

Bro do you even supplement?

Filed under: DNAGeeks — Razib Khan @ 12:08 am


For a while now I’ve been telling my cofounders at DNAGeeks.com that we need to do a shirt about reading supplements.

If you don’t know what I’m talking about, you’re a heathen. Basically, if I blog about a paper, I try and read the supplements, because there’s a lot of good stuff (often the method or provenance of samples) in there that can’t be put into the paper proper. The restrictions of modern publishing are kind of crap, but they are what they are.

Also, supplements are usually a better guide to future research and directions if you look close. Better than the “discussion” section.

I’ve already bought one of the t-shirts. This is obviously a “niche” product, but who knows? I’m definitely going to wear it at ASHG 2018.

March 26, 2018

Open Thread, 3/26/2018

Filed under: Open Thread — Razib Khan @ 9:17 pm

Does anyone have a galley or review copy of She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity? The book is long, and review copies are in short supply. Would be nice if I could see it before it’s released at the end of May. Just use my contact email if you have a copy.

Pretty excited about it! The use of the word “heredity” is a clue to me that this is going to be a book with a really long historical narrative.

How Genetics Is Changing Our Understanding of ‘Race’. Everyone is talking about this David Reich op-ed in The New York Times. Well, at least in my corner of Twitter.

It’s adapted from a chapter of Who We Are and How We Got Here. That chapter is both more subtle and more punchy than the op-ed. Anthropologists will probably dislike it even more than they dislike this op-ed because Reich does not pull punches (though contrary to the impression you might get from the op-ed he clearly prefers to use “ancestry” rather than the word “race”).

There’s not much to say about the op-ed.

I think it’s more interesting to perceive the dynamics of scientific culture at work in the reaction. The Reich lab is an eminent one, and its Diaspora includes other elite institutions now. He is affiliated with Harvard Medical School and the Broad.

Friends of mine who operate outside of human genetics characterize this subfield within genetics as one with sharp elbows and a mafia-like network of pedigree laboratories and superstar professors. It’s probably worse in the explicitly biomedical area, but population geneticists who don’t work on humans still say human population geneticists are different (we’re talking averages here).

There were many criticisms of the op-ed from human population geneticists…but they were subdued, restrained, and often prefaced by praise for Reich’s scientific chops or his generosity as a collaborator. Both true of course. There was also praise.

But the op-ed illustrated the reality of some unpalatable propositions. In Who We Are and How We Got Her David Reich himself makes it clear that some of the ideas he’s mooting are not palatable to him. If it wasn’t clear from the op-ed already.

But it also I believe it illustrated what I like to say about academia from what little I’ve seen and experienced within it: it is a highly feudal culture defined by patronage networks and an ordered understanding of the relationship of superiors to subordinates. As they say: “You come at the king, you best not miss.”

If he was someone less connected, less at the peak of his powers, I believe that David Reich’s reputation would be ground up in a sausage machine. This op-ed reminds me of nothing more than Symmachus’ plea for an old way that is fading before the new. Symmachus was rich and famous. He could dissent from the ascendant orthodoxy that was “passing on to better things.” But his class of the old pagan elite was at its dusk.

Most of the more vociferous criticisms are coming from anthropologists because it’s a different field with an alternative nobility of blood and status. David Reich can be thought of as an alien warlord who as trespassed the boundaries of their kingdom. But Reich is also aiming at the very foundations of their rule, so they can do no other but unleash the dogs of war.

Speaking of that book, my review is up at National Review Online. Hope to contribute more in the future to that publication! Doesn’t look like Kevin Williamson is getting fired from The Atlantic, so there’s space in those pages.

I’ll probably talk more about the book in a spoilerish way next week so that people who purchased the book can read it.

Efficiently inferring the demographic history of many populations with allele count data and Recovering signals of ghost archaic admixture in the genomes of present-day Africans. These deserve close readings.


I assume everyone on this blog has heard about my podcast and are sick of hearing about it. But there are still people who follow me on Twitter who haven’t.

Since nothing has changed in a while, more positive reviews on iTunes and Sticher, please.

I think you’ll enjoy the interview with Stuart Ritchie, though that won’t post until further into April.

In a few days, I’ve going to have a post up on a new shirt which I pushed for at DNAGeeks (we got an artist to do something). But for now, check out the GNXP-helix themes hats and beanies.

The Battle of the Blue Cat Café How an anti-gentrification boycott became a proxy war between the radical left and the alt-right. Hits a little close to home.

The basic outline is that gentrification in East Austin is transforming lower class & lower-middle-class black and Latino neighborhoods into middle and upper-middle-class white neighborhoods. This makes some people really angry because they don’t want their neighborhood to change.

I’ve had some “interesting” discussions about this with locals with deeper roots. It’s fashionable to bemoan gentrification, but when I bring up my experience as an immigrant, and how that naturally results in change and transformation of neighborhoods, people get uncomfortable. The emotions deployed against gentrification aren’t that different from the emotions used against immigration. In many ways, the East Austinites who are being “displaced” can be psychologically analogized to middle and lower-middle-class Trump voters who feel they’re being “displaced.” Both groups feel they are being marginalized by people who are changing the world that their ancestors created with their own labor. And they probably are.

I don’t have a good answer to this. The free-market person in me says that gentrification has to happen, and the neighborhoods are going to change no matter what. But another part of me actually understands the argument by making an analogy to the national level: too much migration into a polity can result in a transformation of its institutions and dispossession of its majority. Pretty soon East Austin will mean something very different from what it has traditionally meant.

If you haven’t had wood ear salad, you haven’t lived. I highly recommend it as one of the major experiences of Sichuan cuisine (and of course don’t go to the place if their green beans are not recommended.

Humanity’s Genes Reveal Its Tangled History

Filed under: Culture,History,science,Science & Tech — Razib Khan @ 2:30 am
Reality, it turns out, is more complex and interesting than scientists ever imagined.

Communities only exist only in the Minds of Europeans

Filed under: History,Imagined Communities — Razib Khan @ 12:28 am

I read Benedict Anderson’s Imagined Communities: Reflections on the origins and spread of Nationalism because other people read it. This is a book that is routinely alluded to in discussions by pundits of various stripes. On the back of the 2006 edition, the publisher notes that over 250,000 copies have been printed of this short academic work. Time put this as 48th out of 100 all-time great nonfiction books. It’s one of the most assigned works to undergraduates at universities.

There are two things about Imagined Communities that drove me crazy. First, there’s a tendency to just assert something that is perhaps profound, perhaps inscrutable. Honestly, I just don’t know. I randomly opened to page 23, and found this:

Figuring the Virgin Mary with “Semitic” feature or “first-century” costumes in the restoring spirit of the modern museum was unimaginable because the medieval [sic] Christian mind had no conception of history as an endless chain of cause and effect or of radical separation between past and present.30

But wait, there’s a note! What does it cite? “For us, the idea of ‘modern dress,’ a metaphorical equivalencing of past with present, is a backhanded recognition of their fatal separation.”

This is pretty typical throughout the book. I’m really skeptical of this strong assertion that medieval Christians didn’t understand cause and effect, and the past or present, considering that they periodically went through millenarian enthusiasms about the End of the World. But perhaps I misunderstand Anderson? It wouldn’t surprise me. He’s just not that clear a lot of the time.

About ten years ago Jonathan Gottschall observed that often in literary scholarship all their “experiments” confirm their theories. Imagined Communities follows this model. I’m very confused why pundits with backgrounds in political science are citing a work which is basically a long analysis of literature, with some historical references thrown in. Though there are numbers in the book, there are no graphs or tables. This is a work of literary scholarship.

Second,  Anderson likes to use a lot of words which are very obscure. For example, “the philological-lexicographic revolution and the rise of intra-European nationalist movements, themselves the products, not only of capitalism, but of the elephantiasis of the dynastic states….”

I understood what the author meant by “elephantiasis.” But that’s a really unnecessary word. If it was the exception, I’d shrug it off. But this reliance on overly obscure terminology is pretty common in this book, and again, it makes me wonder what undergrads are getting out of it. Not to brag, but I have a pretty big vocabulary, and the lexical flourishes were obscuring the point of whole passages. If that’s how I feel, what about someone with a smaller vocabulary?

Probably the most intellectually creative thing about Imagined Communities is that the author begins by examining the emergence of nation-states in Latin America, and the role of white Creole communities in the rebellion against the Spaniards. Anderson contends that this model influenced Europeans. The United States as well showed much of Europe that a large continental republic could actually flourish. From here Imagined Communities digs deeply into the various intricate details of how the Empire of the Romanovs began to assert a more clear Russian identity, or the nationalities trapped into the Habsburg polity.

Much of this material is interesting and has clearly percolated to other areas of scholarship, as I was familiar with it. Again, the author has a tendency toward abstruse phraseology or obscure word choices, but the portion on Europe was relatively coherent and familiar, though there was a strong bias to present nationalism as novel and new, rather than primordial.

But when the story moves to Asia it lost me. This is strange insofar as Anderson has a background in Asian scholarship, with a focus on Indonesia. He devotes a fair amount of time to Southeast Asia for these reason. And perhaps it wasn’t intended, but Imagined Communities depicts the emergence of Southeast Asian nation-states as an outcome of the agency of Europeans. The British created Burma. The French created Vietnam (Anderson makes much of the name changes that “Vietnam” has undergone over the past few centuries). China was a diverse motley of dialects before being dragged into the modern world by European-influenced intellectuals. Japan was given form with the Meiji revolution. Thailand created itself due to its engagement with colonial powers. Indonesia was stitched together by the Dutch.

Non-Europeans have no agency or originality in creating their own national identities. They were blank slates upon which European colonials drew something.

Luckily for me, I don’t come into reading Imagined Communities totally ignorant of other viewpoints. I’ve read Victor Lieberman’s Strange Parallels, which makes the case that mainland Southeast Asia resembled Europe in the coalescence of distinct proto-national identities one to two thousand years ago.

The same is true to the north. China was arguably a nation-empire long before Europeans arrived. Though the Chinese peasantry spoke different dialects, it was united by a ruling class with a sense of coherency. The modern Japanese nation-state state is modeled on Western nation-states, in particular, Prussia. It strikes as bizarre to hold that this unique and isolated nation didn’t exist in the imagination of Japanese when the Europeans first arrived.

Anderson, like many scholars of his ilk, gets carried away with the novelty and power of European rationalism. For example, he focuses on European censuses with the clear implication that they somehow created many ethnicities. Not to sidetrack, but modern genetics shows that this is just false. It’s false in India. It’s false in Southeast Asia. It’s probably false more or less everywhere.

Western science and the bureaucratic machinery of the Western nation-state, were novel and revolutionary. But peoples existed with a self-identity long before Europeans arrived. To be honest I found Anderson’s treatment of the Vietnamese almost insulting. The first edition of Imagined Communities was written in the early 1980s, and the work is pervaded by Cold War concerns. Though Vietnam has been a catspaw in the game of great power, the fact that they began adjuncts to, but did not become absorbed into, the Chinese system highlights that their national identity in some inchoate way is very old.

Overall it is worth reading Imagined Communities because of its purported cultural significance. But much of it is so garbled and unclear I’m not sure what people are taking from it, aside from the proposition that the modern nation-state was invented in the last few centuries due to modernity. In the end the book is kind of a long tautology.

March 25, 2018

“Because we could”

Filed under: Genetics — Razib Khan @ 9:53 am

March 22, 2018

The origin of the Ashkenazi Jews in early medieval Europe

Filed under: Ashkenazi Jewish Genetics,Ashkenazi Jews — Razib Khan @ 9:27 pm


Last year’s The time and place of European admixture in Ashkenazi Jewish history is very close to the last word on the genetics of the ethnogenesis of Ashkenazi Jews. Here’s the author summary:

The Ashkenazi Jewish population has resided in Europe for much of its 1000-year existence. However, its ethnic and geographic origins are controversial, due to the scarcity of reliable historical records. Previous genetic studies have found links to Middle-Eastern and European ancestries, but the admixture history has not been studied in detail yet, partly due to technical difficulties in disentangling signals from multiple admixture events. Here, we present an in-depth analysis of the sources of European gene flow and the time of admixture events by using multiple new and existing methods and extensive simulations. Our results suggest a model of at least two events of European admixture. One event slightly pre-dated a late medieval founder event and was likely from a Southern European source. Another event post-dated the founder event and likely occurred in Eastern Europe. These results, as well as the methods introduced, will be highly valuable for geneticists and other researchers interested in Ashkenazi Jewish origins.

Roughly the Ashkenazi Jews are a half and half mix of a Middle Eastern population and various European groups. The majority of the European ancestry is “Southern European,” probably something like Italian. But, a minority of the European ancestry is like “Eastern European.” Additionally, the former admixture pre-dated the bottleneck, and probably dates to ~1000 A.D., while the latter event post-dates the bottleneck.

For years I had thought that Isaac Bashevis Singer’s excellent novel The Slave was interesting but implausible. The reason being that Ashkenazi Jews and their gentile neighbors did not mix by this time, as the European ancestry in Ashkenazi Jews dates to the Roman period.

These results reject that model…the tract-length evidence is persuasive to me that admixture with Slavs did occur.  Some Italian groups are more north shifted, but the most parsimonious explanation while the Eastern European like ancestry came in later is that it tracks Jewish migration into Germany and Poland-Lithuania later.

The dating of admixture is something I’m less sure of. At 625 to 1,250 years before the present, it puts the emergence of the Ashkenazi community firmly in the Christian era. I don’t want to get into too many details, but from what I have read the Church and local authorities frowned on Jews owning Christians slaves, and tried to suppress instances where Christian slave women became concubines to Jewish men or even Judaized.

I had long assumed that these records reflect elite paranoia. If the dates of admixture are right they may reflect a real concern and a phenomenon (the Y and mtDNA evidence strongly point to the likelihood that the pattern was generally partnerships between Jewish men and gentile women).

And to be frank they tell us less about Jews than they do about the nature of “Christian Europe” in the early medieval period. There is one school of Reform Protestant which takes a dim view of how deeply Christian medieval Europe ever was. I think these results support the thesis that Christianity was an elite religion whose grasp upon the masses was more tenuous and illusory than we might imagine. There is also the reality that the feudal Christian state never had totalitarian authority over the population.

In theory Jewish assimilation of Christians to their identity, Judaizing, could be a capital crime. But if these results are correct it was quite common in the formation of the early Ashkenazi community before it moved north and then east. This decentralization and relative weakness of the early medieval Church and state, the superficially of mass Christianity, might also explain how vast regions of France defected from orthodox Christianity for decades in the 12th century during the ascendancy of the Cathars.

On a final note, I decided to do a little probing on the Middle Eastern forebears of the Askhenazi. The paper says that Levantine populations are the most likely source, which is entirely unexpected. But I wanted more detail, so I used the Human Origins Array dataset. You can see on the PCA above that the Ashkenazi Jews are shifted toward the European (Basque) population away from Middle Easterners, but if you project the line outward it lands on Christian and Muslim Lebanese. Haber et al. last year showed that there was continuity between the modern Lebanese and Caananites, and the Jews were likely originally a form of Canaanite. Curiously, Palestinian samples in the data are strongly shifted away for the Lebanese, toward groups like Saudis.

I understand it’s a hot potato politically, but if I didn’t have a dog in this fight I’d say that the contention that Palestine and Jordan (look at the Jordanian sample positions) underwent some population turnover is likely true (though I’d be curious about the data on Palestinian Christians).

The peopling of the Indian subcontinent at the dawn of knowing

Filed under: Indian Genetics — Razib Khan @ 8:47 pm

A few people have been pointing me to a new paper, A Bayesian phylogenetic study of the Dravidian language family, which implies that the Dravidian language family diversified ~4,500 years ago. I don’t have much to say about the paper itself since it aligns with my own conclusions, but it’s well outside of any field that I can judge (though it does use standard phylogenetic packages I’ve used).

Recently I’ve been going back to old posts of mine on South Asian population genetics because no matter how much some people drag their feet on this question, we’re pretty close to knowing how South Asians came to be. Here’s what I said in December of 2010:

Who were the Indo-Iranians? I lean toward the proposition that they do derive from the Andronovo culture of the Eurasian steppe. This would date the entrance and expansion of Indo-Aryans in northern India 3-4,000 years ago. I also contend that the dominant element of ancestry among modern South Asians is not Indo-Aryan. Rather, it is an ancient stabilized hybrid of pre-agricultural societies in the Indus valley and Neolithic farmers who originated from what is today western Iran and eastern Anatolia. Therefore, I posit that the “Aryanization” of the Indian subcontinent is properly modeled as the same processes which led to the emergence of an Anatolian and Rumelian Turkish identity; a small elite population which forces an identity shift among the majority.

Where was I wrong? Where was I right?

Even looking at ADMIXTURE plots which don’t always give an accurate sense of population history it seemed likely that “Ancestral North Indian” (ANI) was not one thing. Some South Asian populations seemed to have much stronger affinities to West Asian populations. And in particular those from highland West Asia, toward the Caucasus. These include groups in southern Pakistan, but also to some extent in South India. In contrast, other groups had affinities with Eastern European populations, in particular, high caste North Indians, and to a lesser extend Indo-European peoples more generally.

I think I got the dynamic correct. Subsequent analyses comparing ancient DNA from the Caucasus and Iran suggest that all South Asians have a lot of shared drift (ergo, ancestry) with highland West Asians, while a smaller subset has high shared drift (ergo, ancestry) with pastoralists from the Eurasian steppe. The groups match up with what the ADMIXTURE plots were suggesting.

There was more than one pulse of ANI-like ancestry and that one of them was like West Asians and one more like Europeans. Remember, this is before we knew the acronyms ANE, WHG, and EEF. Or CHG and Eastern Middle Eastern Farmers and Western Middle Eastern Farmers.

But, I think I was wrong about the magnitude of the admixture. This was before ancient DNA had revolutionized our understanding of population movement and turnover. I was still resisting the mass migration of a whole folk across huge distances. I’m more open to that now. I am not sure I still believe the very high steppe fractions implied in some of the recent analyses, but it’s certainly higher than I would have believed back then.

Finally, the recent diversification of the Dravidian languages supports the model that their current distribution is not primordial. Rather, they probably expanded relatively recently from the northwest of the subcontinent. Probably earlier than the Indo-Aryan expansion into the Gangetic plain, but not that much earlier.

Additionally, because the Dravidians were not primordial, but expanding only somewhat ahead of Indo-Aryans, they were part of an interactive social-cultural sphere with the Indo-Aryans. I think the very high frequency of R1a1a-Z93 in some non-Brahmin South Indian groups, even tribal ones, suggests to me that the expansiveness of some paternal Indo-Aryan kin networks across the whole subcontinent.

Addendum: Much of the attention goes to the ANI dynamics. But though recent work attests to the overwhelmingly diversity, and basal character, of South Asian mtDNA lineages, we can’t be entirely sure that they are indigenous without ancient DNA. If a migration from the east at the Pleistocene-Holocene boundary was characterized by gradual diffusion of groups with reasonable effective population sizes they could have brought over their diversity.

March 21, 2018

Diving into Chinese philosophy

Filed under: China,Chinese philosophy,philosophy — Razib Khan @ 11:59 pm

Back when I was in college one of my roommates was taking a Chinese philosophy class for a general education requirement. A double major in mathematics and economics (he went on to get an economics Ph.D.) he found the lack of formal rigor in the field rather maddening. I thought this was fair, but I suggested to him that the this-worldy and often non-metaphysical orientation of much of Chinese philosophy made it less amenable to formal and logical analysis.

I recalled this when a friend of mine, from an Indian background, asked what I would recommend for him to learn a bit about Chinese philosophy. What I suggested was that he read A Short History of Chinese Philosophy, and then read The Analects and something like Confucius: And The World He Created.

As someone who lives in the West from a Hindu background, I didn’t think it was worth it for him to explore Chinese Buddhism, or even Neo-Confucianism, which emerged out of the reaction and accommodation with Buddhism.

Thoughts? Recommendations?

Henan, the heart of China

Filed under: China,Henan — Razib Khan @ 11:43 pm

I haven’t posted on one of these in a while. Mostly because I don’t know what to say about Henan. Henan is where China began. As noted in Wikipedia four of the eight ancient capitals of China are located in this province, in the heart of the North China plain. Chineseness, as we understand it, coalesced in this province. The first historical dynasty, the Shang, had the core of their domains in Henan. Though we don’t have historical evidence of earlier legendary Chinese dynasties, many believe that they are likely recollections of the archaeological cultures which flourished in Henan before the Shang (e.g., the Eritlou culture as the Xia).

Originally a land of millet, Henan is China’s number one wheat producer. Whereas the staple of the south is rice, in the North China plain is it noodle.

The agricultural focus of Henan indicates its relative lack of development. In some ways, it resembles Bihar and eastern Uttar Pradesh in India, which were the core of South Asian polities at the dawn of recorded history, but are now backwaters. With 94 million people Henan is China’s third most populous province, but it turns out that more people in China have origins in Henan (103 million) than any other province. This reflects nearly 10 million migrants who work in other provinces, generally coastal ones.

Being the locus and origin of Han Chinese culture it is no surprise that the province is overwhelmingly ethnically Han. But curiously it also seems to have an overrepresentation of Christians compared to other Chinese provinces.

The Others were people too

Filed under: Genetics,Human Evolution,paleontology,science — Razib Khan @ 12:25 pm
Neanderthals, cousins we knew.

In 2010, our understanding of Neanderthals, our human cousins, changed forever. Before this year, there was a live debate about whether they were human at all, whether they had fully elaborated language, or even culture.

When A Draft Sequence of the Neanderthal Genome was published in Science, we found out that all humans outside of Africa, and some within Africa, had some ancestors who were Neanderthal. In the wake of this finding, a renaissance of Neanderthal humanization occurred. Previously, Neanderthals were just a ‘dead-end’ in our ancestral lineage.

Denisova Cave

In December of the same year, Nature published Genetic history of an archaic hominin group from Denisova Cave in Siberia. While Neanderthals had been part of our cultural landscape for over 150 years, these hominins discovered in Denisova cave were a shot out of the dark. Debates about Neanderthals’ humanity raged for years, and this discovery certainly promoted more.

Called Denisovans, after the Siberian cave they were discovered in, what we know about these mysterious people comes from only a few bones and teeth.

The Denisovans were a total surprise scientifically. The result was not answering any questions because there was no foreknowledge of them. It turned out that about 5 percent of the ancestry of people in places like Papua New Guinea came down from the Denisovans!

Later work, which looked far more closely at mainland populations, showed that there were traces of Denisovan ancestry across the whole of South, Southeast, and East Asia — as well as into the New World. All these populations presumably descend from an African migration which swept east until it reached the Pacific, and then north and south. While Papuans had about 5 percent Denisovan ancestry, these groups had less: 0.1% to 0.5%.

Oddly, the only evidence we have for the Denisovans is in Siberia, but the greatest proportion of their ancestry is found beyond Wallace’s Line, in Oceania. It is very likely then that the Denisovan sequence from Siberia is from a particular population, and this species ranged far and wide across eastern Eurasia — just as Neanderthals did to the west.

A new paper in Cell, Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture, adds a further twist by reporting that there were two interbreeding events with Denisovans. One group of Denisovans contributed to Papuans, Southeast Asians, South Asians, and some of the ancestry of East Asians. It turn out, however, that another group contributed ancestry only to East Asians — up to half the Denisovan ancestry is in Han Chinese.

The way the authors did this is by first compiling a list of sequences, which likely came from Denisovans or Neanderthals. They did this by looking for regions which were anomalously different from modern Africans, who have no Denisovan or Neanderthal ancestry. Once they had this list, they compared them to the genomes of the Neanderthals and Denisovans.

Not surprisingly, Europeans had matches with Neanderthals only. Papuans had more matches with Denisovans than Neanderthals. South, Southeast, and East Asian populations had many more matches with Neanderthals, but a small number with Denisovans.

So far so good.

But the authors noticed that some of the populations had Densiovan matches to the Siberian sequence that were much better than those in other populations. In South and Southeast Asia, and Oceania, there were no high quality matches with the Denisovans. In the Han Chinese, about half the matches were much better with the Siberian Denisovan genome — while half the matches were similar to the ones found in other populations.

This could mean that in Northeast Asian populations, two groups of Denisovans contributed their ancestry, while in southern Asia and Oceania only one did.

These results show us that the human past was complicated even if the early genetic results painted a simple picture. Modern humans in eastern Asia interacted with Denisovans twice. We know from a genome in Europe that there were several admixture events with Neanderthals, but it seems only one persists down to the present — as the first Europeans with additional admixture left no descendants. Perhaps the same is true in Asia, maybe there were more than two admixtures with Denisovans.

The pattern of where Denisovan admixture is found is intriguing. It is found in highest frequency among Han Chinese and somewhat lower in Japanese and the Dai people of South China. It is entirely absent in the Vietnamese. Combined with the fact that Tibetans obtained a high altitude adaptation from Denisovans, this is circumstantial evidence that the admixture occurred in the interior of Eurasia.

Denisovans are a major twist in the understanding of our species, but their widespread distribution, and multiple interactions with modern humans, points to intriguing possibilities. Perhaps the Denisovans persisted down to relatively recent times, and interacted a fair amount with modern humans? We know they interacted enough to mix with us twice. Denisovans complexify our understanding of the past, but they may simplify and illuminate myth!

Maybe you have some Neanderthal or Denisovan in your DNA. Discover your story today with Neanderthal by Insitome.


The Others were people too was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

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