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12_01_2016_Alice_headshot The new Alice Roberts documentary is going viral. Or at least its spin is.

E.g., Western contact with China began long before Marco Polo, experts say:

However, Chinese historians recorded much earlier visits by people thought by some to have been emissaries from the Roman Empire during the Second and Third Centuries AD.

“We now have evidence that close contact existed between the First Emperor’s China and the West before the formal opening of the Silk Road. This is far earlier than we formerly thought,” said Senior Archaeologist Li Xiuzhen, from the Emperor Qin Shi Huang’s Mausoleum Site Museum.

A separate study shows European-specific mitochondrial DNA has been found at sites in China’s western-most Xinjiang Province, suggesting that Westerners may have settled, lived and died there before and during the time of the First Emperor.

Let’s go with the easy part first: there were no “Western” people when the Afanasevo culture was pushing into the fringes of what is today Xinjiang.

There are two extreme polarities of definition of what Western is. One is cultural.

516C6LMzGTL As outlined in David Gress’ From Plato To NATO: The Idea of the West and Its Opponents, the West did not emerge fully grown like Athena from the head of Zeus in the 6th century BCE along the Aegean. Rather, the West evolved organically as a synthesis over time of Classical Greco-Roman elements, Christianity, and later the post-Roman societies, often dominated by barbarian martial elites. By this definition it is clear that a blue-eyed Sogdian merchant who was resident in Xian in the 7th century was not Western. Their only affiliation with the West would be adherence to Christian Church derived from Persia, and even here this stream of Christianity was relatively marginal that of the Western variety (most Sogdians were probably Zoroastrians of course).

A second definition of being Western is racial, whether explicit or implicit. That is, there is an association with being Western and white. This is certainly true, but the problem with this formulation is that though Western people were invariably white, white people were not invariably Western. To give a concrete example, Buddhist Tocharians who had light hair and eyes, and flourished as late as 1000 A.D, were white people by any definition, but they were not Western in anything but the most reductive and biologistic sense. The cultural valence of what it means to be Western is clear on the southeastern fringes of Europe, where Muslim populations are often considered non-Western, even when they are genetically similar to their Christian neighbors.

The mtDNA they found is probably of haplogroup U, or perhaps H. Its presence in Eastern Asians is unsurprising, as skeins of migration seem to have laced themselves across the landscape of Eurasia across the whole Holocene, and earlier.

Finally, I think the media is misleading its depiction of Greek influence. Greco-Bactrians were culturally influential for several centuries in Asia. The Greek influence then did not come from the Mediterranean, but from the furthest outputs of Hellenistic society. Still noteworthy, but not so spectacularly surprising.

 
• Category: History • Tags: History 
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n20307 Taking a break in my work of the day I stumbled upon the fact that Bernard Cornwell’s series based on King Alfred’s period, which began with The Last Kingdom, is a Netflix series. To be honest I much preferred the three volume Warlord Chronicles, set more than three centuries earlier, in post-Roman and pre-Saxon Britain. A retelling of the Arthurian romance with not too much romance, George R. R. Martin admitted to me in correspondence in the late 1990s that he quite enjoyed it as well. The protagonist of The Last Kingdom is peculiarly similar to the one in Warlord Chronicles.

As a fan of alternate history I’ve occasionally stumbled upon the “what-if” scenario whereby Alfred’s Wessex is conquered, and England becomes Daneland. Would we today be speaking another Scandinavian language? Would Christianity disappear, and the pagan rites of the Norse come to rule the day? It seems broadly likely that that would not be cause at all.

First, the victory of Christianity in Europe was overdetermined by the 9th century. Even in this period there was a Christian presence in Scandinavia. A Scandinavian ruled England would almost certainly be a Christian one. And in fact in the century before the Norman conquest the Scandinavians created a hybrid society with the native English. Harold Godwinson had a Danish mother, and connections to the Danish monarchy.

The second issue is one of language. The English language of Alfred’s time was much more Germanic, so the gap between it and the tongue of the Danes was not that large in any case. And, from what I have seen, it seems that the number of Scandinavians in relation to the native population was much smaller than that of the Saxons in relation to the British, though even in the latter case it must be acknowledged that the Germans who arrived in the 5th to 6th centuries were numerically outnumbered by the native Romano-British (see PoBI results).

Perhaps if the kingdom of Wessex fell England’s identity would be more indubitably aligned with Scandinavia, as it was arguably in the decades before Norman conquest in any case. But cultural identities can be curiously resilient. The Finns endured nearly 600 years of Scandinavian domination, but maintained their language, while the long Irish interaction with the Vikings still left the Irish identity intact.

 
• Category: History • Tags: History 
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41ezBQHrx7L Spencer Wells, along with many others, such as Jared Diamond, argued that agriculture was a disaster in terms of what it wrought for the quality of life for the average human in his book Pandora’s Seed. This is broadly plausible to me. On the other hand, I also think it is highly likely that agriculture and civilization were basically inevitable.

The “great leap forward” in cultural complexity and explosion of symbolic expression ~50,000 years ago, give or take, seems likely to have been only the culmination of a process of encephalization and increased sophistication which had proceeded over millions of years. The precursors to the agricultural life were likely already there before the Holocene.

To a great extent the hypothesis of inevitability has been tested: in the Americas much of the dynamics which characterize the Old World were recapitulated. Agriculture, civilizations with writing and class stratification, and monumental architecture, all with analogs in the Old World, are there. In fact, this National Geographic piece, In Search of the Lost Empire of the Maya, is fascinating to read, because it seems to me that it likely parallels developments in the Old World two thousand years before. The Snake Kings were warlords in a manner which would have been familiar to the “Great Kings” of the ancient Near East.

There are two great schools of history from the pre-modern era. Those which are cyclical, and those which exhibit some intuition that there is an endpoint or progress. The “independent” experiments of human history suggest that both are true, with an arc of history on the macroscale scaffolded by innumerable cycles of rise and fall.

 
• Category: History • Tags: History 
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620px-Agry(ararat)_view_from_plane_under_naxcivan_sharurIt all began in the hillocks to the north of the plains of modern Syria and Iraq. Agriculture that is. Or more precisely, the West Eurasian package which would wash all the way to the Atlantic, and deep into Eurasia, and in innumerable ways influence most human societies. The standard model until recently was that this was a cultural, rather than genetic, revolution. That is, the idea of agriculture took root among people as they emulated their successful neighbors. An analogy here can be made to writing. Early Egyptian forms of what became hieroglyphs much more resemble Mesopotamian cuneiform than they later did. The idea of writing was critical, to the point where we know that it occurred at least one other time (East Asian writing may have been independent, there is debate about this).

51IZQjMbVlL._SX346_BO1,204,203,200_ But there’s a crucial difference. Writing is complex, but the idea is simple enough, symbolic representation of language, that one can imagine imitating it. Additionally, originally literacy was a monopoly of a small class of scribes. One can imagine that these people were highly skilled and perhaps initially mobile, but they made little demographic impact among the polities which they traversed. Agriculture is different. It is not just a technology, but it is a lifestyle. One of the insights of Peter Bellwood’s First Farmers is that the there aren’t too many instances of modern ethnographic instances of hunter-gatherers or nomadic populations happily settling down to the farmer lifestyle. The work of cultural evolutionists more recently reinforces the fact that there is a great deal of tacit norms which are both functionally critical toward many traditional lifestyles, and, whose utility and contingent integration are not reflectively understood by those who practice a given lifestyle.

That’s just a way to say that many people do what they do because they’re going through the motions of traditions which they have internalized over their whole life, and they couldn’t even tell someone else in any rational way why they were doing what they were doing. If you were trying to imitate them you’d probably discard a lot of functionality without understanding its importance to the whole system.

So how did farming spread? It didn’t, farmers did. Endogenous population growth in the simplest formulations resulted in a natural replacement of hunter-gatherers with farmers. More recently works such as War Before Civilization have convinced me that early agriculturalists engaged in a lot of inter-group competition. In other words, it wasn’t just passive demographic replacement, but proactive expansion of clans, tribes, and confederacies into the “empty frontier.” This makes more sense of the reality that ancient DNA is witness to quick rapid disruptions, and later equilibration (perhaps as residual hunter-gatherers slowly become assimilated to the new society which is more self-confident in itself).

An implication of this model is that the chrysalis of later genetic and cultural variation was already preexistent rather early on. That is, if you looked at the ancient Near East, where several communities stumbled upon agriculture, perhaps in concert, you will see in these the “womb of nations.” The idea struck me as crazy when the blogger Dienekes Pontikos presented it in the late aughts based on patterns in admixture analyses. It strikes me as far less crazy after half a decade of ancient DNA. Now in the comments David points me to an abstract at SMBE which shows this all coming to a head:

The shift from hunter-gathering to food production, the so-called Neolithic Revolution, profoundly changed human societies. Whilst much is known about the mode of spread of people and domesticates into Europe during the Neolithic period, the origin of this cultural package in the Ancient Near East and Anatolia is poorly understood. By sequencing the whole genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, we show that the eastern part of the Ancient Near East was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus but distinct from the Neolithic Anatolian people who later brought food production into Europe. Despite their key role in developing the Neolithic package, the inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting they were somewhat isolated from other populations in this region. Their high frequency of short runs of homozygosity, comparable to other early Neolithic farmers, suggests that they overwintered the Last Glacial Maximum in a climatically favourable area, where they may have received a genetic contribution from a population basal to modern Eurasians. Thus, the Neolithic package was developed by at least two genetically-distinct groups which coexisted next to each other, implying a degree of cultural yet little genetic exchange among them.

As I’ve said before, the the hunter-gatherers of the Caucasus share a lot of drift with South Indians. I’m betting that the woman from Ganj Dareh is part of the root population of what later became the dominant contributor to “Ancestral North Indians,” as well as the major vector of “Basal Eurasian” into the Yamnaya people.

Addendum: This site is very close to ancient Elam. This nation has been very speculatively associated with Dravidian languages. The Copper Age commercial ties with the Indus Valley Civilization in the Persian Gulf may be less surprising if many of these routes dated back to the early Neolithic expansion.

 
• Category: Science • Tags: Genetics, History 
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Screenshot 2016-06-03 12.15.55

51OftfuYlSL._SX316_BO1,204,203,200_The Monkey’s Voyage is a book I’ve spotlighted before. Probably the main reason is that it highlights the importance of migration/dispersion on an evolutionary timescale. That is, change is the norm, and turnover is ubiquitous. The Tuatara is the exception, not the rule, when it comes to the biogeographic diversity of New Zealand.

As I’m not particularly focused on macroevolutionary dynamics, I’ve taken a microevolutionary lesson. That is, attempts to understanding variation within species. Updating one’s priors with the above the finding that Palearctic wolves descend from a core founder population which flourished after the Last Glacial Maximum is a lot less surprising. Wolves have been around a lot time, but meta-population dynamics and local extinctions may be the rule.

The same probably applies to another Ice Age megafauna, humans. For a long time it was something of a mystery why macro-haplogroup M, so common in South Asia, East Asia, the New World and Oceania, had no presence it Europe. Turns out it did, at least during the Pleistocene. Some of this is is just drift acting on smaller effective population size of uniparental markers. But, we know now some of this was population turnover.

This explains my casual comment below that I think “Ancestral South Indians” may have origins outside of India itself. My theoretical expectations have just shifted over time. Imagine that you have population X in a constrained geographic region. It is divided into two components, X0, at 50%, and X1 at 50%, while X1 is just the remainder after you remove X0. When you look at worldwide variation you see that X0 is modal in the region in question that you are focusing on. From this can you conclude that X0 is indigenous to/originates from this region?

I don’t think that that is necessarily true for a variety of reasons. More concrete, if you looked at ancient DNA 5,000 years before the present in the region I think X0 is probably likely to be dominant. 10,000 years before the present though I’m sure. At 20,000 years before the present I’d be skeptical. Finally, at 40,000 years before the present I’d think continuity is unlikely.

That’s the theoretical/abstract reason why I think ASI are likely to be intrusive to India. But there’s a concrete reason. The table above is from a preprint, Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. What you see is that the coalescence for M lineages, which are the modal haplogroups in South Asia, seem higher to the east than in South Asia itself. The authors take that to suggest M probably diversified in Sundaland and even Sahul before it became prominent in South Asia.

A few caveats. First, the paper is quite uneven, and there’s a lot of talk about “Out of Africa” routes which I think are neither here nor there (Y/mtDNA work isn’t going to resolve this issue, ancient DNA is). Second, these coalescence dates aren’t “proof” of anything, they simply make the case for shifting priors. Finally, the differences between South Asia and Southeast Asia are modest, suggesting that there was a very large effective population of females in both areas. In all likelihood there were multiple waves of migration west…and east, during the Pleistocene (some of the M in Northeast South Asia is almost certainly very recent Holocene gene flow from Burma).

 
• Category: Science • Tags: Genetics, History 
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41ncnodwApL._SY344_BO1,204,203,200_ My main gripe with Inventing the Individual: The Origins of Western Liberalism, is that I don’t think individualism is a sui generis invention of Western civilization (the author, Larry Siedentop, gives particular pride of place to Western Christianity as the mother and midwife of liberal individualism). It’s hard to generalize about human nature and history without portraying cut-outs, but I’ve contended for over ten years now that basal, constitutive, and modal, human nature is already quite individualistic. Western liberalism is a rediscovery or excavation, not a novel creation.

Yes, as per The Secret of Our Success humans are very social creatures. But ultimately that sociality redounds to individual success (e.g., positional games/status hierarchies take up more time and energy than coordinating to achieve group success). Western civilization’s individualistic ethos is to my mind a reversion to a more primal norm, as dense human living became less constrained by the eternal Malthusian traps of the agrarian civilizations which arose after the Neolithic. Individualism and wealth go hand and hand.

41ezBQHrx7L“Traditional” customs and values which were handed down to early moderns by their ancestors were cultural adaptations to novel ecologies that were the product of dense existence on the Malthusian limit. There may be limitations to the classical evolutionary psychological conception of the “Pleistocene mind,” but I suspect that the emotional importance of friendship and pairbonds between mates existed during that period, and were ubiquitous. I say this because platonic and romantic love don’t seem to be learned in any deep sense, but are naturally evoked out of our cognitive hardware. And yet norms, values, and rituals over the past 10,000 years have constrained the importance of love, because individual interests can sometimes be at cross-purposes with group/social interests. The friendship between Cú Chulainn and Ferdiad should naturally transcend divisions of honor, obligation, and nationality. Yet in early Iron Age Ireland they do not. The dramatic tension at the heart of Romeo and Juliet, or Tristan and Iseult, arises because of the reality that almost everyone can relate to the individuals whose preferences and needs are constrained and thwarted by considerations of family, religion, or ethnicity (the substitution of divine love for most is probably not an equal value substitute, with all due to respect to god).

The_10,000_Year_Explosion_(Cover) Complex societies are a big deal. They’ve changed the genetic makeup and characteristics of humans a fair amount. But cultural evolution is even more plastic, pliable, and adaptive. Human cultures are protean, and rearrange preexistent cognitive furniture in a manner which makes them functional for a particular time and place. Much of this comes together during the Axial Age with the evolution of “higher religion.” These cultural innovations fused multiple strands together into a very robust alloy. Philosophy compelling to the literate castes was deftly interleaved with devotionalist theism which appealed to the masses and proffered fictive kinship, hammered together by mass ritual, and scaffolded in the institutional frameworks of the despotisms and oligarchies of the age.

41YXHblIQEL._SY445_QL70_ I doubt that humans are naturally egalitarian. We strive for excellence, and engage in individual and intergroup competition. But our penchant for rank and status exhibits constraint and moderation. Humans are social apes, and if an “alpha male” gets too big for his britches, then a coalition of subordinate males is likely to topple him. I presume this sort of equilibrating system operated for most of the Pleistocene…but things began to change during the Holocene. Big men became despots. Peter Turchin has argued in UltraSociety that the despotisms of the Bronze Age were unstable, with the consequences for toppling catastrophic. Universal religion, which allowed for constraint on autocrats by positing an ethical principle or supernatural agent above the king or emperor, was a cultural innovation that allowed for greater stability. Sometimes the adaptation was peculiar; both the Imperial Romans and early Muslims avoided the term “king” for rhetorical reasons, even though the princeps and caliphs were kings in all but name.

Evolutionary processes in complexes species generally involves an element of intraspecific competition. Some would even posit that in many cases this is the dominant dynamic driving evolutionary change. But the invention of a caste of slaves, and masses of servile peasants, to serve a small elite, was a feature of agricultural civilization. This was no natural consequence of natural competition.

We know all this happened. The current project has to be to understand how it happened. Why it happened.

A new paper in Nature Genetics sheds light on a critical piece of the puzzle, Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. The figure below communicates the main results:


Screenshot 2016-04-25 21.40.08

In some ways this seems an incremental improvement over last year’s A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Much of the detail of this current paper, and why it adds to earlier work, can be found in the supplements.

The major takeaway is again you see evidence in Y chromosomal male lineages of incredibly rapid and explosive demographic growth. This is the rise of patriarchy, the arrival on the scene of despotic lineages which monopolized access to a disproportionate amount of the goods and services of many societies, including women.

In the plot above three lineages jump out at you. E1b, R1a, and R1b. The first is associated with the Bantu expansion, that occurred over the last 4,000 years. The second two are likely associated with Indo-Europeans in both Asia and Europe, respectively. The timescale is on the order of 4 to 5,000 years in the past. The association between culture and genes, or the genetic lineages of males, is rather clear, in these cases. In other instances the growth was more gradual. For example, the lineages likely associated with the first Neolithic pulses, J and G. Interestingly, the authors of the paper notice that the same is true in East Asia. Here one sees a more gradual accumulation of genetic mutations as lineages branch out from each other at a stolid pace, a sharp contrast to the explosive “star phylogeny” that is the case for R1b and R1a. This is almost certainly due to the differences in the cultural revolutions, and the reproductive success that that allowed a given male.

Finally, the authors suggest that haplogroup E, which is today the dominant lineage within Africa, though it is found in the Middle East and Europe, is the product of a back migration ~50,000 years ago. The argument is from parsimony. E and D are clearly a clade, and D is found in Japan (and also Tibet and Southeast Asia). If E originated in Africa, and later spread to Europe, so did D. Rather, the authors favor the model that E is a basal Eurasian haplogroup which percolated back into Sub-Saharan Africa during the Pleistocene. It would not be surprising that Southwest Eurasian humans would maintain contact with nearby African populations, but this sort of phenomenon does seem to point to the possibility for a Levantine origin for modern humans!

This is all based on contemporary DNA, and contemporary distributions of populations. There may have been mass extinctions which hide from our perception other demographic revolutions. Additionally, if there is one thing that ancient DNA has taught us, it is that modern distributions may not reflect ancient ones. Nevertheless, this is a good step in understanding the cultural changes which have resulted in the world we see around us.

 
• Category: Science • Tags: History, Y chromosomes 
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The_10,000_Year_Explosion_(Cover) In light of David Reich’s interview I have been thinking about how genetics will shed light on many questions in the near future, and what my particular expectations are. The interview prompts me to collect some of my thoughts into one place, and outline a tentative thesis that I’ve been pointing to for the past few years. My friend Greg Cochran wrote The 10,000 Year Explosion: How Civilization Accelerated Human Evolution in the late aughts, and some of his predictions have come to pass (e.g., Neanderthal admixture, and likely adaptive introgression according to many analysts of the data).

Others have not, and one of those that needs to be heavily modified was the idea that a mutation for lactase persistence allowed for the Indo-European expansion. That is, the original Indo-Europeans were simply biologically superior at extracting calories from the land, and so succeeded due to that advantage (at least in large part). The ancient DNA tells a different story; the Indo-Europeans may have originated the mutation, but it came to be at higher frequency after their demographic replacement and absorption of the European first farmer populations. That is, genetics post-dated the cultural shift, rather than initiating it.

Though understanding the biological basis of human behavior remains important to me, over the past decade or so I have become more and more convinced that the missing piece of the puzzle of the last 10,000 years is about how cultural evolution produced civilization and altered patterns of human genetics, rather than the other way around. This is somewhat a change in tack for me. One of the reasons I refer to Richard Klein’s Dawn of Human Culture so much is that ten years ago the book’s thesis that a biological change in our cognitive architecture allowed for the “Out of Africa” expansion was moderately persuasive (also see Steven Mithen’s Prehistory of the Mind). My acceptance was probably inadvertently tempered by the fact that Klein seemed to have only a rudimentary idea as to the details of formal evolutionary theory, appealing as he did to punctuated equilibrium.

It may be that anatomically modern humans changed in some fundamental way 50,000 years ago. But the bigger picture seems just too complicated to reduce in this fashion right now. Rather than focus how human culture was shaped by the genes, I am now more curious about how genes were shaped by human culture.

k8488 Last year a paper was published, A recent bottleneck of Y chromosome diversity coincides with a global change in culture, which reported that it seems that a major recent change had occurred in the composition of Y chromosomes of humans. These are basically records of paternal transmissions across the generations. Ancient DNA shows that many of the very common lineages only appear to have risen in frequency ~4,000 years ago. This was of course thousands of years after agriculture. One can’t reduce this simply to a shift in mode of production, and the demographic excess of farming societies.

UltrasSoc_cover_epub I’m sure most of you can anticipate where I’m going here. The rise of pastoralism, and the emergence of a mobile arms-bearing males changed civilization. It wrecked civilization, but it also created civilization as we know it. If you read The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World, you would already suspect that (or, books going back to the early 20th century). But even the author of that book was shocked by the demographic impact of the Indo-Europeans as evident in ancient DNA. And, anyone who looks at star-shaped phylogenies such as that for R1a1a would have a hard time explaining what might have caused such an explosion in anything but the vaguest detail.

My answer comes from Peter Turchin in Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth. In War in Human Civilization Azar Gat reports that more numerous armies are more likely to win any pairwise conflicts. But in Ultrasociety Peter notes that Lanchester’s laws indicate that superiority with long range weapons on flat territory gives a much greater likelihood of victory to those groups who are more numerous than with simple near engagement on foot. The combination of this with horses to aid in mobility, and I believe you had a revolution on the Eurasian steppe where the outcomes of inter-group competition between coalitions of males became “winner-take-all” affairs.

Because of the inevitability of the drafting of the horse as a beast of burden and transport it was inevitable that the early adopters would undergo a cultural revolution, and trigger a high stakes series of inter-group competition. The winners of that elimination tournament are the Y chromosomes we see around us.* But between 2000 BC and 0 AD the winners decided to cash out, as a new stable equilibrium emerged. “Higher religion,” a shift toward monogamy, and reduced inter-group warfare due to the emergence of state monopoly on violence, was an exit strategy from the melee of the transition between the Neolithic and Iron Age (again, Peter Turchin has discussed this at length). The patriarchy forged on the steppe at the tip of the spear and on the chariot now decided to mature and accrue more cultural adaptations to prevent itself from eating its own young.

* Something similar happened between 1650 and 1850 in Europe. Who have guessed that by the 20th century English would have been the international language? First the British vanquished their Dutch commercial competitors, and slowly ground down preeminence of French political, military, and cultural power on the continent. A dynamic Europe was engaged in competition on a massive scale, and the victorious British obtained the empire upon which the sun never set.

 
• Category: History, Science • Tags: History 
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UltrasSoc_cover_epub Over the past few years one of the major finds of ancient DNA is that human genetic patterns as a function of time often exhibit discontinuity. In plain language, the people who live in a given location are often unlikely to have descendants at that location 10,000 years down the line. This has resulted in an update to long held null and consensus models of of modern human dispersal across the world. To sum it up, that family of models tended to be predicated on a sequence of unidirectional migrations out of Africa in a step-wise fashion. This resulted in the stylized fact that genetic diversity decreased as a function of distance, with groups like Native Americans and Oceanians the most “steps” from Africans. Though all non-African populations are separated by the same number of generations from Africans, one result that would be implied and was seen in the data is that genetic distance from Africans of these populations was often higher than Eurasians, likely a function of their elevated drift (more drift means more divergence from ancestral shared allele frequencies). Once these regions were settled at a given time in the past genetic diversity so partitioned would slowly equilibrate through gene flow between adjacent demes.

F1.large (1) Though this model captures some element of the truth, the reality of sharp local discontinuities in a given region is strongly indicative of the fact that there was no stable state achieved once the initial founders arrived. Geographical reality seems to dictate the sort of pattern of settlement outlined by the model of serial bottleneck Out-of-Africa model, but it seems likely that future population arrivals could be drawn from both closer to, and further out, from Africa. Second, it turns that most of the world’s populations are the product of relatively recent admixtures between very different ancestral lineages. Instead of overlaying a phylogenetic tree over a spatial landscape, one has to conceive of it as a reticulate network. This revised model is outlined in Joe Pickrell and David Reich’s Towards a new history and geography of human genes informed by ancient DNA. In place of diffusion and continuous genetic exchange between adjacent demes, the empirical data seems to point to a non-trivial proportion of “pulse admixtures.” That is, people who were very genetically different arrived, and mixed in with the local population, in a very short period. Sort of what happened in the New World with the arrival of Europeans.

But that’s all talk. A new paper in Molecular Biology & Evolution formally models these processes, Long distance dispersal shaped patterns of human genetic diversity in Eurasia (open access):

…However, it is likely that the Last Glacial Maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite dataset genotyped in 22 populations to estimate the posterior probabilities of several scenarios for the settlement of the Old World by modern humans. We considered models ranging from a simple spatial expansion to others including LDD and a LGM-induced range contraction, as well as Neolithic demographic expansions. We find that scenarios with LDD are much better supported by data than models without LDD. Nevertheless, we show evidence that LDD events to empty habitats were strongly prevented during the settlement of Eurasia. This unexpected absence of LDD ahead of the colonization wave front could have been caused by an Allee effect, either due to intrinsic causes such as an inbreeding depression built during the expansion, or to extrinsic causes such as direct competition with archaic humans. Overall, our results suggest only a relatively limited effect of the LGM-contraction on current patterns of human diversity. This is in clear contrast with the major role of LDD migrations, which have potentially contributed to the intermingled genetic structure of Eurasian populations.

One of the things the authors found is that low population pairwise genetic distances across a wide range of human populations in Eurasia is probably due to LDD events homogenizing the landscape. Continuous gene flow between demes after the initial settlement Out-of-Africa would not have resulted in these patterns. Second, it seems reading the paper that the weak effect of the LGM population reductions on genetic diversity are partly a function of this mixing across long distances. Finally, it is notable in within Eurasia at least (they suggest that the Americans and Oceania may not fit this pattern) a sort of diffusion/wave of advance model does hold for the initial arrival of modern humans in Eurasia. They posit that this might be because archaic populations prevented long distance movements, or, that population fitness became too low when the bands were too small, the reference to the allee effect. Additionally, they also note that the evidence in Europe suggests both replacement with minimal admixture, and then later admixture with the local substrate.

But the details are less important than the big picture. The authors note that there are aspects of the data (dozens of microsatellites) that leave something to be desired, but this is a first pass. At the top of this post you see Peter Turchin’s Ultrasociety. Though the authors don’t get into much specificity in the discussion, I think the solution to what’s going on, and how LDD seems prevalent when you have a populated landscape, is that cultural complexity resulted in sharply increased returns to the victors in inter-group competition. Though some of the dynamics date back to the Pleistocene, the re-patterning of the world with “LDD”, what I call “leapfrogging”, is probably most salient for Eurasia during the Holocene. And, as the story about the Yakutian horses implies, this is also relevant to many domestic lineages.

 
• Category: Science • Tags: Demography, Genetics, History 
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He under whose supreme control are horses, all chariots, and the villages, and cattle; he who gave being to the Sun and Morning, who leads the waters: He, O men, is Indra.

To whom two armies cry in close encounter, both enemies, the stronger and the weaker; whom two invoke upon one chariot mounted, each for himself: He, O ye men, is Indra.

Rig Veda

Sons of Indra

Sons of Indra

Five years ago I found out that my friend Daniel MacArthur and I are members of the same Y chromosomal haplogroup, R1a. Both of us thought it was rather cool, that ~5,000 years ago there lived a man who was ancestral to us both on the direct paternal line. Five years on, and both Dan and I have sons who continue this lineage. True, surely Dan and I share more than one lineage of connection over the past ~5,000 years, the Y chromosomal one is simply the one that is genetically irrefutable since recombination does not break apart the sequence of variants, the haplotype, allowing the inference to be as simple as taking candy from a baby. The common ancestral information is transmitted as a whole block, excepting the mutations which separate us from our common forefather. Additionally, since he has attested South Asian ancestry (< 200 years), we probably share many lines of descent over the past ~3,000 years (one of Dan’s ancestors was stationed in Bengal in the 19th century, so I think our genealogies intersect a decent amount for non-related individuals).

Screenshot - 10272015 - 03:41:22 PM But there’s something special about R1a beyond the fact that it binds me paternally with a host of people who I know from all around the world. The figure to the right is from the supplements of a Genome Research paper, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. You see that R1a1 diverges by very few mutational steps, and a rake-like pattern defines the phylogeny. That is in keeping with a history of relatively recent diversification, and rapid population expansion. The Genome Research paper found that R1a, along with a host of other Y chromosomal lineages, have undergone very rapid demographic expansion over the past when put through the sieve of phylogenomic inference. This is similar to what you see with the Genghis Khan haplotype. Remember, this is a very specific signature of direct male descent. It does not necessarily extrapolate well to the rest of the human genome. So, though Daniel MacArthur and I share a common Y chromosomal lineage, he is Northern European and I am South Asian, with all that implies for the set of genealogies which come together to contribute to the patterns of variation we see in our whole genomes.

Screenshot - 11012015 - 11:20:26 AM But recently we’ve been gaining even more understanding at the phylogeography of R1a, and its likely history. To the left is a figure from the supplements of Reconstructing Genetic History of Siberian and Northeastern European Populations. You see in this chart a few important things. First, the sister to the haplogroup R, which includes R1b and R1a, and therefore huge numbers of European, West, and South Asian men, is Q, an Amerindian one. The Mal’ta boy, who lived ~24,000 years ago, seems likely to have carried a basal R1 lineage. This is reasonable because most people peg the divergence of R1a and R1b ~20,000 years ago (or somewhat more recently). A major takeaway here is that the dominant lineages across much of western Eurasia today on the male side seem to derive from a group with central Eurasian affinities. The two R1 lineages are very rare in Europe before ~4,000 years ago, according to ancient DNA. This is also concomitant with the arrival of “Ancient North Eurasian” (ANE) ancestry, which is closer to that of Mesolithic European hunter-gatherers than East Eurasians, but still rather anciently diverged, on the order of ~30-40,000 years before the present. Amerindians also have substantial admixture from this group, as do many groups in the Caucasus, and South Asia.

 

The second major issue that is evident from this figure is that Western and most Eastern European R1a diverge from South Asian and Central Asian R1a. The Altay population in this paper are Turkic, but “trace approximately 37%…of their ancestry to another unknown population, which the model predicted to be related to modern Europeans.” And, its R1a looks basal to the South Indian sample, which because it is from Singapore, is likely to be Tamil. Nearly 15 years ago in The Eurasian Heartland: A continental perspective on Y-chromosome diversity, Spencer Wells reported R1a at reasonable frequencies even among non-Brahmin South Indians. More recent work using more markers suggests that R1a has two very common major lineages in Eurasia, with one very common in Eastern Europe, and decreasing in frequency west, and another common in South Asia, with appreciable fractions in regions of Central Asia such as the Altai mountains. Going back to the earlier work, and connecting the dots, it looks like these two “brotherhoods” of R1a diverged on the order of ~4,000 years ago, both undergoing rapid expansion in different regions of Eurasia.

Oh, but there’s more! Eight thousand years of natural selection in Europe has been updated with new ancient DNA results form Iosif Lazaridis’ work. As you might know by now it seems likely that the Indo-European languages were brought into Europe by peoples related to (descended from?) the Yamna culture of the trans-Caspian steppe. The Yamna were genetically a compound population, with about half their ancestry being derived form “eastern hunter-gatherers” (EHG), who themselves were a equal compound between “western hunter-gatherhers” (WHG), the latter presumably descendants of the Pleistocene populations which had retreated to the habitable fringes of the continent, and the previously mentioned ANE group, with Siberian affinities. The other half of the Yamna peoples’ ancestry derives from something similar to that of the early European farmers (EEF), but somewhat different. In particular, rather than western Anatolian affinities, this ancestry seems more trans-Caucasian or eastern Anatolian, with Armenians and Kartvelian groups either being source population, or related to the source populations.

Intriguingly, the Yamna carry the R1b haplogroup, today rather rare in Eastern Europe, but common, and modal, in Western Europe, with extremely high frequencies along the Atlantic fringe. The new version of the preprint now reports some ancient DNA results form the successor culture to the Yamna, the Srubna. There are two intriguing aspects to the new results. First, the Srubna have nearly ~20% ancestry from a population related to the EEF. There are two possible options here. One, that there was back-migration from Europe after the initial migration west. Second, that an EEF-like migration occurred directly from the Middle East to the steppe. But now, from the preprint:

Srubnaya possess exclusively (n=6) R1a Y-95 chromosomes (Extended Data Table 1), and four of them (and one Poltavka male) belonged to haplogroup R1a-Z93 which is common in central/south Asians…very rare in present-day Europeans…and absent in all ancient central Europeans studied to date.

First things first. There are some “Out of India” theorists who posit that R1a derives from South Asia. If you take a very deep time perspective this may be true; recall that much of Eurasia was not habitable during the Last Glacial Maximum (LGM), so the distribution of populations was very different from what we see today. But, on the scale of ~4,000 years ago it seems that one can say that the very common variant of R1a found in the eastern Iranian world and South Asia likely derives from the steppe. The reasoning here is that while peoples in South Asia have elements of ancestry across their genome with affinities to the steppe people (e.g., ANE), there is little evidence for South Asian distinctive ancestry (e.g., ASI) in the steppe people. Additionally, the majority of South Asia mtDNA does not have a West Eurasian profile, but is closer to the lineages of eastern Eurasia. This is strongly suggestive of mostly male migrants. What we can say definitively is that it looks as if male lineages overturned each other multiple times on the steppe. First, R1b was dominant. Then in the same region one lineage of R1a came to the fore, only to later be marginalized by another lineage of the same haplogroup. Finally, in Central Asia more generally the Turkic migrations reshaped the whole ethnographic landscape within historical memory.

F5.mediumThough I begin this post with Y chromosomes, I will not end with them. My belief though is that the Y chromosomal story gives us a deep insight into the nature of social relations over the past ~5,000 years. More on this later. But, the constant turnover of the Y chromosomal record should clue us in to the fact that human demographic history exhibits punctuated turnover events, which reshape the genetic landscape radically over a few centuries. This is a far cry from a model of a set of serial founder events from Africa, dispersing outward as a phylogenetic tree overlain upon a spatial map over a time-scale of tens of thousands of years in Fisher waves.

Specifically, I’m referring here to the 2005 paper, Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Currently, the best rejoinder to this model is probably Towards a new history and geography of human genes informed by ancient DNA, by Joe Pickrell and David Reich. In this review the authors show that though the serial founder bottleneck framework is consistent with the data at a certain level of granularity, it is not the only possibility. What ancient DNA in particular is telling is that local geographic continuity of lineage is often very rare. This result then should make us skeptical of taking contemporary genetic variation, inferring phylogenies, and then overlaying those phylogenies upon the spatial distribution of particular ethno-linguistic groups. Of course, on a coarser scale of granularity the “Out of Africa” model inferred from older genetic work from the pre-ancient DNA era is probably correct. That is, African populations tend to harbor lots of genetic variation, and are basal in relation to non-African lineages. Or, put another way, non-Africans are a derived lineage of Africans. ~100,000 years ago almost all of the ancestors of non-Africans would have been in Africa (or perhaps the biogeographic extension of Africa in the Middle East).

But the story beyond that scale is more complex. At least some of the first settlers of Europe have no modern descendants in Europe. In fact, these populations are nearly as close to East Asians as they are to modern Europeans, suggesting that the modern east-west and north-south axes in Eurasia are products of events of the last few tens of thousands of years at most. In fact, the synthetic origins of Europeans and South Asians is strongly suggestive of the likelihood that inferences from modern genetic variation only have time depths back ~4-5,000 years or so in much of Eurasia. A recent paper in Science, Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, suggests widespread back-migration to Africa itself from Eurasia! Though I disagree with the interpretation in some details (I don’t believe that this occurred ~3,000 years ago), the circumstantial evidence from this and other studies is strong that there has been several waves of migration of Eurasian groups back to Africa. Excepting the northern fringe of the continent in no region is this preponderant, so that the status of Africa as the home of the original population of modern humans from which others derives, remains unshaken. For now.

Nevertheless, both ancient DNA and whole genome sequencing are fleshing out surprising and enigmatic details in relation to how human genetic variation came to distribute itself around the the world today. Here we can come back to Europe. Mostly because there has been a lot of genetic work on this continent, and the ancient DNA is probably thick enough that we won’t find any major new surprises. In short, the phylogenomic history of the continent over the past ~10,000 years has been “solved” more or less. What did we find out? What can it tell us about the more general human story?

nature14317-f3 We can start with the present. As noted in The History and Geography of Human Genes Europe is a very genetically homogeneous continent. The distances as inferred from allele frequency differences between two given populations is very low, and Northern Europe between the Atlantic fringe and the great Eurasian plain in particular is very uniform in terms of the total genome. Today, we know why. As outlined in Massive migration from the steppe was a source for Indo-European languages in Europe, Northern Europe was demographically shaken ~4,000-5,000 years ago by population movements triggered by peoples which left the steppe. It was not a total replacement. But the world of the first farmers, who had issued out of the Middle East ~8,000 years ago, was rocked in the north. The male Y haplogroups associated with these old farming groups, such as G2a, are found at low, though relatively even, proportions all across Northern Europe today.

One interesting aspect of the story is the huge genetic distance between some of these ancient groups. For example, that between the first farmers from the Middle East and their nearby hunter-gatherer neighbors ~8,000 years ago was of the same order as between Europeans and East Asians! This is more than ten times the larger genetic distances you can find in Europe today, but this persisted for thousands of years, though it seems that hunter-gatherer ancestry increased over time among the farming populations, likely through admixture with the local substrate. The reason for this high genetic distance is because the early European farmers carried ancestry which has been termed “Basal Eurasian” (BEu). This points to the fact that these people seem to have diverged first away from all other non-Africans when it comes to Out-of-Africa populations. In other words, ~40% of the ancestry of early European farmers is from a population which is more genetically distant from European hunter-gatherers than Andaman Islanders are. It was the arrival of the steppe people which resulted in the leveling of the genetic distances across much of Europe, overwhelmingly so in the north, and to a non-trivial extent in the south.

nihms132060f1 So if Europe went through a great homogenization and leveling ~4,000 years ago, why does the “genetic map of Europe” exist? That is, why does geography predict variation in genes so well? There are three things one might say about this. First, PC 1, the larger dimension of variation is north-south. This comports with the idea that the heritage of the early farmers persisted in the south to a far greater extent, and the Indo-European demographic impact was more modest, if not trivial. An earlier explanation I had seen floated around was that there was a north-south gradient due to expansion from the post-Pleistocene refugia, via the serial bottleneck effect. The real explanation for the north-south difference though seems more likely to be the differing proportions of Indo-European ancestry, overlain upon the early farmer and hunter-gatherer ancestry.

The second issue to consider is that the underlying genetic variation in Europe was absorbed into the expanding population. Even if the steppe invaders differed little from east to west, there were differing levels of absorption of the substrate, and after several thousand years there had likely been some divergence between the different early farmer groups, perhaps due to differing levels of admixture with hunter-gatherers. Basically, PC analysis could still pick up the signal of underlying variation even if that component was minor if the dominant element was not particularly structured (you can pick up indigenous structure in Mestizo populations in Mexico for this reason).

Finally, after the initial punctuated change, there was an equilibration as isolation by distance dynamics resulted in divergence across the North European plain. We have enough historical records to know that aside from the Slavic migrations there seems to have been little change in the population structure of Europe since the Roman period (the Saxon migrations were not trivial, but they were neither preponderant nor continent-wide in impact).

What general inferences can we glean from this specific European case? As Graham Coop’s group has noted, one must account both for continuous gene flow via isolation by distance dynamics, and pulse admixture events between very distant populations. Consider the metaphor of a forest expanding over the landscape. There will be local structure, accrued over generations, hundreds and thousands of years. But perhaps periodically a fire will sweep through the landscape and clear huge swaths of territory. Into this virgin landscape may expand forests which derive from isolated reservoirs which escape the flames. Over time geographic structuring will be evident again, and depending on the number of refuges the jigsaw puzzle of genetic islands expanding into the gaps will fade somewhat as migration smooths the edges.

The reference to fire here is conscious, insofar as fire can immolate structure which has taken generations to develop. Before the steppe people arrived in Northern Europe the first farmers had established a long-standing cultural commonwealth of sorts. Their legacy had persisted for thousands of years. Then, in a period of centuries, it all changed. Why? Culture.

Outright genocide with weapons is a dangerous business. Societies which engage in endemic long-term warfare as a primary male vocation, such as highland New Guinea, have high mortality rates. But in the context of the Malthusian world, where villages persist on the knife’s edge of subsistence, marginalization and disturbance of long-held patterns is all that might be needed for cultures to descend into famine and starvation. In 1493 Charles C. Mann notes that the mass death triggered by the arrival of Europeans and Africans to the New World had as much to do with the destabilization of society by illness as much as the illness itself. In a world where all hands were on deck to bring in the harvest, the loss of critical labor during those periods could result in starvation, and high death rates led to the rapid collapse of the institutions which served as scaffolds for the maintenance of everyday life.

The scenario then might be one where populations on the Eurasian steppe develop some of the basic elements which would lead to agro-pastoralism, and undergo population expansion. With numbers, and well fed on the agro-pastoralist diet, these tribes might have poured into the lands of the farmers as rapid mobile groups in their wagons. The pattern in antiquity down to the early modern period, from the Goths to the Mongols, was to extract rents and treat the farmers as cattle. There was no incentive for one to starve cattle, and so the demographic impact of conquests was relatively modest.

But what about a world with less institutional complexity? In a world where the basic levers of rent to extract from the conquered did not exist, the natural path would be to replace them. The story goes that Genghis Khan had hoped to turn North China into a vast pastureland by driving out the peasantry (and almost certainly killing most of them through starvation), but his sage Khitai adviser explained the wealth that could be gained by taxing humans rather than raising stock on land. But the Khitai themselves were a semi-civilized people with centuries of experience milking the Han peasantry, and were heirs to a tradition of pastoralist predation that went back to the Hsiung-Nu. And yet no doubt there was a time when the idea of collecting rents from a conquered people was an innovation in and itself. The genocidal antics of the Israelites in the Hebrew Bible strike us as dark and atavistic, but they reflect a cultural mindset which is nearly contemporaneous* with the arrival of Indo-Europeans to Europe.

This plausible sketch puts into better perspective Steven Pinker’s thesis in Better Angels of Our Nature as well as Peter Turchin’s War and Peace and War. The emergence of state institutions and pacific ideologies in the past ~3,000 years may be a sort of response to the high-stakes inter-group competitions which would level societies and turnover populations on a regular basis in the human past.

And yet not all was as sweetness and light. In terms of their total genome the differences between the Srubna and their predecessors were not very great. Conversely, the differences in the total genome between Slavic people and South Asians are legion. But interlaced more recently across the landscape of a more stable structuring of genetic variation, a great regrowth of the forest through isolation by distance equilibration if you will, has been the explosion of powerful patrilineages which trace out an intriguing skein across the landscape. The total genome signal of these men may quickly decay over the generations, as their female-line descendants lose the golden allure of their status, but their male-line descendants continue to accrue mating prowess by dint of their association with great kinship units which succeeded in a winner-take-all game with other such groups of men. On top of the story of migrations of whole peoples, and the extinction and absorption of others, is the story of bands of men operating as units, related either in truth or fictively, which extract rents across a thickly populated landscape of human cattle. Another way to state this is that the thuggish state which imposed a monopoly of violence on a chaotic world where small-scale conflict was becoming too expensive allowed for the emergence of patriarchy as we understand in its customary form. Like so many hirelings, the men charged with protecting the people, made the whole world their possession and left dreams of their people behind.

John Ross, Cherokee Chief

John Ross, Cherokee Chief

While the cultural and genetic affinities of folk wanderings were tightly coupled, I am not sure that the Y chromosomal lineages are so neat. The Hazara people of Afghanistan exhibit an Asiatic appearance in comparison to other Afghans, and their Y chromosomes suggest a close connection to the Khalkha Mongols, but they are Shia Muslims who speak Persian. It does seem that the R1 lineages ascendant in Europe and South Asia owe their success to the Indo-Europeans, but both R1b and R1a transcend a connection to Indo-European ethno-linguistic groups. In some cases, as in that of R1a in the Levant, one might see in that a submerged Indo-European element, from the Mitanni down to the later Persian and Kurdish peoples. But in other cases, such as R1b among the Basque and R1a among Dravidian-speaking tribal people in South India, what we are seeing is the long arm of the patriarchy reaching beyond bounds of cultural and genetic affinity. The great Cherokee chief John Ross was famously 7/8th Scottish in ancestry. But he was a voice for the Cherokee people nevertheless. In most places where the Mongol hordes washed over they assimilated to the cultural folkways of the people whom they conquered. Like modern corporations the patriarchies were only loosely associated with other units of human organization, even if they used them as their vehicles of choice.

And so the story ties back to the beginning. Many of us are the sons of Indra, Zeus, and Thor. The descendants of Herakles, and of Abraham who haggled with God himself. Of Ishmael, whose hand will be against everyone and everyone’s hand against him. Of Niall of the Nine Hostages, and Temujin. The interests of men like this know no nation, nations are but ends to their will. The tension we see in our modern world, between egocentric plutocratic elites jostling nation-states like playthings, might be simply the repetition of an old pattern. In the Bible Saul was rebuked for not destroying all the capital of the Amalekites, perhaps reflecting the tensions of interests which reflect the leader of a people who must act in the collective good, but have their own selfish needs and dreams of self aggrandizement for their own very particular posterity.

Addendum: Ancient DNA will expand in its ability to discern various patterns in the past. But the general disturbances will fall in line with what I have outlined above, I believe. Rather, the move will be from phylogenomics, to population genomics. Phylogenomics leverages genomic methods to attempt to infer phylogenetic patterns. Population genomics explores the classical parameters which shape the change in allele frequencies in lineages, and ultimately, deep evolutionary questions. We now know from ancient DNA that in all likelihood the phenotype which we associate with modern Europeans is a novel configuration. To some extent this is to be expected, as the basic elements which combine to form the European genome, fusing together lineages which diverged at least ~50,000 years before the present (BEu vs. everyone else outside of Africa) and ~35,000 years before the present (ANE vs. WHG), only came together around ~4,000 years ago. But there is more, as natural selection seems to have changed allele frequencies after these elements came together. That is, selection may have been operating across the European landscape when Hannibal was skirting the Alps!

And again, this is likely a general story. Physical anthropologists have long wondered why classical East Asian skeletal morphology seems to be scarce in the prehistoric past. But what if the classical East Asian appearance is relatively new? The Ainu, who have long been considered at “Lost White Race” turn out to be a basal Northeast Asian group. It may be that they retain more of the “ancestral” features of East Eurasians.

The first age of selection studies in the 2000s was fraught with confusion and false positives. To a great extent we still don’t know what to make many of the signals, which are deposited in the middle of obscure open reading frames. But the real golden age of selection will probably begin when we have more temporal transects with whole genome sequencing of ancient DNA, and with the phylogenomic context relatively robust as an interpretative framework.

* I am aware that the Hebrew Bible coalesced between thousands of the years after the arrival of Indo-Europeans to Europe, but it no doubt distills very ancient folkways. This seems obvious for example in the recollection of the Sumerian flood story.

 
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51IZQjMbVlL._SY344_BO1,204,203,200_ About four years ago the genome blogger Dienekes Pontikos published a post, The womb of nations: how West Eurasians came to be. The argument was that the genetic variation we see around us across western Eurasia and northern Africa has its ultimate roots in the the structure that was extant in the ancient Near East, near to the zone of initial agricultural innovation in the hills above the modern nations of Syria and Iraq. It was similar to the thesis of Peter Bellwood in First Farmers: The Origins of Agricultural Societies. The model as outlined by Dienekes suggested that local substrate was absorbed as these initial agriculture societies rapidly swept outward from their initial focal zone. In the broadest strokes I do think that he, and Bellwood, were correct from what we now know.

Ancient DNA in Europe strongly indicates massive replacement. But, there is also suggestion of admixture with the local substrate. And, unlike the stylized model of Bellwood, it seems that there were multiple migrations after the initial pulse which reshaped the genetic and cultural landscape of human societies in the wake of agriculture. Here is the abstract for Lazaridis et al. at ASHG:

It has hitherto been difficult to obtain genome-wide data from the Near East. By targeting the inner ear region of the petrous bone for extraction [Pinhasi et al., PLoS One 2015] and using a genome-wide capture technology [Haak et al., Nature, 2015] we achieved unprecedented success in obtaining genome-wide data on more than 1.2 million single nucleotide polymorphism targets from 34 Neolithic individuals from Northwestern Anatolia (~6,300 years BCE), including 18 at greater than 1× coverage. Our analysis reveals a homogeneous population that is genetically a plausible source for the first farmers of Europe in the sense of (i) having a high frequency of Y-chromosome haplogroup G2a, and (ii) low Fst distances from early farmers of Germany (0.004 ± 0.0004) and Spain (0.014 ± 0.0009). Model-free principal components and model-based admixture analyses confirm a strong genetic relationship between Anatolian and European farmers. We model early European farmers as mixtures of Neolithic Anatolians and Mesolithic European hunter-gatherers, revealing very limited admixture with indigenous hunter-gatherers during the initial spread of Neolithic farmers into Europe. Our results therefore provide an overwhelming support to the migration of Near Eastern/Anatolian farmers into southeast and Central Europe around 7,000-6,500 BCE [Ammerman & Cavalli Sforza, 1984, Pinhasi et al., PLoS Biology, 2005]. Our results also show differences between early Anatolians and all present-day populations from the Near East, Anatolia, and Caucasus, showing that the early Anatolian farmers, just as their European relatives, were later demographically replaced to a substantial degree.

A somewhat different abstract was submitted for a meeting in Germany:

We study 1.2 million genome-wide single nucleotide polymorphisms on a sample of 26 Neolithic individuals (~6,300 years BCE) from northwestern Anatolia. Our analysis reveals a homogeneous population that was genetically similar to early farmers from Europe (FST=0.004±0.0003 and frequency of 60% of Y-chromosome haplogroup G2a). We model Early Neolithic farmers from central Europe and Iberia as a genetic mixture of ~90% Anatolians and ~10% European hunter-gatherers, suggesting little influence by Mesolithic Europeans prior to the dispersal of European farmers into the interior of the continent. Neolithic Anatolians differ from all present-day populations of western Asia, suggesting genetic changes have occurred in parts of this region since the Neolithic period. We suggest that the language spoken by the homogeneous Anatolian-European Neolithic farmers is unlikely to have been the same as that spoken by the Yamnaya steppe pastoralists whose ancestry was derived from eastern Europe and a different population from the Caucasus/Near East [Haak et al. 2015], and discuss implications for alternative models of Indo-European dispersals.

And now, David has a post up, Yamnaya’s exotic ancestry: The Kartvelian connection. You can read the post yourself, but he presents TreeMix results which strongly imply that the Near Eastern gene flow into the Yamnaya population derives from one with a relationship to modern Kartvelian groups, the most prominent of which are Georgians. This is not entirely surprising. I’ve seen similar things, though I’m not sure what to think of this. Going back to Dienekes’ post he suggests that “It is, perhaps, in the ancient land of the Colchi, protected by the Black and Caspian seas, and by tall mountains on the remaining sides, that something resembling the ur-population survived.” That is, the people of the trans-Caucasian region may preserve elements of the deep ancestral heritage of the Middle East which was to some extent effaced by later migrations. I have some Assyrian genotypes, and this population has strong affinities with Armenians and Georgians. Additionally, I believe that much of the west Eurasian heritage in South Asians is from this same region and source. In Genetic Evidence for Recent Population Mixture in India the authors note that “For all 45 Indian groups on the Indian cline…we find that Georgians along with other Caucasus groups are consistent with sharing the most genetic drift with ANI [Ancestral North Indians -Razib].” Of course in South Asia there was a second intrusion of this sort of ancestry, but in this case as part of the admixed compound brought by Indo-Europeans, who interleaved Near Eastern, ancient European, and Central Asian, all in one.

There are two elements here which need to be noted. First, a genetic one in regards to the Middle East. In Europe over thousands of years the heritage of the first farmers waned, as that of the hunter-gatherers experienced some resurgence, and eventually the Indo-Europeans from the steppe overran vast territories. In the Middle East analogous groups which expanded out of the ancient hillocks and swept south were overwhelmed by a later Arabian reflux. These are perhaps prefigured by the drifting of Amorites into the cities of ancient Mesopotamia 4,000 years ago, and more recently the arrival of Arabs who had been outside of the limes of civilization into the worlds of eastern Rome and western Persia.

Finally, this is about the nature of culture and the advantage which a particular toolkit does, or doesn’t, provide a people. The rollover of European hunter-gatherers, or the fact that “Ancestral South Indians” (ASI) don’t exist in pure unadmixed form, point to the advantages which a fully elaborated agricultural cultural system provided the farmers. But, during the initial stages of the development of this toolkit it does not seem that there was any particular advantage to single group in a narrow delimited zone. To be more concrete, the linguistic diversity of the Caucasus region, or what we see and know from the edges of history in the Near East, may be close to the reality of the period of the early Neolithic in the Near East. Different polities with radically different languages, and likely divergent genetics, were all crystallizing the new lifestyle in a cheek by jowl fashion in the hills between the Tarsus and Zagros mountains. At some point though the system became powerful enough that it was portable and extendable in space. Rather than engaging in inter-group competition against populations which were comparable, the most successful route was to expand outward into the vast “unoccupied” zones of hunter-gatherers.

Because of the nature of climate west and east migrations were probably easiest and more rapid. Likely this resulted in a near total translocation of the ancestral cultures on far shores or distant horizons. But as the groups pushed north or south the agricultural toolkit was less well suited, and so synthesis with the native substrate was necessary. I believe that Indo-European and Afro-Asiatic may both be language families of hunter-gatherer populations who absorbed migrating farmers into a radically different ecology where the competitive playing field was much more level than in the initial zone of expansion.

 
• Category: History • Tags: History 
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51cVPyo9rQL._SX331_BO1,204,203,200_Angkor Wat is an icon of architecture. Arguably one can speak of it in the same breath as the pyramids of Giza or the Taj Mahal. Angkor Wat is a concrete manifestation of the apogee of Khmer civilization, which extended to the Chao Praya to the west, and the estuary of the Mekong to the east, at its height. As is evidenced by the fact that it began its life as a Hindu temple complex, Indian influences bled deeply into the high culture of much of mainland Southeast Asia during the centuries before 1000 A.D.. The king who initiated the building of Angkor Wat had the throne name Suryavarman. Its South Asian cadence is pretty unmistakable.

Today mainland Southeast Asia to the west of Vietnam is dominated by Theravada Buddhism, not Hinduism. But the Indian tincture persists. Theravada Buddhism is the dominant religion outside of Southeast Asia in only nation, Sri Lanka, in South Asia. Additionally, Southeast Asia harbors the world’s only native Hindu ethnic groups outside of the Indian subcontinent. Famously the Balinese of Indonesia, and less well known, the Hindu Cham of Vietnam, as well as various Javanese communities such as the Tenggerese (there are animist groups which are aligning with Hinduism in Indonesia, but that’s a recent phenomenon). The kings of Thailand strongly support the Theravada Buddhist religion, but their courts also sponsor the services of Hindu Brahmins. And the native scripts of Southeast Asia tend to have to South Indian origins.

This world of “Greater India” shattered in the centuries between 1000 and 1500 A.D. The rise of Islam along the Straits of Malacca in the century or so after 1000, and the eventual spread of the religion until it broke through to the interior of Java in the 16th century, is well known. But nearly contemporaneous with the rise of Islam in maritime Southeast Asia mainland Southeast Asia was subject to a massive migration of Tai warbands. Anyone curious about the whole story is recommended to read Strange Parallels: Southeast Asia in a Global Context, c. 800-1830. The author works through the slow process of nation-state formation in the 2,000 years between prehistory and modernity. The varied indigenous polities dealt with the challenge ways. In the west the Tai established a foothold, but could not overwhelm the Burman or Mon societies and political institutions. The Shan states were born. In the east, in Vietnam, the Tai were repelled or assimilated in totality. In fact, the Vietnamese absorbed Champa on the central coast, and began their long push toward the Mekong delta, expanding Sinic civilization at the expense of Indic (the Vietnamese emulated the Chinese model, and their popular religious cults were based on Mahayana Buddhism). In the center the Tai were victorious in near totality. Modern day Thailand, like modern day France, takes the name of its conquerors. And like the Franks the Thai absorbed most of their high culture from the Khmer and Mon whom they defeated. Unlike the Vietnamese, the Thai did not emulate Sinic forms of governance or promulgate Confucian ideology. Rather, the Tai warriors took on the mantles of the Khmer kings, and became sacral kings in an Indian sense, just as the long-haired Merovingians became bathed in Romanitas with their conversion to Catholic Chrisitanity. Though unlike the Franks, and like the Anglo-Saxons, the militarized bands maintained their linguistic identity, until their language superseded the Mon and Khmer dialects previous dominant. Modern day Cambodia only exists in large part because European colonialism sheltered it from total absorption into the Siamese Empire, which was digesting it in pieces when the French absorbed the Khmer monarchy.

Li, Jun Z., et al. "Worldwide human relationships inferred from genome-wide patterns of variation." science 319.5866 (2008): 1100-1104.

Li, Jun Z., et al. “Worldwide human relationships inferred from genome-wide patterns of variation.” science 319.5866 (2008): 1100-1104.

Which finally brings me to the presumption of cultural diffusionism. The impact of Indian culture on Southeast Asia is undeniable. But that does not necessarily entail that Indians, as people, engaged in migration. The Chola invasion of Sumatra in 1025 is viewed as a somewhat singular event. Though there are legends of Indian ancestry of the Khmer kings, these can easily be chalked up to the sort of foundational myth-making which is normal for many cultures (e.g., descent from the House of David or Trojans were common for European noble houses). Though there are plenty of historical references to the ancestors of the Peranakan Chinese going back to Zheng He’s voyage, references to Indians are fewer, and must be gleaned through their cultural influence, both Dharmic and Islamic. After all, Christianity spread in Europe not through migration, but through conversion. Similarly, Islam also spread through the conversion of elites in Sub-Saharan Africa, and Central and Southeast Asia.

I no longer think cultural diffusion is the only explanation for why Hinduism and Indian civilization struck such deep roots in Cambodia. Rather, I think it is clear that there was a migration of people whose ultimate origins were in South Asia. The arrival of South Indian motifs to Southeast Asia was accompanied by South Indian people, and in some areas lots of them (or at least enough that their outsized demographic impact left its mark). We need to move beyond an excessively strong null hypothesis of cultural diffusionism. Migrations can echo down the generations and across continents. The agro-pastoralism triggered by the expansion of farmers out of the Near East thousands of years ago eventually cascaded all the way down to the South African Cape, and the genetic signal of these Eurasians is present in the Khoe people (almost certainly mediated by Nilotic pastoralists who pushed in from East Africa).

The evidence of Indian genetic imprint on Cambodia has been staring us in the face for nearly 10 years. Above is a STRUCTURE bar plot from the paper which brought the HGDP-CEPH panel into the post-genomic era. They took their 650,000 SNPs, and allowed STRUCTURE to assign ancestral quanta to each individual given a particular value of K populations. One thing that caught my eye immediately was the Cambodian affinity to South Asians. The bar plot generated a component, light blue, which was modal in South Asians from Pakistan. The Cambodians had low levels of this. The other Southeast Asian groups did not exhibit any signal of this ancestral component.

When Joe Pickrell came out with TreeMix he saw this:

Two inferred edges were unexpected. First, perhaps the most surprising inference is that Cambodians trace about 16% of their ancestry to a population equally related to both Europeans and other East Asians (while the remaining 84% of their ancestry is related to other southeast Asians). This is partially consistent with clustering analyses, which indicate shared ancestry between Cambodians and central Asian populations…To confirm that the Cambodians are admixed, we turned to less parameterized models. The predicted admixture event implies that allele frequencies in Cambodia are more similar to those in African populations than would be expected based on their East Asian ancestry.

I asked Joe whether he thought that this admixture had something to do with “Ancestral South Indians” (ASI). He said it was plausible. But I didn’t follow up on this at the time.

Recently a friend asked me to project his genotype on a PCA of Southeast Asian and Northeast Asian populations. For kicks I decided to throw in people who were not of non-East Asian ancestry. Myself, and a few friends who were mostly European. What I did was place the individual genotypes on top of the variation of the target populations. If I didn’t do this then my white friends and myself would just hog up the first PC as non-East Asian vs East Asian. To my surprise all of us non-East Asians landed right on top of the Cambodian cluster (I was shifted toward other Southeast Asians though, which is reasonable given my genetic background). I had naively assumed that we’d just land on the (0,0) position, except for me, who would be somewhat shifted off, because most of us would be symmetrically related to all these East Asian groups.

What was happening though was that something in the Cambodians was capturing genetic variation in individuals with West Eurasian ancestry. We now know that groups in the STRUCTURE plot above which are nearly 100% “South Asian” are actually highly skewed toward “Ancestral North Indians” (ANI), which is a West Eurasian group. It seemed implausible that the Cambodian signal would be due purely to shared ASI-like ancestry which was present from the Indus to the South China Sea before the incursions of agriculturalists from the northwest and northeast.

An initial hypothesis is that these individuals are admixed with Indians who arrived during the period of European colonialism. But there are problems with this. Historically there were many Indians who arrived in Burma and Malaysia. But far fewer in eastern mainland Southeast Asia. Additionally, observe that the Indian admixture in the Cambodian samples is relatively similar in fraction across all the individuals. That’s a major tell that the admixture is old enough for it to have distributed itself across the population.

As I implied above I have a private data set of Cambodians, with a sample size larger than the HGDP. I also have Filipinos and Vietnamese. I combined them with 1000 Genome data sets, and produced the plot below:

Rplot12 Click the figure to see what’s going on, but it’s pretty straightforward. PC1 separates Eurasia on a east to west axis. My North Indian population of Punjabis is at the top right. Then at the far left are crammed Japanese, Koreans, and North Chinese. At the bottom are Papuans from the HGDP. What’s interesting to me, and suggestive, is that the Cambodians are the most West Eurasian shifted of the East Eurasian populations. The Filipinos also exhibit a cline, but they are shifted toward the Papuans. As you may know there are “Negritos” in the Philippines, and their non-Austronesian ancestry has affinities to that of Melanesians. Following the convention in archaeology I will refer to the Negrito people as “Austro-Melanesian.”

In a 2011 paper David Reich’s group posited that there are two major groups of Austro-Melanesians. One clade consists of the Andaman Islanders and the Negrito people of inland Malaya, and another component is found among the Philippine Negritos and the peoples of Near Oceania, the Melanesians and Australian Aboriginals. These results are not consensus. But, they suggest that the history of pre-agricultural Southeast Asia is likely to be complex.

Of course I ran TreeMix on the data (170,000 markers with very little missingness):

CambodianOut.10 CambodianOut.9 CambodianOut.8 CambodianOut.7 CambodianOut.6 CambodianOut.5 CambodianOut.4 CambodianOut.3 CambodianOut.2 CambodianOut.1

First, a minor point. I included the 1000 Genomes Bengali data set mostly as a positive control. I wanted to make sure TreeMix was behaving right. Well, I think I found out something new that pushed forward the conclusion I came to in my earlier post, the East Asian ancestry in Bengalis can’t just be due to old Austro-Asiatic admixture. I didn’t add any Chinese samples in the original analysis because it seemed clear to me that they wouldn’t be relevant. Well, if you look through these TreeMix results you see that the gene flow edge is actually often between the Southeast Asian groups and the Southern Chinese! I think this points to something of the composite nature of the admixture. It was probably a Tibeto-Burman group which had absorbed Austro-Asiatic elements along the way.

The second issue is that the Cambodians consistently have a gene flow arrow coming from a population that is related to the Indians. I added the Papuans specifically to pick up the Austro-Melanesian signal. The archaeology and mtDNA strongly indicates that a substantial minority of the ancestry of Southeast Asians derives from the pre-agricultural Austro-Melanesians. The Austro-Asiatic groups were the first to arrive, so it makes sense if they have the highest fraction of Austro-Melanesian ancestry. Stereotypically Cambodians are darker skinned and curlier haired than their Thai and Vietnamese neighbors.

That being said, how can we rule out the possibility that this gene flow isn’t due to ASI-like ancestry shared between Indians and Cambodians? After all the gene flow edge derives from near the root of where the Indian and Papuan clade diverge. I decided to add another population, which I will label “ASI-rich Indian.” I basically took the data from the Estonian Biocentre and yanked out individuals which didn’t have East Asian ancestry but had more ASI than my middle-caste South Indian data set. Most of these populations where South Indian Dalit or Tribes. Perhaps this population would be a better fit to the donor group for the Cambodians?

Cambodian3Out.7 Cambodian3Out.8 Cambodian3Out.9 Cambodian3Out.10 Cambodian3Out.4 Cambodian3Out.5 Cambodian3Out.6 Cambodian3Out.1 Cambodian3Out.2 Cambodian3Out.3

Well that didn’t help! Now the Cambodians are often just a basal Indian populations with a lot of Dai admixture. Adding the ASI-enriched group just made the tree more Indo-centric, so it put the Cambodians on the Indian clade. Let’s narrow the set of populations under consideration.

CambodianNarrowOut.9 CambodianNarrowOut.10 CambodianNarrowOut.2 CambodianNarrowOut.3 CambodianNarrowOut.4 CambodianNarrowOut.5 CambodianNarrowOut.6 CambodianNarrowOut.7 CambodianNarrowOut.8

OK, that’s better. Two things:

1) The Indian-like gene flow to the Cambodians is clear. It’s more Indian-than-Papuan.

2) The Filipinos now have a Papuan-like gene flow. This could be because of the Austro-Melanesian connection between these two groups. Remember the Reich paper above indicated that they had shared ancestry which was distinctive from that of the Austro-Melanesians who contributed to the ancestry of mainland groups (and distantly to Indians).

Next I decided to add Australian Aboriginals and Taiwanese Aborigines into the analysis. These are related populations to some of the ones already in the data set.

CambodianOzOut.10 CambodianOzOut.3 CambodianOzOut.4 CambodianOzOut.5 CambodianOzOut.6 CambodianOzOut.7 CambodianOzOut.8 CambodianOzOut.9 CambodianOzOut.1 CambodianOzOut.2
CambodianNarrowOut.1

OK, the patterns reoccur, and the relationship between the sister clades is what we’ed expect. Though TreeMix does not tell us time, the fact that the gene flow into the Filipinos from the Oceanians is below the node where Papuans and Australians diverge probably suggest that the Austro-Melanesians of maritime Southeast Asia diverged more than 10,000 years ago. That’s pretty reasonable if you follow the natural history.

Finally, I’m going to remove Indians, and put in a true West Eurasian population: Armenians. I select Armenians because I think they’re close to the ancestral population of ANI which resulted in the non-Brahmin populations of Southern Indian (and to a large extent Northern India). I believe that the Indo-Aryans were a secondary migration which had an impact on the upper castes and the Northwest. Since the cultural connections of Southeast Asian Indian culture are to southern, not northern, India, the West Eurasian affinity would ultimately be from this region. I don’t have Y or mtDNA data on most of the Cambodian samples, but I do have Y on three of them. And one of those is Y chromosomal lineage J2. That’s commonly found in West Asia, and among some groups in South Asia. Additionally, Y haplogroup group H is found among the Khmers. This haplogroup is modal among low caste and southern Indian populations.

CambodianNWAsiaOut.2

CambodianNWAsiaOut.3

CambodianNWAsiaOut.4

CambodianNWAsiaOut.5

CambodianNWAsiaOut.6

CambodianNWAsiaOut.7

CambodianNWAsiaOut.8

CambodianNWAsiaOut.9

CambodianNWAsiaOut.10

CambodianNWAsiaOut.1

It’s not consistent, but it does look like the gene flow into Cambodians has West Eurasian affinities. Remember, the PCA that I mention above already suggests this. ASI, of whom the Andaman Islanders are a cousin lineage, are not any closer to Europeans than East Asians. East Asians and Southern Eurasians seem to form a very deep clade as contrasted to West Eurasians. The affinities are deep in the Pleistocene, but they’re there (e.g., mtDNA haplogroup M instance). That’s why those South Asians with more ASI ancestry get pushed “east” along the PCA plane. Mind you, I think that really there are two admixture events in rapid sequence. First, the Austro-Asiatic farmers spread across Southeast Asia 3 to 4 thousand years ago, and mixed with Austro-Melanesian groups. These are sister lineages to ASI and Andaman Islanders. Then, 1 to 2 thousand years ago you have a gene flow event mediated by a large number of South Indians. The admixture is probably smaller in magnitude than that of Austro-Melanesians. That’s probably why the gene flow edge keeps getting dragged toward the Papuans: you are seeing a composite edge of two admixture events which occurred sequentially.

This is all rather strange, and I hope that those with some knowledge of Southeast Asian history can not take in the new evidence and wonder how it affects previous interpretations. Those Indian warlords in Khmer myth may not be so mythical after all!

51NYNCV761L._SY344_BO1,204,203,200_ When making the case for the monopoly of Christianity on the public space of late antiquity St. Ambrose famously declared to the pagan senator Symmachus that “There is no shame in passing to better things.” St. Ambrose more broadly was setting the precedent for religious intolerance of falsehood, and exclusive promulgation of one singular truth from on high. The Christians of that period were clearing away the organically accrued institutions and folkways of pagan antiquity, sweeping aside the detritus and making it clean in their eyes. They believed that history was on their side, and they did not look backward. How times change. Just as the most confident of the New Atheists declare that humanity’s childhood is nearing an end, and so the need for God, so the Christians of antiquity believed that in their religion the revelation of the prophets and insights of the philosophers came to maturation. It was time to put childish things behind us.

In some ways Thor Heyerdahl is one of those “childish things.” Heyerdahl was active in my childhood. And despite being an old man his imagination was still fertile. I recall reading some of his books, and laughing even then. It struck me that his bizarre theories were no better than speculations about Lemuria. Here was a Madame Blavatsky for our age!

To some extent I’m being unfair to Heyerdahl. Some of his ideas were genuinely crazy, but he was pushing the envelope of speculative possibilities. He was a thinker who would have been more at home in the late 19th century, though no doubt his life would have been at risk since he almost certainly would attempt to discover “Lost Civilizations” in the heart of Africa. Heyerdahl was attracted to those “blank spaces” on the map, and in his adulthood those zones were filled in. The eye of the satellite became the all-seeing eye of Sauron. So he fled to the past, and wove speculations from his amorphous diffusionism. He posited strange and implausible contacts leading to syntheses between diverse peoples.

Well, he had a point. I believe that perhaps it is time to turn time back. Just as the Christ of St. Ambrose is now receding from the public spaces of Western civilization, becoming another cult among cults, so the clean and singular vision of archaeology and prehistory after World War 2 needs a reformation. Here is a question: would we believe that the Malagasy could exist if they did not exist? That is, would we think it possible that a small group of Austronesians from southern Borneo would somehow be the first humans to settle the great island off the southeast coast of Africa? It’s so fantastical I doubt it. The clear cultural impact of Malayo-Polynesians on East Africa is only plausible because the Malagasy exist. Otherwise they’d have been explained away. In addition, there is now suggestive evidence of pre-Columbian Polynesian and South American contact.

On the edges of history, in the lacunae between where text speaks to us, there were occurrences which would surprise us. The genetics sends clear signals that our race of adventurers and travelers continued to mingle and find ways to interact even after the emergence of great agricultural civilizations.. We have always sought out the “blank spaces” on the map, and filled them in our imaginations.

Postscript: Well, this post took half my day. About half running the analyses and generating the input data sets. And the other half writing. It’s a pretty strange world we live in! Special thanks to Chris Chang, whose new version of Plink is so fast and has so much incredible functionality. It really speeds up the process of data exploration. And similarly, a shout out to Joe Pickrell, whose TreeMix is truly addictive.

 
• Category: Science • Tags: Cambodia, History 
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TaylorSwiftApr09 William Dalrymple in The New Yorker has a reflection up on the 1947 partition of the subcontinent, The Great Divide. It is fine so far as it goes. He reminds us of the scale of the tragedy, millions of deaths, as well as the depravity of the barbarity, as “infants were found literally roasted on spits.” Some day I will have to educate myself about this period, as I only have vague recollections of reading fragments of Freedom at Midnight as a child. I recall stopping at the point where the authors reported how a group of men broke into an obstetrics unit at a hospital and took a newborn who had just breathed their first and smashed its brains out on the walls, while the mother and hospital staff watched in horror. That was enough to get a flavor of the “action.” Fortunately my family did not suffer during this period, Bengal was relatively quiet in comparison to the atrocities washing over Punjab (as many of you are aware, my family experienced more hardship in the 1971 war, though as they were relatively privileged Muslims who were also not very involved in the arts or politics they were not actively targeted).

But there is one section whose assumptions and implications rub me the wrong way. Let me quote:

In the nineteenth century, India was still a place where traditions, languages, and cultures cut across religious groupings, and where people did not define themselves primarily through their religious faith. A Sunni Muslim weaver from Bengal would have had far more in common in his language, his outlook, and his fondness for fish with one of his Hindu colleagues than he would with a Karachi Shia or a Pashtun Sufi from the North-West Frontier.

Many writers persuasively blame the British for the gradual erosion of these shared traditions. As Alex von Tunzelmann observes in her history “Indian Summer,” when “the British started to define ‘communities’ based on religious identity and attach political representation to them, many Indians stopped accepting the diversity of their own thoughts and began to ask themselves in which of the boxes they belonged.” Indeed, the British scholar Yasmin Khan, in her acclaimed history “The Great Partition,” judges that Partition “stands testament to the follies of empire, which ruptures community evolution, distorts historical trajectories and forces violent state formation from societies that would otherwise have taken different—and unknowable—paths.”


k7191
Ten years ago I read Nicholas Dirks’ Castes of Mind. It is a work of history which shows how many caste identities were fashioned de novo under the impetus of British bureaucratic taxonomic impulse (see Census of 1891). Though Dirks is too subtle to assert that the caste system was created by the British, the general thrust of the work is clearly one which emphasizes the role of recent historical contingency in establishing the social order of South Asia as we understand it. The subhead is after all: “Colonialism and the Making of Modern India.” The British are then the agents who operate upon the formless void of the Indian subcontinent’s amorphous peasant culture. They came, they saw, and they created.

Even when I read Castes of Mind I was moderately skeptical of the narrative, as there had been enough genetics done to suggest that South Asian populations were stratified by caste. By this, I mean that caste status as much, or more, than geography predict the genetic structure of Indian society. It was already evident, for example, that South Indian Brahmins were closer to North Indian Brahmins than they were to South Indian Dalits when it came to genetic relatedness. Brahmins and Dalits are two caste groups which are clear and present throughout South Asia (the “middle castes” tend to vary from region to region, and the classical warrior and trader castes do not exist in South India, though there are notionally Sudra groups which occupy their roles). Even those who prioritize the role of the British would accept that the Brahmin and untouchable categories predate the reification of the colonial period. But what the latest genetics is telling us is that caste endogamy has been a feature of Indian life for at least 2,000 years, and perhaps longer. Not only are Brahmins distinct from Dalits, but castes with a less clear position in the classical varna typology, such as the Reddy community of South India, clearly have had long histories as a coherent groups. The British could not have been the dominant causal force in shaping caste as a ubiquitous feature of Indian life if they were already genetically endogamous even before the Muslims arrived.

And so with religion. The contemporary revisionism, which now is approaching mainstream orthodoxy, is that South Asian religious life before the arrival of the British, and the Western outlook more generally, was characterized by a quietist syncretism where communal boundaries were fluid to the point of confessional identity being a flimsy veil which could be shed or shifted dependent upon context. An alternative history then might be proposed of a united subcontinent, where Hindus and Muslims were coexistent, or, perhaps where a Hindu and Muslim identity did not even exist. The cognitive psychologist Pascal Boyer likes to characterize a theory as giving you “information for free.” You don’t really have to know anything, you can simply deduce from your axioms. Though the model of South Asian ethno-religious history I allude to above obviously integrates ethnographic and historical realities, it constructs a post-colonial fantasy-land, where South Asian religiosity was without form or edge before the arrival of Europeans and their gaze collapsed the wave function. Before the instigation of Europeans people of color were tolerant of religious diversity, varied sexual orientations, and practiced gender egalitarianism. In other words, India was like the campus of Oberlin college, except without the microaggressions, and more authentic spirituality!

51J39W7ZRFL._SX306_BO1,204,203,200_ The first problem with this model is empirical and specific to South Asia. Before white Europeans arrived in the Indian subcontinent to roil and upend its social order, to transform its culture, there was already a ruling race of self-consciously white people doing just that. They were the Turks, Persians, and a lesser extent Arabs, who introduced Islam to the subcontinent. As alluded to in Dalyrmple’s piece in some ways Islam was conceived of as a sect of the foreigners by the natives, as well as the Muslims themselves. This is not an entirely strange state of affairs, in the first century or so of Islam the religion was the tribal cult of the Arab ruling caste of the Caliphate. Only with the rise of the Abassids and maturation of Islamic civilization as a pan-ethnic and post-ethnic dispensation did the “converted peoples,” in particular the Persians and Turks, become full members of the Ummah, and turn it into the universal religion that we understand it today (though even today there is an ethnic dimension in Islam, for example, the Islamic State accepts that the Caliph must be an Arab of the Quraysh tribe).

For many centuries Islam in South Asia recapitulated this pattern ancient pattern, whereby those who descended from converts were received as second class citizens (and still called “Hindus,” which simply meant a native of Hindustan). And to this reality must be added the dimension of race, for the Muslims from the west viewed the native peoples as black, and many elite families with origins in Persia and Central Asia maintained their endogamy for generations partly as a matter of racial hygiene. When Muslim elites did intermarry with the descendants of converts, it was invariably with those descended from high caste groups. The Mughal Emperors did wed women from Hindu backgrounds, but these were the daughters of powerful Rajputs, whose values and armies fused with the Muslim invaders to create what we understand as Islamicate civilization.

Yet there are many other stories besides the standard one of the rise and fall of Mughal India. In Crossing the Threshold: Understanding Religious Identities in South Asia, the author shows how the arrival of Islam in the subcontinent often involved a complex process of cultural interaction mediated by esoteric strains of the Ismaili sect. It is not relevant for the purpose of this post to review the nature of Ismaili Islam, but it is important to note that Sunnis view this group as deviant and marginally Muslim. With the arrival of the Mughals there began a long period of persecution of Ismailis in the Indian subcontinent as the new arrivals attempted to enforce conformity on the Muslim population. Both Crossing the Threshold and Mullahs on the Mainframe, an ethnography of a particular Ismaili sect in Gujarat, report that many of the Sunni Muslim communities of the subcontinent may be descended from people who entered Islam via Ismailism. Under the Mughals heterodox Muslim sects like the Ismailis were subject to more persecution than non-Muslims (this echos a similar dynamic in Late Antiquity, where more of the Christian animus was directed toward heretical sects than pagans). In Gujarat this resulted in mass conversions to Sunni Islam. In other regions it might have resulted in a “compromise” state of shifting to a Twelver Shia identity, which though not Sunni, was generally accorded more respectability than Ismailism. These people would be anticipating the life of Muhammad Ali Jinnah, whose recent ancestors (most accounts state his grandfather) converted from Hinduism to Ismailism, but who himself was an entirely irreligious man who avowed a Twelver Shia faith for purposes of formality.

The author of Crossing the Threshold suggests that for many centuries there existed in the subcontinent under the more tenuous and patchwork pre-Mughal Islamic rulers many liminal communities, which straddled the line between Muslim and Hindu. So long as the Muslims of the Indian subcontinent viewed themselves as strangers in a land which offered them opportunities for profit, there was a certain freedom in being viewed as an amorphous black-skinned mass of “Hindus” whose only importance was in the tax that they provided their overlords. The Mughals changed that. Though they were in origin Timurid princes from Central Asia, their long ascendancy in the subcontinent produced a genuine synthesis with the indigenous substrate. By the later years of the dynasty their symbolic and ceremonial roles as Emperors of India became so entrenched that even resurgent Hindu groups such as the Marathas retained the Mughals as figureheads, much as the Zhou dynasty persisted for centuries after its genuine preeminence had faded.

516ZEEEK2XL._SX332_BO1,204,203,200_ Over the 150 years that the Mughals dominated South Asia with their armies they also changed the nature of Islam in the subcontinent thanks to their broader connections. The Naqshbandi Sufi ordered was associated with the dynasty, and objected when rulers such as Akbar bent or rejected what they perceived to be Sunni Islamic orthodoxy. And the Naqshbandi were in a place to judge what was orthodox, as they were an international order with branches across Sunni the Muslim world. The historian S. A. M. Adshead discusses the role of what he calls the “Naqshbandi International” in binding the Islamic world back together after the shattering of the Mongol invasions in Central Asia in World History. It was no coincidence that attempted to root out deviancy and enforce what they saw to be uprightness.

China was another zone of Naqshbandi influence. Unlike India China proper had (and has) never been ruled by Muslims. After period of prominence under the Yuan (Mongols) the Muslim groups became another minority, tolerated by the Han Chinese, but viewed with curiosity and confusion. While the Muslims of what is today called Xinjiang were part of the Turkic world, and even when conquered by the Manchus administered as a separate domain from China, those resident in the east were relatively isolated from the Ummah, and swam in a Han sea. The Dao of Muhammad: A Cultural History of Muslims in Late Imperial China tells the story of the intellectuals among the Muslims of eastern China, who were confronted with accommodating the reality that they existed at the sufferance of non-Muslims, and could only advance to prominence and prosperity playing the game according to the rules of the Han majority. At the popular level in places like Ningxia there emerged Muslim apocalyptic movements which bore a striking resemblance to heterodox variants of Pure Land Buddhism, but among the intellectuals there arose the conundrum of how to render compatible orthodox Islam and Neo-Confucianism. So long as China was reasonably isolated from the rest of the world, this process dynamic proceeded without interference and followed its own logic. What emerged can reasonably be described as a synthesis between Islam and Neo-Confucianism, which resembles in its broad outlines the sort of fusion which occurred in early Christianity after the ruling elites took up the religion and imparted upon it their own philosophical presumptions. Just as some Christians perceived in their religion the completion of the project of the ancient Greek philosophers, so Hui Muslim intellectuals in the cities of eastern China in the 18th century saw in Islam not the overturning of Chinese culture, but its extension and perfection.

Suffice it say this movement among educated Chinese Muslims did not give fruit to a vital modern tradition. Several waves of Islamic reform have blasted into China from the outside world, first from Central Asia, and later from the Middle East proper in the age of modern transport and pilgrimage. The Islamic-Confucian synthesis in its full elaboration was a stillborn sect, pushed aside by the popularity of world normative Islam and the decline in prestige in the 19th and 20th century of Neo-Confucianism. Similarly, the Islamic-Hindu synthesis championed by the Mughal prince Dara Shikoh and prefigured by his great-grandfather Akbar, was forestalled by the emergence of Aurangzeb. Remembered as pious and steadfast by many modern day Muslims, he is reviled by Hindus, and most Western historians, who perceive that the sun set on religious pluralism due to his actions, seem to take a dim view of him. But Aurangzeb was closely associated with the Naqshbandi over much of his life, and he may be less important to the broad social movement of South Asian Muslims being drawn into an international system, with a standard set of beliefs and practices, than we think. Rather, Aurangzeb’s life arc may be consonant with both the indigenization of Islam in the subcontinent, and its need to align itself with external norms.

513yXnWcqDL._SX322_BO1,204,203,200_ Though I use the Indian subcontinent as my primary illustration, the dynamic is likely more general. In The Next Christendom: The Coming of Global Christianity Phillip Jenkins notes that though many claims are made for indigenous African churches, that is, those which have no connection to global denominations and movements and tend to more freely integrate African practices, as African societies become more Christianized they tend to become more mainstream and orthodox in their affiliation. What Jenkins is observing is that with development and modernity indigenous and local practices tend to fade into the background, as African Christians become influenced by the ideas and traditions of Christians from other regions of the world. Individuals who consider themselves part of a religious community start to adhere to the practices and norms of that community’s history.

Despite the homogenization and delineation of identity categories in India there are still liminal communities in the mode envisaged by Crossing the Threshold. The Meo people of Northwest India are Muslims who maintain many Hindu traditions. But the trend among the Meo is to become progressively “more Muslim,” and those Meo who leave their homeland assimilate into the conventional Sunni Muslim milieu and lose their distinctiveness. The Ismaili Khoja community of India is another example of a Muslim group with many Hindu customs and beliefs which has become more “orthodox” within historical memory. In this case the arrival of their spiritual leader, the Aga Khan, from Iran in the 19th century seems to have triggered an Islamic reformation of views and mores. And just as there may have been many groups which moved toward a more standard Muslim identity, there were likely those who became more self-conscious in their Hinduism, as that tradition coalesced as a negation of the exclusive confessionalism of Islam. The Hussaini Brahmins customarily participated in Shia Ashura, and have an origin story which places them at Karbala on the side of the sons of Ali. As noted above it was not unknown for high caste Hindus to enter Islam and intermarry with the Muslim nobility. Over time their Hindu origins may have been obscured, as they constructed wholly Muslim origin narratives. The Hussaini Brahmin community might illustrate a case where the process was halted, and reversed, albeit with a retention of some of their Islamic practices and beliefs. In Crossing the Threshold the argument is made that it the critical aspect for the Sunni Muslim eminences enforcing the new orthodoxy was that Muslim and non-Muslim be clear and distinct categories. Therefore, better a Hindu than a heretic.

51k6n6ma-NL._SY344_BO1,204,203,200_ What have I left out of the story? Note that white Europeans are notably absent from the narrative. To some extent this is an artificiality. European “factories” were present on the margins of Mughal India. Jesuits supplanted Muslims as astronomers in the court of Ming China, and were disputants on religious topics in the court of Akbar the Great. Christianity, Islam, and Buddhism, were all closely associated with each other in Central Asia, to the point where it is difficult to tease apart the arrows of causality. In China it seems likely that some varieties of Christianity with ultimate roots in Persia and Central Asia were subsumed into strands of Pure Land Buddhism. But, the point is that history and peoples are subject to general patterns and dynamics, and European colonialism may be thought of as just one important contingent factor. A critical one, but one factor nonetheless.

41JdP75Eu8L._SX321_BO1,204,203,200_ It is hard to deny the influence of European culture and Christianity on Indian national and religious worldviews. Consider Hindutva. Conceived of as a form of Hindu racial nationalism by Vinayak Savarkar, himself an atheist who advocated the dismantling the caste system, it is difficult to understand it without considering the dominant winds of culture in the early 20th century. Those winds invariably blew out of Europe. The colonial imprint, the mirrored reflection of British racial nationalism, is real. Today the intellectual descendants of Savarkar promote bizarre beliefs like the idea that ancient Hindus had flying machines and nuclear weapons, and that astrology is a true science and Ayuvedic medicine is superior to that of the West. It is hard not to see in these beliefs a funhouse distortion of Western movements, such as Christian Science and Creationism. Similarly, the Islamic Creationism of Harun Yahya is explicitly indebted to American evangelical Protestants!

And yet within South Asia the broad trend of confessionalization predates the arrival and dominance of Europeans. It seems entirely likely that a division between Islam and what became Hinduism in the subcontinent was inevitable, as modernity and globalization seem to produce crisper identity groups, which are not diffuse, inchoate, and locally rooted. Yes, illiterate peasant naturally practice syncretistic traditions, but when the illiterate peasant becomes a town dweller a different sort of religious practice takes hold. There is a reason that the city-dwelling Christians of the Late Antique world were contemptuous of the marginally Christianized peasantry, the pagani. The last European people to convert to Christianity were the Lithuanians, in the late 14th century. But the peasantry retained enough of their customary religion that veneration and recollection of sacred groves seem to have persisted down to early modernity.

51W2mxRBC9L._SX326_BO1,204,203,200_ The Reformed Dutch scholar Atonie Wessels wrote a book titled Europe: Was it Ever Really Christian? His thesis is that from an orthodox Protestant perspective which privileges the beliefs and practices of the individual, it can be argued that much of the European peasantry was operationally pagan down to the Catholic and Protestant Reformations of the 16th and 17th century, followed by the secularization of the continent that began after the Peace of Westphalia. In short, during the period after the fall of Rome and Renaissance the elites were steadfastly Christian, but peasants were only nominally so, with their spiritual life dominated by superstitions rooted in local traditions. In contrast, the emergence of Protestant and Catholic identities during the Reformation resulted in a broad based Christian feeling and identity among the populace. So much so that when the Hohenzollerns converted to Calvinism in the early 17th century their subjects remained steadfast in their Lutheranism. But as the populace became more conventionally Christian, the elites began their long slide toward secularism, finally resulting the rise to power of Frederick the Great, who in matters of religion was apathetic at best.

The European example is important, because it shows that even without exogenous European colonialism confessionalism occurs as a society modernizes. The seeds of this confessionalization are clear in South Asia even before the rise to power of the British raj, as Hindu rulers such as Shivaji privileged their own native traditions as against that of the Muslims, while earlier the rulers of Vijayanagar had served as patrons of native religion while the north of the subcontinent was dominated by Muslim polities. It does seem fair to state that Sanatani is not comprehensible without it dialectic with Islam. But, it is important to remember that Buddhism as an organized religion with a missionary impulse predates Christianity by centuries. Obviously institutional religious identity in the subcontinent is not dependent upon the ideas of Europeans and Muslims. What differed with the arrival of Islam is that it was a Weltanschauung which was not digestible to the native cultural traditions.

Though the various Muslim ruling warrior castes held themselves aloof from the people of India, being within the subcontinent, but not of it, it seems inevitable they presumed that their domains were now a permanent part of the Dar-ul-Islam, just as Iran or Central Asia was. Certainly Ibn Battuta could travel in an entirely Muslim India, which operated in parallel with the practices of the vast majority. Over time no doubt the Muslims assumed that the subcontinent would be won over as Iran had. It is hard to remember now, but in the first few centuries of Islamic rule there were periodic anti-Muslim nativist religious eruptions which attempted to overthrow the Muslims, who were perceived as aliens. Prophets arose which told of a time when Islam would fall, and the old religion of the Iranians would come back to the pride of place that it had had. A detailed exploration of this lost world can be found in Patricia Crone’s The Nativist Prophets of Early Islamic Iran, but these movements always make cameos in even traditional works of early Islamic history, such as Hugh Kennedy’s When Baghdad Ruled the Muslim World. But by 1000 A.D. the majority of Persian peasants were Muslim, and Zoroastrianism and its affiliated movements slowly went into their long decline (though still retaining influence through various heterodox Islamic and post-Islamic religious movements).

61H+zZL41QL._SY344_BO1,204,203,200_ In India you have a world where the vision of the Iranian prophets came to be, where Islam which seemed eternal and ever waxing in numbers and influence, lost its hold on power and native dynasties which championed local religious traditions arose. There are many differences between the situation of Iran and India. In no particular order, India is far more populous than Iran, local non-Muslim rulers always managed to retain independence at the far corners even at the height of Islamic power and dominion, and the cultural distance between the Muslims and the natives of India was arguably greater than that between the Arabs and the Persians. Even though the Iranians and northern Indians share Aryan cultural roots and influence, reflected in language and religious ideas, those are distant affinities. In contrast, the Arabs had long been present on the margins of the western Iranian world, and the ecology of much of Iran and Mesopotamia was familiar to them.

One peculiarity of the historiography of India under the Muslims is that many scholars claim that local intellectuals, mostly Brahmins, behaved as if their conquerors did not even exist. This sort of involution though may be less strange than seems on first inspection. Ashkenazi Jews in Central and Eastern Europe are to a great extent a people without a history, as their intellectual class devoted its energies to Talmudic commentary, not recording the history of their people. India was massive, and transformations were pregnant within its cultural matrix in response to the Islamic challenge. The Sikh religion seems an obvious case of synthesis, which while that of Hindu reformist movements such as Arya Samaj seem to sublimate the external variables.

61LXo6U7a4L._SX331_BO1,204,203,200_Though the British may have been a proximate cause for the communal conflicts that tore apart the subcontinent in 1947, they were not the deep cause. As Victor Lieberman observes in Strange Parallels: Europe, Japan, China, South Asia, and the Islands, after 1000 AD there arose several polities dominated by cultural aliens along the edge of Eurasia, such as that of the Muslims in India, the Tai in Southeast Asia and the Manchu in China. But unlike the latter two cases the Islamic elites never sufficiently rooted themselves in the local culture to establish a coherent and unified national identity. While the Manchu racial sense of distinctiveness persisted down to their overthrow, their cultural assimilation to most Han mores was so total that rulers such as Kangxi Emperor arguably became exemplars of Confucian rulers. Though the Tai imposed their language of the Mon and Khmer people whom they conquered, they fostered a genuine cultural synthesis by patronizing the Theravada Buddhism of their subjects and espousing it as their national religion. While the kings of Thailand patronized Brahmins to give their rule a tincture of Hindu legitimacy, the Mughals were styling themselves as Padishahs.

If Dara Shikoh had defeated Aurangzeb and the British had never brought India into their Empire, would history have been different? I would like to hope so, but I doubt so. Akbar had attempted to create a new religion, but it did not last beyond his life. By the 17th century what was becoming Hinduism, and Indian Islam, were already sufficiently developed that they were becoming cultural attractors. Not through cognitive bias, but the weight of inertia of their cultural history and precedent. The transition from Akbar, to Jahangir, to Shah Jahan, and finally Aurangzeb, is one from an individual who brooked the displeasure of Naqsbhandi shiekhs, to one who worked hand in hand with them. An alternative vision is one where the heirs of Akbar turn their back on their dreams of Fergana, and rely upon Rajputs to dominate their lands instead of a mix of Central Asians and native Indians, Hindu and Muslim. Perhaps the Mughals would have become indigenized enough that they would transform into that they would have become fully Indian in their religious identity. Ultimately the answers of history are more complex than can be dreamt of in your post-colonial philosophy, and the white man is neither angel nor the devil, but a subaltern of historical forces.

 
• Category: History • Tags: History, India, Religion 
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51KHpfTVbiL._SY344_BO1,204,203,200_ Let’s start at the beginning. If you read a book about Indian history in the 1980s it might begin with this sort of stylized narrative: in the beginning were the Mundas. Then there were the Dravidians, then finally the Aryans (and as an afterthought various East Asian groups on the fringes of northern and eastern Aryavarta). The thesis, broadly, was that the Munda people, who speak an Austro-Asiatic language, were the closest that the Indian subcontinent had to genuine aboriginals. The oldest of old. Supporting this contention is the fact that the languages of the Munda people, with distant affinities to Cambodian and Vietnamese, are very alien in comparison to Dravidian and Indo-Aryan (if Dravidian has any connections outside of the subcontinent, they are always posited to the west, in ancient Iran. The Munda languages clearly have eastern connections). The supposition then was that from the Munda arose various peoples of eastern Eurasia. To cut to the chase this model is probably wrong. The genetic structure of South Asia seems to have arrived at its current outlines relatively recently. In regards to the Munda people their origin is in Southeast Asia. They are not the progenitors of Southeast Asians, they are in part derived from Southeast Asians. Part of the broader expansion of “first farmers” in Southeast Asia from southern China. Their Y chromosomal lineages and autosomal heritage both imply this. Additionally, they carry the Northeast Asian derived variant of EDAR. Though much of their culture is almost certainly exogenous, and of relatively recent vintage, they are clearly highly admixed with the South Asian substrate. In particular, the fusing of an ancient West Eurasian population (“Ancestral North Indians”, or ANI) and a deeply rooted indigenous group with distant affinities further east (“Ancestral South Indians”, or ASI).

Chaubey, Gyaneshwer, et al. "Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture." Molecular biology and evolution 28.2 (2011): 1013-1024.

Chaubey, Gyaneshwer, et al. “Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture.” Molecular biology and evolution 28.2 (2011): 1013-1024.

One of the reasons that the ancient character of Munda residence in South Asia was persuasive is that they are resident in upland zones, which perhaps refuges after being marginalized by later arrivals. Their fragmented distribution is a tell that they occupied wider territories than is the case today. One thesis is that the Gangetic plain was inhabited by Munda people before the Indo-Aryans arrived. Rather than Dravidians, the indigenes in the Vedas may have been Mundas. But I’m interested in a more parochial question: can Munda ancestry explain the high fraction of East Asian ancestry in Bengalis, particular eastern Bengalis?

We can address this question a bit with genetics thanks to the resources we have in terms of population coverage. As readers know I’ve started to work with the 1000 Genomes data set. Luckily it has a large number of Bengalis within it. Meanwhile, the Estonian Biocentre has put its genotype data online, and there are Munda samples in there. I merged the data together, and removed pretty much all missing alleles. At the end of it I had 185,000 SNPs. To explore the questions I had in mind I decided to look at several populations. Bengalis and Telegu speakers (their genetic position would put them as “middle castes”; not Brahmins, but not Dalits or tribals). Georgians (from the Caucasus) as an outgroup. For Southeast Asian groups, Burmese, Cambodians, Filipinos and Dai. Finally, a small number of Munda. I plotted them on a PCA and removed those individuals who were not easily assigned to a cluster. The first PCA: MundaPC1

This isn’t really telling you much you don’t know. Let’s look at PC 3 now: Rplot

As you can see the Munda show a cline toward the Cambodians. This makes sense if the Munda descend from Austro-Asiatic agriculturalists. The Austro-Asiatic expansion in Southeast Asia probably dates to 4,000 years ago or so. Peter Bellwood has stated that archaeologists have excavated villages in northern Vietnam which catch the process of ethnic transition in action at this date (e.g., 75% of the burials are of gracile individuals, whille 25% very robust individuals). Such dates might put a ceiling on how early the Munda arrived inthe Indian subcontinen. In these results the Filipinos are representative of Austronesians, who have their roots in Taiwan and the Fujian coast, while the Dai are the forerunners of the Thai who arrived in Southeast Asia over the last few thousand years, taking over the uplands of Burma (Shan) and Laos (Lao), and swallowing the Khmer civilization which once flourished in the Chao Phraya basin (becoming Thailand). But it’s hard to make out what’s going on with the Bengalis…to me it isn’t clear that they’re shifted as much toward the Cambodians as they should be if the Asian ancestry was due to Munda being absorbed by Indo-Aryan speaking farmers.

So next I ran Admixture. I ran supervised and unsupervised and they showed the same qualitative result. Below is a bar plot of the unsupervised result, K = 5.

plinkAA_htm_mf149510

The Munda ancestry which is Southeast Asian here is overwhelmingly Austro-Asiatic. That is not the case with the Bengalis, who exhibit a range of fractions. There is very little Austronesian ancestry, which is something one might expect. But, there’s a balance of Austro-Asiatic and Daic ancestry in many individuals, though there is inter-individual variation (my mother has one of the strongest Austro-Asiatic skews among the Bengalis, while my father is among the most Daic; previous runs of admixture consistently show that her eastern Eurasian is more Southeast Asian than his, which has suggestions of Northeast Asian). This is not consistent with Munda being the sole source of East Asian ancestry in modern Bengalis.1 Using rolloff based methods researchers have estimated that admixture into Bengalis occurred on the order of 1,000 years ago. There’s nothing here that would contradict that, and the admixture can easily be explained by the Burmese in the data above, or Khasi and Garo people, who live to north and and east of Bengalis.

Finally, I ran TreeMix on the data. I removed the Georgians and Filipinos because they didn’t add much. Additionally, for kicks I broke apart the Bangladeshis into two groups defined by the 25 most Daic, and 25 least Daic. Below are the ten plots from the ten runs.

MTree.9 MTree.10 MTree.1 MTree.2 MTree.3 MTree.4 MTree.5 MTree.6 MTree.7 MTree.8

I don’t think breaking apart the Bengalis did any good. There were runs with the full fused sample, and the results were similar. It is clear that TreeMix also suggests that Munda are not a singular donor to Bengalis of their East Asian heritage. The source of the donor migration arrow is always shifted more toward Southeast Asian groups proper. Breaking apart the Bengalis into Austro-Asiatic and Daic skewed groups did result in the source of the gene flow being somewhat different. But not appreciably. I also ran the f3 and f4 statistics. There’s nothing surprising about who mixes with who…though it is notable in these and the above results that Burmese show nearly as high a gene flow from South Asians as Bengalis show from Southeast Asians. There have long been suggestions of gene flow from India to Cambodia, perhaps associated with the ancient mediation of South Asian cultural forms across Southeast Asia. But the Burmese evidence of gene flow is tragically ironic in light of the fact that modern Burmese are virulently racist toward dark skinned Muslims who clearly have South Asian origins.

51MGYd330tL._SY344_BO1,204,203,200_ So what happened in Bengal? At the top of the post I have an illustration of The Rise of Islam and the Bengal Frontier, 1204-1760. The thesis of this book is that the Islamic nature of eastern Bengal is in large part due to its relatively recent settlement by Indo-Aryan farmers. Though Bengal has always been a marchland, on the fringes of Aryavarta, before the Islamic conquest of the 13th century its center of gravity, culturally and demographically, was in what is today in the Indian state of Bengal, to the west of Bangladesh. The author of The Rise of Islam and the Bengal Frontier, 1204-1760 suggests that Islamic elites were instrumental in opening up the lands to the east of the old core, and the peasant cultivators who came to cultivate the new territory under their leadership identified vaguely with the religious identity of this new elite (though in general practicing on a day to day level their own folk beliefs), as the old organically developed institutions of Hinduism and Buddhism were poorly moored in the virgin lands. To me this is reminiscent of Michelle Salzman’s data in The Making of a Christian Aristocracy, which suggests that Christian elites arose on the frontiers, rather than the old cores, under patronage of the new religious dispensation (these data are predicted by Peter Turchin in War and Peace and War). In contrast the old Roman elite was relatively late to Christianity, as they were attached their own customs and traditions, which had thick and deep roots in the heartlands of the Roman world. Similarly, Hinduism (or what became what we term Hinduism) between the Doab and western Bengal seems to have resisted Islam’s attempt to destabilize local institutions and interpose itself as the dominant religious ethos of the sub-elites. Only on the destabilized fringes of the west and east, where old orders did not exist or were totally torn down, did Islam find purchase as a majority dispensation.

Finally, the high component of East Asian ancestry among the peasants of eastern Bengal is probably a function of the fact that there were groups from the east also pushing into the fertile territory. If the initial population density was low then a modest inflow at the early stages, ~1,000 years ago, could have a major long term impact. The crushing population densities of “Golden Bengal” was centuries into the future. A lack of cultural memory of this admixture is curious, but to a great extent shifting to the new religion meant that the proto-east Bengalis were creating a new identity. Things get lost….

 
• Category: Science • Tags: Bangladesh, History 
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51VGBO04szL._SY344_BO1,204,203,200_ In the year 2000 I watched the film The Patriot. Some British observers protested that the depiction of frankly Nazi-like behavior by the redcoats in the film was total fiction. There are scenes in the film where slaves are promised freedom in the revolutionary cause. Even those with a cursory knowledge of history during this period know that that was a painfully ahistorical element of the plot (I vaguely recall a few people laughing at this part of the movie in the theater). Finally, the historical individual upon whom the protagonist was based was a nasty fellow.

There is a tendency to compress the past, and turn it all into a blurry equivalent haze. Consider the American Civil War next to the Revolutionary War. Though people of the North were no more angels than those of the South, it eventually came to be that the sectional chasms of the 1850s culminated in the Dred Scott v. Sandford decision, as well as a war in the service of a peculiar institution (do note, I accept the proposition that the upstream causes were structural-economic, even if their cultural manifestations were ideological; see Clash of Extremes: The Economic Origins of the Civil War). As I have noted, as a child who came to consciousness in Greater New England there was never any doubt as to who was on the “right” side in the Civil War. Looking back with hindsight it does seem to me that by and large the armies in blue singing “John Brown’s Body” are more prophetic of a modern outlook than those who fought for the Southern way of life.

OrnamentalismTo be unequivocal about the American Revolution is more difficult for me. Unlike the Lost Cause, Britain did not disappear. Britain is still here. In fact, for a century Britain and the United States of America have been fast friends on the international stage. In the game of “what-if” it is natural that one look to the course of events in the British Empire and consider if that was perhaps a road not taken that might have been a better one at that. Vox offers 3 reasons the American Revolution was a mistake. They are, in order:

– Abolition would have come faster without independence

– Independence was bad for Native Americans

– America would have a better system of government if we’d stuck with Britain

One can agree or disagree with these assertions. The first two do seem more probable than not, though I am not entirely confident. The last is a matter of some complexity which I will set to the side. The key concern that immediately crops up in my mind is that the retention of the thirteen settler colonies would have irrevocably altered the course of British history. History is made up of contingent events, even if there are broad trends, and the addition of the massive dominion of the American colonies, and their likely demographic arc toward parity with the metropole just across the Atlantic, would have changed British culture. As Kevin Philips observed in The Cousins’ Wars the independence of the American colonies and the demographic collapse of Ireland in the wake of the famine resulted in a British population stripped of a large number of dissenting Protestant elements as well as a huge Catholic minority. British national consciousness as an Anglican country was definitely enabled by the independence of the American colonies, which were strongholds for heterodox and dissenter factions.

9780199604548 There is also a line of economic determinism that argues that American secession from union with the metropole was inevitable. That is because of the distinctiveness of the American Northern economy as it progressed in the early 19th century, the conditions of which were already in place by the 18th. While dominions such as Canada and Australia, and the erstwhile Southern colonies and the non-white possessions, were geared toward producing raw inputs for British manufacturing (one reason that the British elite were pro-Southern in their sympathies for much of the Civil War), the North was almost certainly bound to become an industrial rival (this explains the fixation on tariff policy in American politics up until the middle of the 20th century). It is hard to imagine the existence of a Dominion dominated by groups with dissenting Protestant sympathies and economically ascendant in a manner which competes with England not being a major question in the 19th century in lieu of the American Revolution. It may be that many of the things distinctive in British history as opposed to American, and preferred by the sort of people who write at Vox, may not have occurred in the same way if America and Britain remained politically fused, due to greater cultural exchange.

51VLZmyVmRL._SY344_BO1,204,203,200_ Second, there is the likelihood that British elite culture would influence the United States. Within the American experiment there was pregnant a panoply of radicalisms, some of which were resisted by broad swaths of America itself. Britain has a hereditary aristocracy, and class has a particular valence in British culture which it does not in the United States of America. The economic realities of the frontier suggest to me that some of this is structural and not conditional. After all, Canada and Australia are less fixated on class than England. But, it seems that a tighter integration between British and American society could not but help dampen down the populism of American culture in its orientation. Additionally, a quick survey of the population statistics for Canada and Australia show that they are much more British in origin than the white population of the United States. The massive waves of German immigration to the United States may have been much more modest in an America under the Empire, and the Anglo-Saxon demographic character of much of the North would have been more thoroughly preserved (one can imagine knock-on effects, such as a larger wave of German migration to South America and Eastern Europe?)

Reflecting on history is important. And thought experiments, counter-intuitive, even shocking, are to be welcomed. Political correctness should be abhorred in intellectual discussion. But we live in the year 2015, and the past is the past. What has been done can not be undone. So tomorrow I’m going to celebrate the American Independence, because whether the omniscient scales of history judge the arc of utility positive or negative, without it we wouldn’t be who we are, and we can always make the future better no matter the substance of the past.

 
• Category: History, Ideology • Tags: History 
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51qciM4cBhL._SX258_BO1,204,203,200_*The past after the word*

If science is hard, history is harder. Harder in that the goal is to understand what happened in ages which are fading away like evanescent ghosts of our imagination. But we must be cautious. We are a great storytelling species, seduced by narrative. The sort of empirically informed and rigorous analysis which is the hallmark of modern scholarship is a special and distinctive thing, even if it is usually packaged in turgid and impenetrable prose. It is too pat to state that history was born fully formed with the work of Thucydides (or Sima Qian). In fact Thucydides’ pretensions at historical objectivity despite obvious perspective and bias lend credence to the assertions of those who make the case that the past is fiction (in this way Herodotus may actually have been more honest). The temptation is always great to paint an edifying myth which gives succor to national pride or flatters our contemporary self-image. The fact that modern nation-states in the technological age have vigorous debates about details as to the nature of periods of history in the recent past, when the people who lived during those times are still here to bear witness, is telling in terms of the magnitude of the task before us. Fraught questions must be answered with far fewer resources.

Much of history we see only vaguely through chance and contingency, known through happenstance and the whims of our ancestors. In the West the documents which shed light upon antiquity come to us through tunnels of finite transmissions, a furious period of textual transcription in the last few centuries before 1000 A.D. The Carolingians, the Byzantines, and the Abbasids all engaged in sponsoring the capital intensive project of taking ancient texts and making copies for posterity. The vast majority of the works of antiquity we have today can be traced back to this period[1]. Biases and concerns of the elites who sponsored these projects were critical in determining the nature of the source material which serves as the foundation for our understanding of the deeper past which we take for granted today. We know how little was copied because the extant material make copious reference to a vast body of work which was circulating in the ancient world on assorted topics (and even many of the works we do have are only portions of multi-volume endeavours, such as that of Livy).

brotherhoodBut what about pushing beyond what the text can tell us, and transitioning from history to prehistory? Here is where matters become opaque and conditional upon the nature of the texts (or lack thereof). This is clear when you observe that there are very early periods of human history when our knowledge of individual actors and daily life is actually greater than later epochs due to regress of civilization, or, changes in technology which mitigated against preservation of texts[2]. The “Dark Ages” of Greece between the Mycenaeans and the Classical Greeks are the purview purely of archaeology (and even during the Mycenaean period most Linear B were of a bureaucratic nature; I do not know of narrative literature such as we have for Egypt or Babylon). For the Classical Greeks the rupture was traumatic enough that their Mycenaean past became the subject of legends. The citadels of the Bronze Age warlords were viewed as “cyclopean” works, as if only giants could have created them. Similarly, the period in Britain between the end of central Roman rule and the Christianization of the Anglo-Saxons, about two centuries, is perceived only faintly because of the paucity of written records (this also explains why this period is often utilized as the setting for historical fantasy).

9780192807281_p0_v1_s260x420 Yet when text is silent one still has material remains. Their collection and analysis are the domain of archaeology, a historical science. The fact that history as we understand it deals in the written word, and so limits its focus to the period when we have texts, is itself a historical coincidence. Ideally traditional history and archaeology should work in concert, and critically, words have a way of deceiving and misleading. Most obviously we have a major ascertainment bias in our understanding of the past when we listen only to the perspectives of those who can speak through words, because they who were literate or had access to literate professionals were a very small subset of the broader human experience. Archaeology has less of this bias, because all classes leave behind their material evidence (though if one wants textual representations of a broader cross section of the Roman populace, the novel The Golden Ass is a good place to start). An excellent illustration of this for me, as readers know, is the extended argument in the book The Fall of Rome, which brings material evidence to buttress the position that the decline and fall of the unitary Roman state in the 5th century coincided with a genuine degradation of what we might term civilization. Revisionists looking purely at textual materials have long argued that the classical view was misleading, and to reduce their argument down toward its essence, suggest that classical civilization evolved and transformed, channeling its energies into different activities (e.g., the rise of Christian theology as a successor to the classical liberal arts, see Peter Brown’s The Rise of Western Christendom). But what material remains tell us is that there was indeed an economic and demographic collapse, despite apologia that one can make as to the reshaping of high culture in texts. One may choose to weight these facts, or not, but the facts nevertheless remain, no matter how many glosses one wishes to upon them. The Rome of 600 may have had many more Christian theologians than the Rome of 400 (which was then a mainly non-Christian city), but the Rome of 400 probably had a population on the order of 10-20 times greater.

41hdiv6SmHL._SY344_BO1,204,203,200_ In a world without text, which is almost all of human history, the material remains are all that we have to grasp upon. Though we can attempt to glean the minds of people long gone from paintings and scratches in stone, the reality is that what they hunted with, what they ate with, and the dwellings in which they lived, are going to give us concrete information where leaps of imagination are unnecessary. Moving beyond the text can allow us to truly illuminate the vast dark oceans of human history with more than our dreams, from the dawn of our species, down to even recent periods when literacy was the privilege of the few, and the experiences of the many were dead to us. Despite this, the paintings have only a few colors on the palette, because archaeology is filled with enormous gaps in perception. Pots not cloth. Caves not tents.

Which brings us to biology, and specifically genetics, as it turns out that DNA is actually one of the material remains that one can extract from archaeological field sites. It’s a robust macromolecule, and today researchers believe that it is feasible that some information can be drawn from remains as old as 1 to 2 million years, though that’s a best case scenario. When it comes to questions of demographic change genetic insights are key, and present data in a way that allows for more rigorous analysis. As has been the case in previous posts I must now give a nod here to L. L. Cavalli-Sforza and The History and Geography of Human Genes. Cavalli-Sforza’s magnum opus reopened the book in attempting to understand history through demographics. It was the first page, and the first chapter. Prior to this before World War II there was a cottage industry which attempted to do what Cavalli-Sforza achieved in the late 20th century. But these endeavors were hobbled by two problems. First, they was not scientific, often relying upon intuition derived from their erudition (they were not hypothetico-deductive, though that’s overrated if you have lots of data). Second, the reliance upon intuition meant that many of the conclusions dovetailed rather neatly with the ideological preferences of the day, National Socialism most horrifically, but much more widely than that was a shoddiness of nationalism inflected prehistory. Scientific romance without the genocide (see Pat Shipman’s The Evolution of Racism). After World War II archaeologists reversed course and decoupled cultural evolution and change from demographic variation. Works such as the Races of Europe became anachronistic when decades before they’d have been mainstream, and there was a strong bias toward a null hypothesis that pots, that is cultural traditions, migrate, but people do not.

 

k7442 Into this intellectual climate stepped Cavalli-Sforza and his students, triggering a minefield in academic explosions (see The Human Genome Diversity Project: An Ethnography of Scientific Practice). Molecular anthropology in its earliest incarnations focused on deep time. In particular, there was a recalibration of time depth of the origin of apes and humans, where the molecular biologists clashed with paleontologists, and came out the victors (see The Monkey Puzzle for a history of these controversies). Then, there was the “Out of Africa” debate (see The African Exodus). Though these were somewhat fractious and personalized arguments, the emotions around the implications of these contests of ideas were often limited to scholars (though the scholars themselves may not have felt the fallout was limited; apparently at Stanford in the late 1990s a cultural anthropologist gave a presentation where he juxtaposed a photo of Cavalli-Sforza with Josef Mengele). What Cavalli-Sforza did was bring genetic science toward addressing more contemporary phenomena, to answer questions which come to the cusp of the present, tackling issues of relevance to living human people on the scale of nations and peoples. Over many decades his lab collected enough information from hundreds of genetic loci to arrive at the sum totality of inferences which were eventually presented in The History and Geography of Human Genes.

CosttoSequenceaGenome-e1409924136899 Let’s take a step back here. Cavalli-Sforza and his colleagues had access to hundreds of markers at best. Note that ~2% of the human genomic codes for proteins, but there are 3 billion positions in terms of bases. Today anyone who wants to pay can get millions of positions through SNP-chip services. My son has billions of positions, because he’s been whole-genome sequenced. For phylogenetic purposes you don’t need billions, millions, or even thousands, depending on the nature of the questions you have in mind. But, it puts in perspective how far we’ve come in literally 20 years. Even 5 years.

As is the nature of science there was much that Cavalli-Sforza got wrong in The History and Geography of Human Genes. But there was much that he got right, because the results were so clear and strong on particular points of contention. In short, very broad patterns on the continental level jumped out when analyzing even hundreds of neutral (that is, not subject to natural selection) markers. For example, the data confirm a gradient of genetic diversity which implies human origins from an African locus, as well as the relative homogeneity of Europe (aside from Finns, European populations have a surprisingly low between-population pairwise genetic distance in most cases). But, more subtle counterintuitive relationships were often not robust (e.g., North and South Chinese do not bifurcate in the manner that he reported in the 1990s). And, most critically for the purposes of this post inferring past demography from current phylogeographic patterns had serious limitations.

*The present as a window into the past*

downloadm511NSSGQNWL._SY344_BO1,204,203,200_ The basic idea behind historical population genetics (archaeogenetics) which was pioneered by Cavalli-Sforza at the HPGL at Stanford was to look at patterns of diversity and relatedness among modern populations, and intersect that with what was and is known about history, as well as geography, and then allow those intersections to peal back the palimpsests of human history (see his The Great Human Diasporas). Though Cavalli-Sforza focused initially on autosomal markers scattered through the genome, in the period between 1995 and 2005 there was a great deal of work using uniparental data., the markers on the Y and mtDNA. The mtDNA is passed through women only, is copious in terms of quantity on a cellular level, and has a highly mutable region of utility for molecular phylogenetics. The Y chromosome exhibited some technical difficulties in comparison to mtDNA, but with the emergence of better extraction techniques as well as a focus on highly mutable microsatellite regions, it came to be set next mtDNA as a critical tool in the forensic reconstruction of human population history. In addition, both had the virtue of being nonrecombining, so that the generation of a phylogenetic tree was not an artificiality, but a reflection of the nature of the transmission of these two regions of the genome (congenial to a coalescent framework as well).

Human_migrationIn the end this line of research often resulted in a transposition of a phylogenetic tree upon a world map, outlining patterns of human migration. It also aligned well with another line of research which explicitly modeled the expansions of humans out of Africa as a “serial founder bottleneck” process. That is, each population which left Africa progressively branched out in a unidirectional manner, resulting in reduced genetic diversity as one progressed out of Africa.

Ramachandran, Sohini, et al. "Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa." Proceedings of the National Academy of Sciences of the United States of America 102.44 (2005): 15942-15947.

Ramachandran, Sohini, et al. “Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.” Proceedings of the National Academy of Sciences of the United States of America 102.44 (2005): 15942-15947.

In its broadest strokes this model is not without validity. It does seem that most of the ancestry of modern humans can be traced to a population which flourished around or in Africa ~50-100 thousand years ago. Much of the inter-continental racial variation that we see in extant populations does nicely fit onto a bifurcating tree-like model (e.g., Non-Africans branch off from Africans, West Eurasians and East Eurasians diverge, Amerindians branch off from East Eurasians). The problem though is that the branches themselves turn out to be brambles which turn back in on themselves, and in some cases twist with other branches, creating lineages with very diverged ancestral roots. The yield of the earliest efforts by Cavalli-Sforza and his heirs was on a very coarse continental grain, where the effects of the dynamics were so striking that they would exhibit themselves across most neutral markers without much difficulty. But, when the questions were narrower, and the temporal and spatial scope more constrained, the earlier methods were not perceptive enough to smoke out the real dynamics.

Li, Jun Z., et al. "Worldwide human relationships inferred from genome-wide patterns of variation." science 319.5866 (2008): 1100-1104.

Li, Jun Z., et al. “Worldwide human relationships inferred from genome-wide patterns of variation.” science 319.5866 (2008): 1100-1104.

By the middle years of the 2000s researchers had gone back to a focus on recombining autosomal markers. But now they had a whole human genome to compare it to, as well as SNP-chips which quickly yielded large troves of data with little effort. In 2008 a paper was published which took the origin HGDP data set collected by Cavalli-Sforza and his colleagues, and utilized the new technologies to make deeper inferences. First, instead of hundreds of markers you had 650,000 SNPs. Second, the emergence of powerful new analytic and computational resources allowed for the complemention of tree-based and PCA visualizations of genetic relationship with model-based understandings of genetic variation and population structure. By “model-based,” I mean that the algorithm posits particular parameters (e.g., “3 ancestral populations”) and operates upon the data (e.g., “650,000 SNPs in 1000 individuals”) , to generate results which are the best representation of the fit of the data to the model.HGDPme This different from PCA, which has fewer assumptions, and represents genetic variation geometrically (each axis represents an independent dimension of variation within the data). Model-based clustering is very clear and aesthetically appealing. It gives precise results. But, the model itself is not necessarily right.

Anyone who uses these methods understands their limitations. If you use PCA to project variation of the data set, then the composition of the data you input is going to influence the largest principal components. Therefore, if you are asking questions on a broader spatial scale you should be careful about the possibility that you are overloading the sample set of interest with particular populations. More data in this case might result in less insight. Similar issues crop up with model-based clustering you don’t appropriately weight the populations. Another major problem is that the models are imposing limitations which might produce false inferences (false in that they do not accurately reflect demographic history). Most simply you might ask for many more population divisions than is realistic for the demographic and genetic history of the data. Consider a data set of Irish from Cork and Nigerians from a small village. PCA would no doubt show you two very tight and distinct clusters. With a model-based framework you could look for divisions and structure beyond K = 2 (two ancestral populations). The method is devised in such way that you would get results. But, they wouldn’t be very informative, and they’d be forced. They wouldn’t be robust. The model would be a poor fit to reality.

*From model to reality*

Obviously no model captures all elements of reality. But when the model deviates so much from reality that you get a false sense of what is true then that model is not nearly as useful. Being wrong is a definite bug. Aside from model-based admixture analysis, which posits a finite number of ancestral populations which come together to produce the genetic variation in the data set, you notice that the 2008 paper also had a tree representation of genetic variation. These two together give real and substantive results that can be useful. But, they mislead to the point of falsity in many specific cases.

nihms137159f3

Reich, David, et al. “Reconstructing Indian population history.” Nature 461.7263 (2009): 489-494.

This can be illustrated by the instance of South Asians, who are about 20% of the world’s population. A 2009 paper, Reconstructing Indian Population History, utilized both the higher autosomal marker density sets and new analytic frameworks to come to some specific conclusions which resolve many confusions about the nature of the genetic history of the peoples of the Indian subcontinent. So what did we know before? If you go back to the ideas of the old physical anthropologists they observed that many South Asian groups had an affinity to the peoples of West Eurasia (Europeans and West Asians). This varied as a function of geography and caste. In other words, there was a cline to the northwest, as well as up and down the caste system. You can see it in a PCA, where Indian groups vary in distance from Europeans, while Europeans form a very tight cluster. It also shows up in admixture based analyses. There is usually a K value where a South Asian modal cluster emerges, and it is near fixation in South Indian non-Brahmins, declining in frequency as one moves toward Pakistan, or, in North India up the caste hierarchy (the residual are West Asian and European clusters, except Bengalis, who have East Asian admixture). In The History and Geography of Human Genes South Asians form an outgroup to Europeans and Middle Eastern populations using older distance measures.

So far all good. One can imagine then a cline of genetic variation, with South Asians at one end, and West Eurasians at the other. On a PCA between East Asians and Europeans South Asians usually fall in the middle, but closer to Europeans. But there have long been major problems with this model when you drilldown into the details. The mtDNA and Y chromosomes of South Asians give very different results. The former classes them as distinct from West Eurasians, with distance affinities to East Eurasians. The latter on the other hand are quite a bit more like West Eurasians. Second, South Asians exhibit a lot of variation as a function of both geography and class in terms of their relatedness to word populations. If South Asians were deeply rooted in the subcontinent, as the migration maps above would imply, then we’re talking about massive barriers to gene flow which have persisted for tens of thousands of years. An alternative explanation is that South Asians are the product of recent admixture between two very different groups, which is what is often the norm when there is a lot of inter-individual variation in ancestral components and PCA position within a putative population group (e.g., African Americans). Finally, tests of natural selection geared toward detecting very recent sweeps have indicated a commonality between South Asians and Europeans and Middle Easterners on the haplotype of SLC24A5, which implies either extreme connectedness, or, recent admixture and migration (on the margin these two models are going to be hard to distinguish, since connections are mediated through migration).

I will sidestep the technical issues at this point, and just offer up that the work on South Asians has presaged much of what we’ve learned over the past decade when it comes to the genesis of modern population structure. The puzzles about South Asian genetic variation are resolved when you admit a model where a West Eurasian population mixed with a local indigenous group with distant affinities with other East Eurasians (see Genetic Evidence for Recent Population Mixture in India). The high level of between population variance within South Asia is due to the recent nature of the admixture event and the high genetic distance between the source populations. This may actually be the story of much of the world over the last 10,000 years. Instead of a regular branching process, imagine branches that periodically fuse back together, in a reticulated pattern. Another way to conceive of it is that the last 10,000 years have been a story of the destruction of population structure accrued over the past 100,000 years. A survey of this field can be found in the review Toward a new history and geography of human genes informed by ancient DNA.

*Inference made concrete, ancient DNA*

Up until now we have been talking about increasing the power of analysis of genetic variation in existent populations. Processes like bottlenecks and positive selection leave footprints in the genomes of modern peoples. But these methods of inference have limits. And, to a great extent they necessitate a simplicity of population dynamics to allow for them to have utility in painting a portrait of the past. Researchers had to assume that the past was simple, or the methods that they had wouldn’t be able to tell them as much as they claimed. The complexity of the demographic palimpsest could never race beyond ability of the genetic methods to peel it back, so there was a ceiling on the number of layers imposed upon the model.

41ePHetk1dL._SY344_BO1,204,203,200_ Ancient DNA was a game changer, because it did not come with these limitations. Instead of just inferring the past from the present, the past could now be inferred from the past! That is, a temporal transect in time could be generated which explicitly explored the trajectory of genetic variation across time and space. As if to recapitulate history the earliest work was with mtDNA, just as it had been with “mtDNA Eve” in the 1980s. The sequence target here is small and mtDNA is copious. The immediate upshot though is that massive discontinuities were detected. Populations replaced each other repeatedly in many regions. Pulse admixture events being inferred with novel methodologies on extant populations now could be understood to have been the natural result of migration and population change over the past ~50,000 years. Thanks to the work of researchers such as Svante Paabo and Eske Willerslev the number of samples we have from ancient DNA for humans has grown to such an extent over the past 5 years that a bright line is shining into what had been a dark cavern of prehistory.

*European man, made and unveiled*

Because of both the concentration of researchers in Europe, as well as suitable preservation conditions in Northern Eurasia, ancient DNA has totally changed how we understand the genetic history of this continent most especially. Two new papers have expanded the sample set to 170 individuals, and many major questions have now been answered, and other new questions have been triggered by perplexing results. A few years ago I was talking to Spencer Wells about the age that we are privileged to live in. Spencer is a history and genetics buff (he was one of Richard Lewontin’s last grad students). So naturally as genetic science has emerged to shed light on history we’ve tracked its developments very closely. Spencer professionally, he’s a genetic anthropologist. Many questions which in the past would have been unanswerable are now answerable. Truth is coming at us so fast that it is hard to even respond to all of it (if you wait too long to publish, everything might have changed).

Carl Zimmer’s piece in The New York Times, DNA Deciphers the Roots of Modern Europeans, is accurate as to the current state of the accelerating research in this area. This is the equivalent of having a Rosetta Stone. The ancients are now coming back to life. They speak! Everything has changed. In Nature Ewen Callway quotes a scientist stating in plain language, “Christ, what does this mean?” I’ll try and flesh out further what it means, but the papers themselves do a good job. These are first steps, but they’re very big steps. There’s only so much more to go, and truth will be at hand.

First, the two papers, Massive migration from the steppe was a source for Indo-European languages in Europe, and Population genomics of Bronze Asia Eurasia. As might be suggested by the title the latter paper has coverage of populations outside of Europe, while the former focuses on Europe. The samples sizes are 69 and 101 respectively. The first paper uses a methodology which yields many SNPs, while the latter relied upon whole-genome sequencing (variation is variation, so really this is a minor detail for the results, though it matters a lot for the working scientists who are generating the data). Both agree broadly on the major results. Additionally, there is a third work, a preprint, Eight thousand years of natural selection in Europe, which has results in line with the second paper above (it has a section on selection as well as phylogenomics).

*European genetic structure is younger than the pyramids*

51IZQjMbVlL._SY344_BO1,204,203,200_

The old debate whether Europeans are descended from farmers or hunter-gatherers was always somewhat incoherent. All humans are descended from hunter-gatherers. Rather, the issue was whether modern Europeans descend primarily from people who were resident within the continent of Europe at the end of the last Pleistocene, or, whether they descend from peoples who developed agriculture in the Middle East ~10,000 years ago. That is, did farming spread through cultural diffusion or migration? Plants or people? The answer is actually not straightforward, but, the results are not controversial today.

First, migration seems to have been the dominant dynamic which defined the spread of farming, especially early on. These first farmers who arrived in Europe were genetically very different from the hunter-gatherers of Europe’s north and west. Some of their ancestry had been isolated by long distances for tens of thousands of years before contact. The people of the Iberian peninsula today have less genetically in common with the hunter-gatherers which were present in the region when the farmers arrived than do modern Northern Europeans, who harbor a greater fraction of ancestry which derives from the Pleistocene people. The main qualifier I’d put on this though is that the farmers themselves seem to have picked up European hunter-gatherer admixture on their way out of the Middle East. The fraction is on the order of ~50%. The other component has been termed “Basal Eurasian,” because this element is an outgroup to all other Eurasians, including the European hunter-gatherers. That is, the Basal Eurasians are an outgroup to a clade that includes such as diverse populations as Andaman Islanders, Australian Aborigines, Japanese, and European hunter-gatherers.

Lazaridis, Iosif, et al. "Ancient human genomes suggest three ancestral populations for present-day Europeans." Nature 513.7518 (2014): 409-413.

Lazaridis, Iosif, et al. “Ancient human genomes suggest three ancestral populations for present-day Europeans.” Nature 513.7518 (2014): 409-413.

The figure to the left is from the paper Ancient human genomes suggest three ancestral populations for present-day Europeans. WHG = “Western (European) Hunter-Gatherers.” EEF = “Early European Farmers.” You can see that EFF is a compound. I don’t think there’s too much clarity right now with where the EEF got its WHG-like ancestry. It could have been structure in the Middle East. Or it could have been in Southeast Europe. In the supplements of Haak et al. they test a Hungarian sample, and it does seem that the EEF individuals are closer to it than the Western European hunter-gatherer samples. So there might have been structure in the ancestral European population, but the confidence here is low. And from what I can tell Basal Eurasian is still something of a mystery, almost occupying the role of “Planet X” before the discovery of Nepture. To make the patterns make sense they have to exist, but much isn’t known about them in detail. And of course there seems to be a huge lacunae right now in terms of exploring the population genetics of the Middle East in a similar fashion as has occurred in Northern Eurasia (my understanding is that Carlos Bustamante was an important person in getting Latin American populations in the 1000 Genomes; unfortunate that there wasn’t someone else to advocate for including a Middle Eastern group, since this is such an important part of the world for human history).

With all that said, if one assumes that the West Eurasian admixture in EEF was from European hunter-gatherers, then it is clearly obvious that most of the ancestry of modern Europeans can date to the Pleistocene (i.e., EEF + Yamnaya likely means more than half the ancestry is WHG-like if you look back 10,000 years). But, this proportion obscures the fact that massive migrations and population turnovers have occurred, so that a simple model of expansion out of Ice Age refuges no longer holds. Cavalli-Sforza has long argued that pure proportions of ancestry are less important than the dynamic, as population growth driven “waves of advance” will over time dilute the initial genetic signal anyway (though the final proportion of non-WHG-like ancestry is actually higher in much of Europe than Cavalli-Sforza conceded in the early 2000s). Whether the ancestry of modern Europeans derives predominantly from those of European hunter-gatherers, the idea of dominant local continuity in a given region has been thoroughly refuted. The hunter-gatherer ancestry in the British Isles, for example, may be mostly from admixture into agricultural groups far to the south and east during the initial waves of advance, not from the people who initially recolonized Northern Europe in the early Holocene.

k8488 The second demographic turnover event which has been highlighted by the papers cited so far is from the east. The migration from the steppes. This event had disproportionate, even dominant, impact across much of Northern Europe. Culturally it is often rooted in the Yamnaya complex, which gave rise to various disparate and wide ranging “daughter” societies. David Anthony’s The Horse, the Wheel, and Language surveys the archaeological terrain thoroughly. If you are interested in this topic, and haven’t read it, do read it. In this work Anthony outlines the spread of Indo-European languages via expansion of a mobile pastoralist elite. He was involved in the retrieval of some of the samples in these studies, and from what I am to understand he was personally surprised that the genetic data imply not just elite migration, but a folk wandering. Not just a band of brothers, but whole peoples on the move.

Haak, Wolfgang, et al. "Massive migration from the steppe was a source for Indo-European languages in Europe." Nature (2015).

Haak, Wolfgang, et al. “Massive migration from the steppe was a source for Indo-European languages in Europe.” Nature (2015).

Focusing on the genetics, these people seem to themselves be a compound of disparate elements. First, some of their ancestry derives from a population which Haak et al. term “Eastern Hunter-Gatherers” (EHG). And the other half derives from a population with affinities to those of the Near East, but different from that of the EEF. There is some disagreement between the two papers in Nature as to the details, but Allentoft et al. admit that they did not have EHG samples, which may have impacted their ability to detect admixture. Allentoft et al. also diverge from Haak et al. in the emphasis they place on the ancestral component among the Yamnaya which some term “Ancient North Eurasian” (ANE) based on the location of the most ancient individual of this line (see Upper Paleolithic Siberian genome reveals dual ancestry of Native Americans). What does seem clear is that this element is deeply diverged from other West Eurasian populations, on the order of ~20 to 30 thousand years. And, they contribute about half the ancestry to the EHG (the rest is WHG-like). The descendants of the Yamnaya people brought this component all throughout Europe, with the exception of the Sardinians and Sicilians, likely isolated because of their position on the Mediterranean littoral (Sicilians have later Near Eastern admixture as well). But this is not limited to Europeans, as a substantial proportion of Native American and West and South Asian ancestral heritage (at least the Kalash) also exhibit connections to this component. Allentoft et al., like Haak et al., points out that there was likely structure in this broader group. That is, the ANE themselves were diversified, with the ancestors of the element in Native Americans and Europeans different from that which contributed to the Siberian component. In fact I have talked to researchers who believe that the term “Ancient North Eurasian” is misleading, as there is little clarity on the distribution of this group (the highest inferred fractions in Eurasia are in the North Caucasus). It is feasible that the Kalash have a different ANE source than Europeans.

A key issue to note, and that confuses some people, is that the ancestry of groups such as Yamnaya exhibited commonalities with other groups across Eurasia. Therefore, if you replaced similar groups then the change in admixture components utilizing model-based programs may not be as extreme as you would think. To illustrate what I’m getting at concrete, the population transfer between Greece and Turkey during the 1920s was far more impactful as a dynamic than simple before and after admixture estimates would suggest to you (since genetically the two groups were very similar). The figure from Haak et al does not use admixture components that break out naturally, but their inferred demographic mixes taking into account the genetic character of the putative ancestral populations. The blue component refers to WHG, but WHG-like ancestry is also in both the green (Yamnaya) and orange (EEF) elements (this is why I’m saying it is likely that modern Europeans are mostly >50% WHG-like).

One temporal dimension that Haak et al emphasizes in particular, but seems clear in Allentoft et al. as well, is that non-Yamnaya ancestry slowly begins to rise again by the Bronze Age. Why? I will address that below. But, Allentoft et al. has broader Eurasian samples, including likely Indo-European populations in the trans-Ural and trans-Altai regions. In both of these areas the successor cultures had EEF-like ancestry. That is, like the Corded Ware population, and unlike the parent Yamnaya group. This strongly implies back-migration by this complex from Eastern Europe, as far east as western China, during the Bronze Age.

warbefore In The New York Times piece David Anthony states two things which puzzle me as an interested lay person without his expertise. First, he seems to think that the amalgamation of the Yamnaya and EEF-descended populations was not a warlike process. Specifically he says “It wasn’t Attila the Hun coming in and killing everybody,”. This is a useful image, but let’s be honest and note that the Huns were not primary producers, and did not aim just to increase pasturage by killing settled peoples as Genghis Khan had wanted to do (see The End of Empire: Attila the Hun & The Fall of Rome). Rather, they conquered and subordinated other barbarian groups, as well as extorted tribute from the East Roman Empire. The demographic impact of the Huns was not directly from them, but the fact that they and their successors (in particular the Avars) facilitated the migration of other groups, first, the Goths, and later the expansion of the Slavs. By the time of Attila barbarian leaders were well aware that the conquered were vital as economic producers whose capture and subjugation would allow them to engage in status competitions of conspicuous consumption. I do not believe that this was quite the case in the Copper and Bronze Ages beyond the limes of the civilized world, which was then an small archipelago of literacy in a sea of barbarism. Both the above papers indicate massive demographic disruption across Europ. Though war as we understand it is necessarily inevitable for our species, between the rise of agriculture and the modern period it seems to have been very common. It is not a coincidence that the Scandinavian Corded Ware culture are also called the Battle-Axe culture. Yes, many archaeologists believe that they were primarily a status symbols. I’m willing to bet many archaeologists are wrong. It’s been known to happen.

gokturk_empire_by_still_ates The second issue which Anthony brings up is the connectedness of the various post-Yamnaya cultures, in particular that of the earliest Indo-Europeans on the fringes of western China, 4,000 miles from their likely point of origin. The genetic characteristics of these eastern groups is also such that it is likely that there was gene flow from Europe, mediated by a common steppe culture. Anthony states that “I myself have a hard time wrapping my head around explanations for that”. This totally confuses me, because he’s a professional archaeologist, so he must know that widespread gene flow and cultural ties cross the vast swath of the Eurasian heartland is not surprising at all! To Carl Zimmer I pointed out the example of the Goturk Empire of the mid 6th century A.D., which expanded rapidly from the core Altai zone, and prefigured the later distribution of the Turkic people, from the Nile to the fringes of the Arctic sea. Language and lifestyle mediate relationships and demographic contact. The peripatetic character of steppe peoples is well known and attested from the historical and semi-historical record. Groups such as the Huns, Avars, and Alans, had inchoate origins in the heart of Eurasia, and moved back and forth along lines of cultural affinity as needed. Alans were serving under the Mongols in China in the 13th century, but 800 years earlier they had accompanied the Vandal tribe to North Africa, and maintained a separate identity there until the conquest of Justinian. It seems entirely plausible that this pattern of hyper-mobility arose with agro-pastoralism along the whole range of continuous ecological appropriateness, only ending with the rise of gunpowder empires and the crushing of the Oirat by the Manchus (with the tacit approval of Russia).

*Northern European archetypical physical characteristics are younger than the pyramids*

Spencer Wells, a new look in the world

Spencer Wells, a new look in the world

Phylogenomics is tangled and complicated still, even with all these new results. I’ve only scratched the surface above. You really need to read the papers, and their supplements, to even get a sense of what’s going on (yes, ideally you’ll know what an f3 statistic is!). But, the population genomics which give us a sense of the character of natural selection and phenotype over time is much clearer. The suite of traits which we associate with white Europeans is quite possibly very recent, as late as post-Bronze Age. White supremacist scholars of the early 20th century who posited that ancient Egypt (in fact, all civilizations) were founded by blonde Nordic people turn out to likely be wrong because these civilizations probably predate the existence of blonde Nordic people, both in their genetic structure, and in their physical type (at least in any number).

nature14507-f4 The genetic architecture of pigmentation is something geneticists know a fair amount about, because genome-wide association has been very fruitful in this area. Unlike traits such as height there is a large amount of between population variation in pigmentation. And, that variation is due in large part to a few genes of large effect. At SLC24A5 there is a SNP which accounts for around 1/3 of the melanin index difference between Europeans and Africans, using an admixed African American population to test the effect. As I have observed before SLC24A5 in its derived form is as close to fixed as you can get in Europeans. In the 1000 Genomes data set of thousands of individuals I found a few samples with a heterozygote and the ancestral copy. In the Middle East this allele is also near fixation, though not quite. As you can see from the figure I adapted from Allentoft et al., among South Asians the derived allele is also at high frequency. My whole family is a homozygote for the “European” variant. There is some suggestive evidence that this haplotype derives from the Middle East. It was only at low frequency among European hunter-gatherers[3]. But, by the Bronze Age had it gone to fixation in Europe, as well as on the Eurasian steppe.

Of more interest to me is the trajectory of SLC45A2. The derived allele is nearly fixed in modern European populations, though not nearly to the same extent at SLC24A5. In Iberian and Sardinian populations the ancestral type is in the range of ~10%. During the Bronze Age in Europe it was only at ~50% frequencies, which is in the range of modern Middle Eastern populations. It was even at lower frequency in the steppe, from which the putative Indo-Europeans migrated.

Finally, in this panel for pigmentation they included a major SNP in OCA2-HERC2 region. This locus is famous for being involved in blue-brown eye color variation, explaining 75% of the variance, and also exhibiting the third longest haplotype in the European genome. Naively projecting from these SNPs one could credibly argue that the ancient hunter-gatherers of Europe at the beginning of the Holocene were dark-skinned and blue-eyed! The Bronze Age European samples, which in this case are biased toward Northern Europeans, had a range of genetic variation equivalent to modern Southern Europeans. The people of the steppe did not seem to have blue eyes at all.

skin2

These results align perfectly with those in Mathieson et al. One thing to observe is that the Paleolithic samples, which have a much deeper time depth, are “ancestral” at all these positions. Even if the sample size is small (N =4), they’re from diverse times and places. Does that mean that they were much darker than even the Holocene hunter-gatherers of Europe? As some have pointed out we can’t just straight-line extrapolate from the genetic architecture of today to the past. Remember that Neanderthals exhibited pigmentation polym]orphism, but of a different sort. A deeper functional analysis may yield the possibility that Paleolithic Europeans had alleles which also resulted in lighter skin, but they were different ones from the ones segregating as polymorphisms today. I have already stated that I doubt much of modern European ancestry derives form before the Last Glacial Maximum. The reason that modern genetic variation in terms of predicting phenotype gives these sorts of results is that they may have arrived at the same trait value via a different set of polymorphisms. Genotype-phenotype maps derived from modern populations may be a poor predictor of the relationship 30,000 years ago. Why would one think that selection upon variation in pigmentation began at the cusp of the Holocene?

But, I do think we can predict with more confidence the nature of phenotypes for populations which are genetically much closer to modern ones. Bronze Age Europeans fit that bill. And, I know something personally about what the appearance of individuals during this period might have been based on genetic architecture: both my children exhibit a genotype profile on pigmentation loci similar to many Bronze Age Europeans. That is, they’re fixed for the derived variant of SLC24A5, and are heterozygotes at SLC45A2 and OCA2-HERC2 (my son, but not my daughter, is a heterozygote at KITLG; it does seem to make a difference in hair color). In terms of just their complexion they could pass as indigenous Southern Europeans, but definitely not Northern European.

*Culture leads genes by the leash*

Another major finding of Mathieson et al. and Allentoft et al. is that the derived allele found across West Eurasians that allows them to digest lactose sugar as adults has been sweeping up in frequency over the last 4,000 years. This allele spans a diverse array of populations, from Basques to South Asians. With pigmentation it seems that we need to consider jointly the impact of ancestry and selection (in South Asia derived SLC24A5 frequencies are definitely a function of both selection and descent). But with LCT it seems likely that selection is paramount. The predominant genetic character of Eurasia was established by the Bronze Age, but the frequency of the lactase persistent allele was still far lower. Tests of natural selection which focus on patterns of haplotype variation long detected a huge hit from LCT so this is not surprising.

51r8Ph-vcaL._SY344_BO1,204,203,200_ Intriguingly Allentoft et al. indicates that though the Bronze Age steppe populations had low frequencies of the derived allele, it seems that they did have a higher frequency than contemporary populations. This suggests that the origin of this haplotype, which spans the whole range of Indo-European speaking populations, and also into Finnic groups and the Basque, may still be attributed to the Yamnaya complex. In 10,000 Year Explosion Greg Cochran proposed the hypothesis that the favored mutation for LCT enabled the spread of Indo-European pastoralists. These results are not strong support for that direct causal relationship; rather, it strikes me that the ascendancy of the pastoralists drive the selection pressures for the allele in question. Biology did not drive culture, culture drove biology. The milk-drinking Celts and Germans encountered by Julius Caesar 2,000 years ago may still have been in the middle stages of adaptation to the agro-pastoralist lifestyle slowly being perfected by their ancestors.

*As the white man is, so shall we all be*

A new look as well

A new look as well

It is a running joke of mine on Twitter that the genetics of white people is one of those fertile areas of research that seems to never end. Is it a surprise that the ancient DNA field has first elucidated the nature of this obscure foggy continent, before rich histories of the untold billions of others? It’s funny, and yet these stories, true tales, do I think tell us a great deal about how modern human populations came to be in the last 10,000 years. The lessons of Europe can be generalized. We don’t have the rich stock of ancient DNA from China, the Middle East, or India. At least not enough to do population genomics, which requires larger sample sizes than a few. But, climate permitting, we may. And when that happens I am confident that very similar stories will be told. Using extant genetics we can already infer that modern populations in South Asia are a novel configuration of genotypes and phenotypes. The same in Southeast Asia, the Americas, and probably Africa. Probably the same in East Asia. Perhaps in Oceania. Even without admixture humans evolve in situ and changed, but with admixture the variation increases, and the parameter space of adaptation becomes richer and more flexible.

In Isaac Asimov’s later Foundation books he touched upon the existence of racial diversity in the future (from what I recall his earlier works from the pulp era were whites-only galaxies). At one point Hari Seldon encounters someone whose physical appearance seems to be East Asian, and they discuss the strangeness of people with East Asian ancestry being termed “Easterners” and those with European appearance being “Westerners.” With a loss of memory of the ancient distribution of these populations on the home planet only the shadow of a semantic recollection exists as a ghost in the galaxy-spanning Empire based out of Trantor. But of course tens of thousands of years in the future, even barring genetic and mechanical modification, it is unlikely that modern racial types will persist in any way we would recognize them.

But these results coming out of ancient DNA are telling us that what is likely to be true for the far future was also true for the recent past. White Europeans are a new type. But so are brown South Asians. Ethiopians have a recent ethnogenesis, as do most North African groups. The Bantu expansion has reshaped the face of Africa on the edge of the historical horizon. And so forth. In the big picture Young Earth Creationists are wrong, but in the specifics the idea that the sons of Noah populated the world ~5,000 years ago is not looking as crazy as it once did! Human genetic variation across Eurasia today may be mostly clinal, but in the recent past it was not. Rather, it was characteristic by sharp discontinuities and isolated local populations with diverged ancestry from their neighbors.

*And culture made man in its image*

51L3op-B8fL._SY344_BO1,204,203,200_ About ten years ago it was common in paleoanthropology to assume that human beings emerged almost fully formed ~50,000 years ago, and wiped out all the others in a genocidal wave of advance. Richard Klein advanced this model in The Dawn of Human Culture. Klein’s thesis was that some stochastic event, a mutation, resulted in the punctuation of a new species, our own. This singular genetic process allowed for the emerged of fully formed linguistic faculties in our lineage, which allowed for the development of the cultural flexibility, which made the rest of the human lineages evolutionary dead ends. It was a single and elegant story. It appealed to the principle of parsimony. The reality of “archaic” admixture was a difficulty for Klein’s model, evidenced by the fact that he voiced his skepticism of genetic claims of admixture in The New York Times after most others had moved on. For Klein a biological change explained the rise and success of our species, not a cultural one.

At the time I found the thesis compelling. We were after all a very special species. Modern Homo made it to Oceania and the New World. Something must have happened. Something big. What else could explain our rapid expansion and marginalization of other lineages? I’m a biologist, and so biology is an appealing causal mechanism.

linear

*The luck of the English facing the ocean*

At about the same time the evidence for Neanderthal admixture came out, Luke Jostins posted results which showed that other human lineages were also undergoing encephalization, before their trajectory was cut short. That is, their brains were getting bigger before they went extinct. To me this suggested that the broader Homo lineage was undergoing a process of nearly inevitable change due to a series of evolutionary events very deep in our history, perhaps ancestral on the order of millions of years. Along with the evidence for admixture it made me reconsider my priors. Perhaps some Homo lineage was going to expand outward and do what we did, and perhaps it wasn’t inevitable that it was going to be us. Perhaps the Neanderthal Parallax scenario is not as fantastical as we might think?

41z97bDZvUL._SY344_BO1,204,203,200_ Consider the case of Europe around 1600. In England and northern Germany (or what was to become northern Germany) you have two Protestant and genetically similar populations. But by 1850 it looked as if England was going to demographically overtake Germany in a broader genetic sense. James Belich’s Replenishing the Earth reviews the history of this period, when England spearheaded a demographic revolution far out of proportion to what one might have predicted in the year 1000. But by 2000 Germany, or Germans, had caught up somewhat. How? Millions of Germans migrated to the United States, starting in very large numbers in the mid-19th century, and were “picked up” by the demographic revolution which was the United States. The point is that contigencies of history, cultural and social, rather than biology, explain the trajectory of the gene pool over time. Much of the human past, and the sharp fluctuations in gene frequencies, might be driven by the long and forceful arm of culture.

In the treatment above I note that the EEF farmers who by and large replaced the indigenous hunter-gatherer groups in modern Southern Europe were themselves a compound. The hunter-gatherer ancestry within the EEF was far more successful than that of those they replaced, but the only reason that this was so was geographic coincidence. The WHG-like groups absorbed into the EEF were positioned further east, and so closer to the initial locus of expansion of Neolithic farmers. Similarly, the Neanderthal admixture into modern populations was almost certainly localized to particular groups. This is not to say that there are no biological differences between human populations which may explain a wide range of phenomena. Anyone looking at the skull of a Neanderthal and a modern human knows there are. There are also likely bio-behavioral differences between extent populations. Gene-culture coevolution is a real process, even if the details need to be worked out. But the interplay between biology and culture is complex, and in many cases cultural changes are driving the biological change, and then fixing differences which are advantageous to the “winners” (lactase persistence seems rather to be a perfect case of this). But just as in the individual case we must also remember that winning is often in part a function of being lucky. Naturally selection, generally thought of as a deterministic process, is also to some extent stochastic[4].

*From genetic islands to a roiling sea of humans*

One of the most shocking things for many of the geneticists working in the area of ancient DNA, and encountering the variation of the past, is the high level of population structure. That is, you have groups co-resident for many generations who nevertheless exhibit genetic distances of intercontinental scale. But as I stated above David Reich himself found the same results for India. And, in Africa you have long symbiotic populations, such as the pygmy groups of the Congo, and their agricultural neighbors, who are genetically very different, and have been for tens of thousands of years. Allentoft et al. dryly observe that “These results are indicative of significant temporal shifts in the gene pools and also reveal that the ancient groups of Eurasia were genetically more structured than contemporary populations.”

castesofmind About 10 years ago I read Nicholas Dirks’ Castes of Mind. Dirks is an eminent scholar who is now the chancellor of UC Berkeley. He emphasizes the power of European categories and systematization in creating the modern caste system. I don’t want to reduce his argument to a caricature. Obviously caste predates European colonialism. Dirks would admit this. But in Castes of Mind it is hard to shake the feeling that he believes that the British imposition of formalization made it what we truly understand it to be today. That caste has to be understood as a contemporary and early modern phenomenon, rather than an ancient one that was a structural feature of South Asian society.

The genetic evidence is clear now, and it paints a very different landscape. Many of the caste, even jati, boundaries we see today are thousands of years old. Endogamy long predates the British. It may predate the Aryans! Rather than the British, or Aryans, inventing caste, this form of ethnic segregation may date to the initial admixture event, to be reinvented and modified with each new population which arrives and imposes its hegemony on the subcontinent. In The New York Times David Reich states “You have groups which are as genetically distinct as Europeans and East Asians. And they’re living side by side for thousands of years.” He then he goes on to say “There’s a breakdown of these cultural barriers, and they mix,” alluding to the rise in WHG ancestry in farmer samples over time. Of course it is interesting to remember Reich’s work on India has highlighted exactly how persistent caste has been, and how it maintains genetic variation in a localized region that is often nearly inter-continental in magnitude.

We can never know if 6,000 years ago the LBK people, the first farming culture of Northern Europe, imposed a caste-like system of segregation when encountering the indigenous hunter-gatherers. Nor can we say with total confidence whether their relationship exhibited a symbiosis analogous to that between the Bantu agriculturalists and pygmies of the Congo (though do note that in these scenarios the Bantu communities are higher status, and the individual pygmies often have a semi-slave status). But, we need to look to what cultural evolutionary models and empirical results can tell us to make sense of these patterns. Ancient DNA can tell us very concretely the details of changes in allele frequencies. We can somewhat confidently reconstruct the faces and complexions of our ancestors. The questions population genomicists ask and answer in relation to animal models are relatively cleanly addressed by these data sets, assuming the sample sizes are large enough. But humans are the cultural animal par excellence, and that is the critical new variable which will require a new set of scholars to come together and create a truly multi-disciplinary understanding of the human past, present, and perhaps future. Powerful genomic techniques which produce results which have implications for the study of human history needs to leverage the full array of scholars who study human historical science.

1 – The three-fold copying is an important matter, because the different cultures had different preferences and goals. The Arab effort for example focused mostly on the philosophical production of the ancients. Without the Byzantines we would have far less of the humanistic production of Classical Greece, in particular the theatrical tradition.

2 – Much of what is known about the diplomatic history of the Bronze Age Near East has been preserved in cuneiform tablets. Though unwieldy, this form of writing on clay tablets is obviously more robust and less dependent upon copying than parchment and papyrus which came later.

3 – I would be curious to know if it is the same haplotype as is currently common in Eurasia.

4 – New mutations will usually go extinct, even if they are favored, in the initial generations. It is only when the frequency becomes high enough due to chance that selection will inevitably drive its frequency up, perhaps to fixation.

 
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713c9hKhvqL._SL1500_ So I just bought the Kindle Version of The Shape of Ancient Thought: Comparative Studies in Greek and Indian Philosophies for $3.99. At 780 pages this is a substantial work, and from what I can tell it’s an academically oriented text (not one of those Kindle “books” which are cut & paste jobs out of Wikipedia). Yet strangely the hardcover edition is much more expensive, at $39.99. That’s a huge discount. Additionally, the “digital list price” is $33.99. Is this incredible deal random? Or does Amazon know that I’m likely to buy this book at this price point? The only non-introductory population genetics text that I know of on Kindle is Matthew Hamilton’s, and it’s Kindle price is $58.99, pretty steep. I generally avoid buying books which might have figures and mathematical symbols in electronic format, because they don’t always render well on a Kindle, but if the Hamilton book was cheap enough I’d go for it (I don’t have a physical copy because I’ve got all the other major population genetics textbooks already).

Also, my friend Ryan Baldini just put up a paper on bioRxiv that some readers might find of interest, Harsh environments and “fast” human life histories: What does the theory say?. I’ll have more comment when I’ve thoroughly read the paper.

 
• Category: History • Tags: History 
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51Jb17R6p6L._SY344_BO1,204,203,200_ Adrian Goldsworthy’s The Fall of Carthage: The Punic Wars 265-146BC is illustrated on its cover with a photograph of a bust of Hannibal Barca. As you may know Hannibal was the general who led the armies of Carthage in the Italian peninsula during the Second Punic War, to great effect. In fact, until the battle of Zama in North Africa, during the last phases of the war, Hannibal did not lose to a Roman army. And yet despite his record of victory in tactical engagements, he was strategically bested by the Romans and lost the war. Unsurprisingly if there is one figure who looms large in the narrative of The Fall of Carthage it is Hannibal. This is striking because almost all of what we know about these wars comes down to us thanks to the Romans, so our perceptions are coloured by their biases, and he was their great antagonist. And yet it is undeniable that Hannibal’s raw tactical genius won grudging admiration and respect from the Romans. He was a singular figure, with no equivalent among the Romans of his era, with all due apologies to Scipio Africanus. And yet Rome won, and Carthage lost.

9780300137194 Goldsworthy is a military historian, so I was aware that he would focus on the minutiae of military logistics as well as outlining numerous set piece battles. Much of his How Rome Fell dealt with the slow decay of the Roman military system of the early empire over the course of the 3rd century, and the reorganization of the 4th century, which temporarily halted the decline, while ultimately undermining it in the long term through a reliance on allies who exhibited less attachment to Romanitas. One could argue in many ways the late antique Roman military complex resembled that of Carthage more than that of Rome during the late republic and early empire. Though the author gives much space to battles and campaigns, aside from the incredible retelling of the battle of Cannae, one can gloss over the details without loss of the general thrust of the narrative. Battles are won and lost, but the lessons from the war can not be reduced down to the battles.

historyofrome It was simply improbable that Carthage could win a military conflict with Rome over the long run because the Roman system conferred upon the Roman state material and ideological advantages which could not be overcome by military victories, even by a general as creative and competent as Hannibal. The Hellenistic king Pyrrhus learned this, and gave us the term “pyrrhic victory”. In ideological terms Goldsworthy argues that the Roman mindset was one where conflicts were viewed as wars of attrition, where only the victors were left standing. In contrast Carthage, like the Hellenistic states, operated in a more classical Westphalian framework where victory and defeat were never final, but simply instances of a continuous game between elites of distinct polities. But, if it was not for the material advantages of the Roman system its ideological orientation would have been suicidal, because wars of attrition can only be maintained when there are resources to feed them. The Romans relied upon conscript armies of free peasantry, committed to the idea of their republic as an expression of collective will, as well as Italian allies of long standing. Goldsworthy notes that no individual of the Roman elite betrayed their city, nor did any of the Latin allies (the cities who went over to Hannibal during his years in Italy tended to be culturally distant from Rome, whether non-Latin Italian or Greek). And, the citizen base of Rome was notoriously broad, because the Roman system was expansive, assimilating allies and elites of foreign polities over time. This is an ancient feature of Roman society, as at least half of the major patrician lineages are not Latin, but Sabine. This is in contrast to organization of Hellenistic or Carthaginian polities, which were not assimilative, but multicultural and cosmopolitan in a manner more resembling the later Roman system of the imperial period, or empires more generally.* The armies of Carthage and the Hellenistic kingdoms were not manned by citizens, but professionals, whether a standing army, or mercenaries and subject peoples. The army deployed by Hannibal consisted of Libyans, Spaniards, and assorted Italian peoples inimical to the Romans (e.g., the Gauls of the Po valley). Until the last of the conflicts between Rome and Carthage, which took place in the immediate environs of Carthage, Roman amateur soldiers lined up against armies in the service of Carthage, not armies of Carthaginians.

warinhumancivilization The robustness of the Roman system to defeat can be put down to the fact that like the armies of the French Revolution Rome threw its citizenry against its enemies to complete a broad mission, while its contemporaries purchased smaller professional armies to achieve specific tasks. In many circumstances these professionals could obtain victory, but the gains did not have the depth to force the concession of the Roman state, because the state was an expression of the populace, which remained defiant. In Azar Gat’s expansive War in Human Civilization the author reports that numbers available to the military are the major predictor of victory in battle and war. In other words, the side that can throw more resources into the conflict can win if it so chooses. Sometimes those resources are not so obvious to contemporaries. For example, Britain’s rise to power in the 18th century has often been attributed to its ability to borrow money to finance its wars (in contrast, many continental polities were not as creditworthy, and so lacked as many financial resources). There are cases where individuals of particular genius and charisma can change the calculus; Gat for example states that Napoleon Bonaparte’s armies were as successful as forces which were nearly 30% bigger. In other words, Napoleon’s particular genius was worth a third again as many soldiers as he actually had at his disposal. And yet ultimately Napoleon lost his wars . The French innovation of the early modern period of conscripting the whole nation for war could only gain them advantages for so long as other Europeans nations did not imitate them. When they did so they ultimately surpassed them in raw quantity, and emerged victorious.

warandpeaceandwar The particular story in The Fall of Carthage dovetails perfectly with the general model in Peter Turchin’s War and Peace and War: The Rise and Fall of Empires. The Romans of the republic had asabiyah, social cohesion. Against their enemies they exhibited a stance where they accepted that the only alternatives were collective victory or collective extinction. One can speculate why this was so, but clearly that is the key variable in the rise of Rome in the world after the death of Alexander. And it explains the fall of Carthage, which in many ways was a Hellenistic polity, rather than an heir to the ancient traditions of the Levant. In the sense of microeconomics the Carthaginians were homo economicus in comparison to the Romans. The years before the Third Punic War were ones of incredible prosperity for the city of Carthage, as documented in the Roman literary sources as well as archaeology. Rome fought Carthage not because it was weak and poor, but because it was strong and rich. And Rome won because its citizens loved their city more than could be accounted for by any rational calculation. Rome rose as an idea, and it fell as an idea.

* Because history is written by the winners we have little direct documentation from Carthage, but it is noteworthy that the city seems to have resembled Rome’s mixed system of governance, down to having a senate.

 
• Category: History • Tags: History, Punic Wars, Rome 
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Cite: Bryc, Katarzyna, et al. "The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States." The American Journal of Human Genetics (2014).

Cite: Bryc, Katarzyna, et al. “The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States.” The American Journal of Human Genetics (2014).

The recent paper, The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States, brings together a lot of results which 23andMe has been letting slip in bits and pieces over the years. Most of the press coverage has focused on racial dynamics at the level we’re used to talking about today in the United States. White, black, and Latino (of whatever race). But as I told the first author at BAPG a few weeks ago the dynamics among white Americans is probably where their massive data set can shine. You see it in the figure above, which confirms what many have suspected: the states of the inland South have retained a predominant Anglo-American settler population down to the present. This is clear in their very high fraction of people of “British-Irish descent” in 23andMe Ancestry Composition nomenclature. Including the black American population the overwhelming majority of the population likely descends from people were already resident in the future continental United States in 1776 in this region. Additionally, you can tell that these results are not crazy because in the north Indiana has higher fractions than either Ohio or Illinois, which is exactly what you’d expect if you knew something about the demographic histories of these states. Indiana experienced less migration from European populations who were not of settler stock than Illinois (Chicago) and Ohio (Cleveland and Cincinnati). Similarly, Maine’s elevated fraction makes sense since rural Yankees are demographic more dominant in northern New England than they are in the southern states. Finally, the states of the old Yankee Empire of the northern Old Northwest have been totally demographically transformed by the massive waves of migration from Germany and Scandinavia.

The distinction between settler and immigrant Europeans is clear in relation to detectable non-European ancestry:

We find very low levels of African and Native American ancestry in Europeans with four grandparents born in Europe. We estimate that only 0.98% of Europeans carry African ancestry and 0.26% of Europeans carry Native American ancestry. These levels are substantially lower than the 3.5% and 2.7% of European Americans who carry African and Native American ancestry, respectively…Excluding countries that had major and minor ports in the Atlantic with strong connections to the slave trade (namely Portugal, Spain, France, and United Kingdom) and Malta, which has been the site of migrations from Africa and the Middle East, we obtain a data set of 9,701 Europeans, where we find African and Native American ancestry is virtually absent, with only 0.04% of individuals carrying 1% or more African ancestry and 0.01% carrying 1% or more Native American ancestry, within the margins of survey error estimates.

32081 The African admixture in places like the American South is almost all a function of admixture in the first 150 years or so of settlement (the exception might be Louisiana, where Spanish Creoles may have contributed some African ancestry). The historical and genetic data seem to align there. Though the racial caste system in the American South had an early origin, it became progressively more calcified and stationary as the decades progressed. But by the late 19th century when Jim Crow laws were enacted the African admixture in many Southerners was a very distant memory and thoroughly diluted. To gauge the social and demographic import, recall that detection of genetic fragments does not reflect the total genealogy. Many people with ancestors who were black American slaves do not carry any segments from those individuals, while the ones being detected in this study exhibit a relative enrichment.

In the future I would be very curious about exploring the patterns of relationship of the Anglo-American folkways, as outlined in works such as Albion’s Seed and the The Cousins’ Wars. A major problem though is that these are genetically very close to begin with. The first author of the above work suggested to me that they would need the People of the British Isles data set to get good reference populations. Perhaps in the near future that will be feasible.

 
• Category: Science • Tags: History 
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k10064 Last week the American armed forces attacked a Syrian branch of al Qaeda which went by the name Khorasan. If you read around the web you’ll be informed that the term, a geographic one referring to the lands of Islam’s east, along the fringes of Persia, Central Asia, and western South Asia, is freighted with historical resonance for jihadis whose ideology is strongly inflected by a romantic vision of Islam’s past. By coincidence over the past few weeks I’ve been reading Lost Enlightenment, a book which chronicles Central Asia’s contribution to early Islamic civilization, and therefore a story in which Khorasan looms very large. Of course you don’t need a book length treatment on an obscure historical topic (though I would argue Central Asian shouldn’t be obscure, it is) to understand why Khorasan is important in the imaginations of jihadis. 41OxoLpuNyL._SY344_BO1,204,203,200_ To keep it succinct, though Salafis and their fellow travelers idealize the period of the Rashidun caliphs which ended ~660 A.D., the real historical basis of their movement in terms of an idealized period which is not mythological is that of the early Abbasids, after 750 A.D., and especially 800 A.D. And it is under the Abbasids that the motor engine of Islamic civilization shifted to the east, to Khorasan, the source of the armies which fueled their initial victories, and later of the soldiers and intellectuals who solidified their regime. Though Baghdad was the capital of the Abbasid Caliphate, the tendrils of influence and power always led back to the east so long as the polity was vigorous.

These extremist Islamic sects and movements always seem to deal in mythology and the legends of their own past. Though much of the fabric of their reality is fiction, there is often a thin scaffold of historical basis which serves as a skeleton around the narrative. I am not sure how critical it is to understand this scaffold, but it probably wouldn’t hurt. To some extent these radicals seem to speak in an inadvertent code, in that Western audiences as totally lacking in the historical consciousness that is necessary to properly interpret and comprehend considered and conscious semantic choices.

 
• Category: Foreign Policy • Tags: History 
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Raptus_EuropaeI’ve mentioned the preprint Ancient human genomes suggest three ancestral populations for present-day Europeans several times, but I thought that I would highlight that there has been a substantial revision as of April 5th. One section I think points to possible future results, and where we are now. The authors conclude (before the methods): Three questions seem particularly important to address in follow-up work. Where did the EEF obtain their WHG ancestry? Southeastern Europe is a candidate as it lies along the path from Anatolia into central Europe. When and where the ancestors of present-day Europeans first acquire their ANE ancestry? Based on discontinuity in mtDNA haplogroup frequencies, this may have occurred ~5,500-4,000 years ago in Central Europe. When and where did Basal Eurasians mix into the ancestors of the EEF? An important aim for future work should be to collect DNA from additional ancient samples to illuminate these transformations As is clear from their results to a first approximation to be genetically European entails ~20 on the order of 10 percent ANE ancestry. If the admixture in most of Europe dates to 5,500 to 4,000 years ago, then it is possible that the basic historical framework which serves as the backdrop for the Epic of Gilgamesh was contemporaneous with the emergence of populations which we would recognize as European! I am rather doubtful as to the power of ancient myths rooted in the Bronze Age to give us deep insights about prehistory, mostly because the myths themselves are often sprawling enough that they can be “fit” to a host of diverse scenarios. But, it does suggest that it is possible that Greek myths which date back to the Bronze Age may actually be somewhat informative, even if by chance, of the origins of the peoples and places of antiquity.

 
• Category: History • Tags: Europeans, Genetics, History 
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"