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Fires in the Forest: The Revolution in Human Evolution

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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  1. Anonymous says:     Show CommentNext New Comment

    I have nothing of value to add, Razib, just thanks for this. I feel it will be one of your classics, it’s exactly the sort of commentaries-cum-syntheses on Indo-Europeans and haplogroups that made me fall in love with your blog in the first place, updated for 2015.

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  2. R1b, me. Interestingly (to me) my mtDNA is U5b1b which I understand is WHG or a derivative thereof and at rather low frequency now, except among the Sami (I mean U5) where it occurs at 50% (and who are now recognised as the only indigenous Europeans), and to a lesser extent among Basques and Berbers. Of course, whole genome I am largely white bread northern European, except for two outliers, one of which I already knew about by tracing genealogy, location, parish records and adding 1+1, and one which came as a total surprise – Iberian, with a lesser portion of North African (at least, I am assuming the North African came as a part of the Iberian).

    So one of my favourite genetic jokes is to wonder if I can claim to be indigenous to two different continents on opposite sides of the world, via two rather small pieces of ancestry. Or maybe even three.

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  3. You speak of replacement, but what I see in this data is the triumph of hybrid vigour.

    So much for the men. But the children of men will be both sexes. If their mothers were different enough, children more heterozygous than either parental line, might also have better immune function, more resistance to trauma, and have longer life-expectancy. Add the support of a male-descent system, and it is not surprising that Y chromosomes show “replacement” – males of all ages are far more fragile, and it is not unlikely that even among the mixed offspring, males whose fathers were among the elite were more likely to survive to adulthood.

    Given that Eurasia (and the Americas and Australia etc) effectively lost diversity in the hypothesized bottleneck (out of Africa was likely to have been a trickle) the recurrent mixing in Eurasia (due to the emergence of economic diversity during the Holocene) has likely been quite beneficial. Disease was probably a potent aspect of natural selection throughout all these complex historical “punctuated turnover events”. I love that phrase, by the way.

    I agree that many hunter-gatherers were probably subject to genocide as their lands were increasingly expropriated by farmers. Is this not the essential narrative of one of the first written histories? The book of Gilgamesh (~2100 BC) tells of the murder of ‎Humbaba – the “guardian” of the forest, and the subsequent destruction of the the great cedar forests of Iraq – the wood was used to build Ur. Agro-pastoral people would require pasture as well as arable land, but tend not to build cities. It might seem that they would be less likely to engage in trade or rent collection and more likely to simply exterminate inconvenient people, however that was not the case in Africa: indeed, it was not even the case in Eurasia.

    Farming and pastoral peoples tend to develop a kind of economic symbiosis, even though the pastoral people, being mobile and often mounted and accustomed to raiding each other (mostly rustling each other’s livestock) and in some cases made stronger by segmentary unification to form very large armies, are often politically dominant no matter what resistance the farmers put up. The desire for complete genocides, described in the old testament, are essentially a cycle of origin myths: it is not clear if they represent real events,let alone some ancient cultural paradigm. Certainly archaeology has not been very successful in substantiated these accounts. Whether the Israelites were a mobile pastoral people who came to dominate sedentary farmers is not even clear, let alone whether they were actually ever slaves in under the Egyptian Pharaohs. As for Abraham and Moses, or Noah, for that matter, please. You might as well claim Adam and Eve, although if you do, they were hunter-gatherers, and ‎Humbaba was their child that stayed in the wilderness.

    You say “And so the story ties back to the beginning” but what beginning do you mean? In the beginning there was a very successful species that had spread all over Africa and then radiated all over Eurasia, a species that survived four or five times longer than our own species has so far. Homo erectus continued to evolve with each shift of drought and ice to warming and wetter spells that decimated some of our co-evoled Pleistocene fauna.. and became, by a quarter of a million years ago, very well adopted to living as a cultural being, a polytypic species throughout the whole of this range. The next wave of radiation out of Africa absorbing the icebound remnants of in Eurasia in the middle of the last glacial period, the rest of the terrestrial globe was occupied.

    Or perhaps we can take it back further, to a small bipedal critter wandering around in Africa 3 or 4 million years ago? I find this longer view kind of poignant, and also it fills me with wonder to think of the little boy in your arms as laying claim to this immense heritage.

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    • Replies: @szopen
    You do not have to engage in genocide to achieve almost complete replacement of the subdued natives.
    , @John Massey
    The recent earlier date for the emergence of Yersinia pestis fits well with this narrative. It is now known that the Yamnaya had it. Early epidemics would have relied on spreading the pneumonic form, probably in small groups. It did not kill everyone infected - the fatality rate is thought to have been about 50%, the survivors likely to have been the younger, stronger and healthier.
    , @Razib Khan
    but what I see in this data is the triumph of hybrid vigour.

    that's a specific genetic term. unless there is massive inbreeding (which actually was the case in some areas) unlikely to be much of this, or depression.

    Disease was probably a potent aspect of natural selection throughout all these complex historical “punctuated turnover events”.

    i didn't explore it. there is some evidence for selection on immune loci for LBK.

    I agree that many hunter-gatherers were probably subject to genocide as their lands were increasingly expropriated by farmers.

    many researchers in ancient DNA have told me they don't think there is much local HG ancestry in most of europe. that the HG ancestry we see is from amalgamation events of a particular population, which later expanded.

    Certainly archaeology has not been very successful in substantiated these accounts.

    archaeology would have to find physical genocides. i'm pretty clear here in this post that simple excess die off can have the same effect.
  4. I wonder when we will see first ancient full genomes from East, Southeast and South Asia. As of know, we have some ancient full genomes from all other parts of the world(Europe, North and South Americas, Siberia, Middle East and even Africa). AFAIK there was full-genome analysis of Jomon samples, but results were not published in a journal.

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    • Replies: @Razib Khan
    I wonder when we will see first ancient full genomes from East, Southeast and South Asia.

    east asia is on deck. there are aDNA researchers moving to china.
  5. @Helga Vierich
    You speak of replacement, but what I see in this data is the triumph of hybrid vigour.

    So much for the men. But the children of men will be both sexes. If their mothers were different enough, children more heterozygous than either parental line, might also have better immune function, more resistance to trauma, and have longer life-expectancy. Add the support of a male-descent system, and it is not surprising that Y chromosomes show “replacement” - males of all ages are far more fragile, and it is not unlikely that even among the mixed offspring, males whose fathers were among the elite were more likely to survive to adulthood.

    Given that Eurasia (and the Americas and Australia etc) effectively lost diversity in the hypothesized bottleneck (out of Africa was likely to have been a trickle) the recurrent mixing in Eurasia (due to the emergence of economic diversity during the Holocene) has likely been quite beneficial. Disease was probably a potent aspect of natural selection throughout all these complex historical "punctuated turnover events". I love that phrase, by the way.

    I agree that many hunter-gatherers were probably subject to genocide as their lands were increasingly expropriated by farmers. Is this not the essential narrative of one of the first written histories? The book of Gilgamesh (~2100 BC) tells of the murder of ‎Humbaba - the “guardian” of the forest, and the subsequent destruction of the the great cedar forests of Iraq - the wood was used to build Ur. Agro-pastoral people would require pasture as well as arable land, but tend not to build cities. It might seem that they would be less likely to engage in trade or rent collection and more likely to simply exterminate inconvenient people, however that was not the case in Africa: indeed, it was not even the case in Eurasia.

    Farming and pastoral peoples tend to develop a kind of economic symbiosis, even though the pastoral people, being mobile and often mounted and accustomed to raiding each other (mostly rustling each other’s livestock) and in some cases made stronger by segmentary unification to form very large armies, are often politically dominant no matter what resistance the farmers put up. The desire for complete genocides, described in the old testament, are essentially a cycle of origin myths: it is not clear if they represent real events,let alone some ancient cultural paradigm. Certainly archaeology has not been very successful in substantiated these accounts. Whether the Israelites were a mobile pastoral people who came to dominate sedentary farmers is not even clear, let alone whether they were actually ever slaves in under the Egyptian Pharaohs. As for Abraham and Moses, or Noah, for that matter, please. You might as well claim Adam and Eve, although if you do, they were hunter-gatherers, and ‎Humbaba was their child that stayed in the wilderness.

    You say “And so the story ties back to the beginning” but what beginning do you mean? In the beginning there was a very successful species that had spread all over Africa and then radiated all over Eurasia, a species that survived four or five times longer than our own species has so far. Homo erectus continued to evolve with each shift of drought and ice to warming and wetter spells that decimated some of our co-evoled Pleistocene fauna.. and became, by a quarter of a million years ago, very well adopted to living as a cultural being, a polytypic species throughout the whole of this range. The next wave of radiation out of Africa absorbing the icebound remnants of in Eurasia in the middle of the last glacial period, the rest of the terrestrial globe was occupied.

    Or perhaps we can take it back further, to a small bipedal critter wandering around in Africa 3 or 4 million years ago? I find this longer view kind of poignant, and also it fills me with wonder to think of the little boy in your arms as laying claim to this immense heritage.

    You do not have to engage in genocide to achieve almost complete replacement of the subdued natives.

    Read More
  6. Before commenting on the article itself, I would like to put a question.

    Do we know when exactly, the paper by Lazaridis et al is coming out ? And are there any major aDNA papers besides Lazaridis et al, that may be published soon ?

    —————-

    Coming to the article, I would not comment on the general theme.

    I would like to point out that the Abrahamic/Sumerian flood myth has strong parallels in the Indian tradition as well in the story of Manu Vaivasavata – https://www.academia.edu/9981910/Some_Observations_on_the_Indian_and_the_Mesopotamian_Flood_Myths

    The Indian flood myth is likely a remnant of a common Indo-European myth. And its parallel with the Mesopotamian/Abrahamic myth is worth investigating.

    There is also a lot of word correspondence between Sumerian and the Indo-European languages – http://new-indology.blogspot.in/2015/05/sumerian-and-indo-european-surprising.html

    So, a possibility of a deep shared origin between the Indo-Europeans and the Middle Easterners dating to the early Holocene should be looked into.

    ——————

    Regarding the absence of ASI into the steppe and elsewhere negating the possibility of an Out of India movement, the EHG (Eastern European Hunter Gatherer) ancestry is nowhere to found in South Asia. Hence, it would have to be argued that a movement from the steppe into South Asia is also not possible. Or else, where is EHG in South Asia ?

    It should also not be forgotten that according to Moorjani et al paper, the ANI-ASI admixture could be dated by them earliest to only 4200 BP. If there was an Out of India movement of Indo-Europeans, it must have already taken place much before 4200 BP because of the early dates we have for Yamnaya. Hence, you are unlikely to find ASI admixture among a migrant population in Europe or Middle East, even if it had come from somewhere in Afghanistan/Pakistan. Now if the assumptions of the Moorjani paper are wrong, thats an entirely different story.

    ——————–

    It may also be worthwhile to note that the West Eurasian mtDNA while not in majority, appears to be very high in South Asia. According to the Palanichamy et al paper of a few months back, mtDNA U alone accounts for 40 % of all mtDNA lineages in India. Besides this, we also have other West Eurasian mtDNA in India such as H, HV, R, T etc. By all indicators this is a very large proportion of mtDNA lineages in India. It is therefore unlikely that only a male-mediated migration took place, whichever direction it was.

    ——————–

    Lastly, it should also be noted that sporadic instances of South Asian mtDNA among ancient Bronze Age (or earlier) samples in the Middle East and in the Tarim Basin have taken place.

    - http://eurogenes.blogspot.in/2015/10/mitochondrial-dna-from-maykop-wolfgang.html

    - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4192148/pdf/pone.0109331.pdf

    - http://www.biomedcentral.com/content/pdf/s12863-015-0237-5.pdf

    This should also be investigated.

    Apologies if I have strayed far off from the subject.

    Read More
    • Replies: @Razib Khan
    Do we know when exactly, the paper by Lazaridis et al is coming out ? And are there any major aDNA papers besides Lazaridis et al, that may be published soon ?

    probably early next year? there are some simon's foundation papers coming up in a month or so. that's first.

    Regarding the absence of ASI into the steppe and elsewhere negating the possibility of an Out of India movement, the EHG (Eastern European Hunter Gatherer) ancestry is nowhere to found in South Asia. Hence, it would have to be argued that a movement from the steppe into South Asia is also not possible. Or else, where is EHG in South Asia ?

    apparently there is WHG-like stuff on the north fringe (and jatts?). the IE footprint in much of s asia even in IE speaking areas is probably pretty low. that's why i emphasized the Y chromosomal lineage. i think it made an outsized impact there, but far less so on the autosome (aside from a few groups in the NW).

    It should also not be forgotten that according to Moorjani et al paper, the ANI-ASI admixture could be dated by them earliest to only 4200 BP.

    their methods detect the last admixture. their paper also implies that there were two admixture events. i think most of the ANI is actually not indo-european, but came with dravidian languages. that's why you see less ANE and anything WHG-like (which would be highly diluted since EHG is only 50% WHG-like) in most of the subcontinent.

    It may also be worthwhile to note that the West Eurasian mtDNA while not in majority, appears to be very high in South Asia.

    i think most of this is probably pre-Indo-European agriculturalists. also, some of it (like U2b, my own mtDNA) may date back to the pleistocene.
    , @Doug Jones
    Flood stories are very widespread. The gods grow angry with humans, send flood waters either from the sky or the earth, almost everyone drowns, but a few survivors, maybe a single family, on a hilltop or a raft survive and repopulate the world: you find this story throughout Eurasia, and in the New World as well. Where these stories come from I don't think anyone knows. They mostly predate missionary influence. https://logarithmichistory.wordpress.com/2015/09/01/mythopoeia/
  7. Anonymous says:     Show CommentNext New Comment

    “Desire for complete genocides, dexcribed in the old testament, are essentially a cycle of origin myths”
    As a liberal, this is attractive

    Read More
  8. @Helga Vierich
    You speak of replacement, but what I see in this data is the triumph of hybrid vigour.

    So much for the men. But the children of men will be both sexes. If their mothers were different enough, children more heterozygous than either parental line, might also have better immune function, more resistance to trauma, and have longer life-expectancy. Add the support of a male-descent system, and it is not surprising that Y chromosomes show “replacement” - males of all ages are far more fragile, and it is not unlikely that even among the mixed offspring, males whose fathers were among the elite were more likely to survive to adulthood.

    Given that Eurasia (and the Americas and Australia etc) effectively lost diversity in the hypothesized bottleneck (out of Africa was likely to have been a trickle) the recurrent mixing in Eurasia (due to the emergence of economic diversity during the Holocene) has likely been quite beneficial. Disease was probably a potent aspect of natural selection throughout all these complex historical "punctuated turnover events". I love that phrase, by the way.

    I agree that many hunter-gatherers were probably subject to genocide as their lands were increasingly expropriated by farmers. Is this not the essential narrative of one of the first written histories? The book of Gilgamesh (~2100 BC) tells of the murder of ‎Humbaba - the “guardian” of the forest, and the subsequent destruction of the the great cedar forests of Iraq - the wood was used to build Ur. Agro-pastoral people would require pasture as well as arable land, but tend not to build cities. It might seem that they would be less likely to engage in trade or rent collection and more likely to simply exterminate inconvenient people, however that was not the case in Africa: indeed, it was not even the case in Eurasia.

    Farming and pastoral peoples tend to develop a kind of economic symbiosis, even though the pastoral people, being mobile and often mounted and accustomed to raiding each other (mostly rustling each other’s livestock) and in some cases made stronger by segmentary unification to form very large armies, are often politically dominant no matter what resistance the farmers put up. The desire for complete genocides, described in the old testament, are essentially a cycle of origin myths: it is not clear if they represent real events,let alone some ancient cultural paradigm. Certainly archaeology has not been very successful in substantiated these accounts. Whether the Israelites were a mobile pastoral people who came to dominate sedentary farmers is not even clear, let alone whether they were actually ever slaves in under the Egyptian Pharaohs. As for Abraham and Moses, or Noah, for that matter, please. You might as well claim Adam and Eve, although if you do, they were hunter-gatherers, and ‎Humbaba was their child that stayed in the wilderness.

    You say “And so the story ties back to the beginning” but what beginning do you mean? In the beginning there was a very successful species that had spread all over Africa and then radiated all over Eurasia, a species that survived four or five times longer than our own species has so far. Homo erectus continued to evolve with each shift of drought and ice to warming and wetter spells that decimated some of our co-evoled Pleistocene fauna.. and became, by a quarter of a million years ago, very well adopted to living as a cultural being, a polytypic species throughout the whole of this range. The next wave of radiation out of Africa absorbing the icebound remnants of in Eurasia in the middle of the last glacial period, the rest of the terrestrial globe was occupied.

    Or perhaps we can take it back further, to a small bipedal critter wandering around in Africa 3 or 4 million years ago? I find this longer view kind of poignant, and also it fills me with wonder to think of the little boy in your arms as laying claim to this immense heritage.

    The recent earlier date for the emergence of Yersinia pestis fits well with this narrative. It is now known that the Yamnaya had it. Early epidemics would have relied on spreading the pneumonic form, probably in small groups. It did not kill everyone infected – the fatality rate is thought to have been about 50%, the survivors likely to have been the younger, stronger and healthier.

    Read More
  9. @Helga Vierich
    You speak of replacement, but what I see in this data is the triumph of hybrid vigour.

    So much for the men. But the children of men will be both sexes. If their mothers were different enough, children more heterozygous than either parental line, might also have better immune function, more resistance to trauma, and have longer life-expectancy. Add the support of a male-descent system, and it is not surprising that Y chromosomes show “replacement” - males of all ages are far more fragile, and it is not unlikely that even among the mixed offspring, males whose fathers were among the elite were more likely to survive to adulthood.

    Given that Eurasia (and the Americas and Australia etc) effectively lost diversity in the hypothesized bottleneck (out of Africa was likely to have been a trickle) the recurrent mixing in Eurasia (due to the emergence of economic diversity during the Holocene) has likely been quite beneficial. Disease was probably a potent aspect of natural selection throughout all these complex historical "punctuated turnover events". I love that phrase, by the way.

    I agree that many hunter-gatherers were probably subject to genocide as their lands were increasingly expropriated by farmers. Is this not the essential narrative of one of the first written histories? The book of Gilgamesh (~2100 BC) tells of the murder of ‎Humbaba - the “guardian” of the forest, and the subsequent destruction of the the great cedar forests of Iraq - the wood was used to build Ur. Agro-pastoral people would require pasture as well as arable land, but tend not to build cities. It might seem that they would be less likely to engage in trade or rent collection and more likely to simply exterminate inconvenient people, however that was not the case in Africa: indeed, it was not even the case in Eurasia.

    Farming and pastoral peoples tend to develop a kind of economic symbiosis, even though the pastoral people, being mobile and often mounted and accustomed to raiding each other (mostly rustling each other’s livestock) and in some cases made stronger by segmentary unification to form very large armies, are often politically dominant no matter what resistance the farmers put up. The desire for complete genocides, described in the old testament, are essentially a cycle of origin myths: it is not clear if they represent real events,let alone some ancient cultural paradigm. Certainly archaeology has not been very successful in substantiated these accounts. Whether the Israelites were a mobile pastoral people who came to dominate sedentary farmers is not even clear, let alone whether they were actually ever slaves in under the Egyptian Pharaohs. As for Abraham and Moses, or Noah, for that matter, please. You might as well claim Adam and Eve, although if you do, they were hunter-gatherers, and ‎Humbaba was their child that stayed in the wilderness.

    You say “And so the story ties back to the beginning” but what beginning do you mean? In the beginning there was a very successful species that had spread all over Africa and then radiated all over Eurasia, a species that survived four or five times longer than our own species has so far. Homo erectus continued to evolve with each shift of drought and ice to warming and wetter spells that decimated some of our co-evoled Pleistocene fauna.. and became, by a quarter of a million years ago, very well adopted to living as a cultural being, a polytypic species throughout the whole of this range. The next wave of radiation out of Africa absorbing the icebound remnants of in Eurasia in the middle of the last glacial period, the rest of the terrestrial globe was occupied.

    Or perhaps we can take it back further, to a small bipedal critter wandering around in Africa 3 or 4 million years ago? I find this longer view kind of poignant, and also it fills me with wonder to think of the little boy in your arms as laying claim to this immense heritage.

    but what I see in this data is the triumph of hybrid vigour.

    that’s a specific genetic term. unless there is massive inbreeding (which actually was the case in some areas) unlikely to be much of this, or depression.

    Disease was probably a potent aspect of natural selection throughout all these complex historical “punctuated turnover events”.

    i didn’t explore it. there is some evidence for selection on immune loci for LBK.

    I agree that many hunter-gatherers were probably subject to genocide as their lands were increasingly expropriated by farmers.

    many researchers in ancient DNA have told me they don’t think there is much local HG ancestry in most of europe. that the HG ancestry we see is from amalgamation events of a particular population, which later expanded.

    Certainly archaeology has not been very successful in substantiated these accounts.

    archaeology would have to find physical genocides. i’m pretty clear here in this post that simple excess die off can have the same effect.

    Read More
  10. @Nicky
    I wonder when we will see first ancient full genomes from East, Southeast and South Asia. As of know, we have some ancient full genomes from all other parts of the world(Europe, North and South Americas, Siberia, Middle East and even Africa). AFAIK there was full-genome analysis of Jomon samples, but results were not published in a journal.

    I wonder when we will see first ancient full genomes from East, Southeast and South Asia.

    east asia is on deck. there are aDNA researchers moving to china.

    Read More
  11. @Jaydeepsinh Rathod
    Before commenting on the article itself, I would like to put a question.

    Do we know when exactly, the paper by Lazaridis et al is coming out ? And are there any major aDNA papers besides Lazaridis et al, that may be published soon ?

    ----------------

    Coming to the article, I would not comment on the general theme.

    I would like to point out that the Abrahamic/Sumerian flood myth has strong parallels in the Indian tradition as well in the story of Manu Vaivasavata - https://www.academia.edu/9981910/Some_Observations_on_the_Indian_and_the_Mesopotamian_Flood_Myths

    The Indian flood myth is likely a remnant of a common Indo-European myth. And its parallel with the Mesopotamian/Abrahamic myth is worth investigating.

    There is also a lot of word correspondence between Sumerian and the Indo-European languages - http://new-indology.blogspot.in/2015/05/sumerian-and-indo-european-surprising.html

    So, a possibility of a deep shared origin between the Indo-Europeans and the Middle Easterners dating to the early Holocene should be looked into.

    ------------------

    Regarding the absence of ASI into the steppe and elsewhere negating the possibility of an Out of India movement, the EHG (Eastern European Hunter Gatherer) ancestry is nowhere to found in South Asia. Hence, it would have to be argued that a movement from the steppe into South Asia is also not possible. Or else, where is EHG in South Asia ?

    It should also not be forgotten that according to Moorjani et al paper, the ANI-ASI admixture could be dated by them earliest to only 4200 BP. If there was an Out of India movement of Indo-Europeans, it must have already taken place much before 4200 BP because of the early dates we have for Yamnaya. Hence, you are unlikely to find ASI admixture among a migrant population in Europe or Middle East, even if it had come from somewhere in Afghanistan/Pakistan. Now if the assumptions of the Moorjani paper are wrong, thats an entirely different story.

    --------------------

    It may also be worthwhile to note that the West Eurasian mtDNA while not in majority, appears to be very high in South Asia. According to the Palanichamy et al paper of a few months back, mtDNA U alone accounts for 40 % of all mtDNA lineages in India. Besides this, we also have other West Eurasian mtDNA in India such as H, HV, R, T etc. By all indicators this is a very large proportion of mtDNA lineages in India. It is therefore unlikely that only a male-mediated migration took place, whichever direction it was.

    --------------------

    Lastly, it should also be noted that sporadic instances of South Asian mtDNA among ancient Bronze Age (or earlier) samples in the Middle East and in the Tarim Basin have taken place.

    - http://eurogenes.blogspot.in/2015/10/mitochondrial-dna-from-maykop-wolfgang.html

    - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4192148/pdf/pone.0109331.pdf

    - http://www.biomedcentral.com/content/pdf/s12863-015-0237-5.pdf

    This should also be investigated.

    Apologies if I have strayed far off from the subject.

    Do we know when exactly, the paper by Lazaridis et al is coming out ? And are there any major aDNA papers besides Lazaridis et al, that may be published soon ?

    probably early next year? there are some simon’s foundation papers coming up in a month or so. that’s first.

    Regarding the absence of ASI into the steppe and elsewhere negating the possibility of an Out of India movement, the EHG (Eastern European Hunter Gatherer) ancestry is nowhere to found in South Asia. Hence, it would have to be argued that a movement from the steppe into South Asia is also not possible. Or else, where is EHG in South Asia ?

    apparently there is WHG-like stuff on the north fringe (and jatts?). the IE footprint in much of s asia even in IE speaking areas is probably pretty low. that’s why i emphasized the Y chromosomal lineage. i think it made an outsized impact there, but far less so on the autosome (aside from a few groups in the NW).

    It should also not be forgotten that according to Moorjani et al paper, the ANI-ASI admixture could be dated by them earliest to only 4200 BP.

    their methods detect the last admixture. their paper also implies that there were two admixture events. i think most of the ANI is actually not indo-european, but came with dravidian languages. that’s why you see less ANE and anything WHG-like (which would be highly diluted since EHG is only 50% WHG-like) in most of the subcontinent.

    It may also be worthwhile to note that the West Eurasian mtDNA while not in majority, appears to be very high in South Asia.

    i think most of this is probably pre-Indo-European agriculturalists. also, some of it (like U2b, my own mtDNA) may date back to the pleistocene.

    Read More
  12. Breathtaking tapestry you waved here Razib.

    BTW in the genomic map what are slovaks doing smack between italians, greeks and turks?

    Read More
    • Replies: @Shaikorth
    There is just one SK on that dataset. That being said, I think a Slovak sample should not be clustering there unless it is fully Jewish.

    re: European components in S-Asia, at least for some Afghanistan and Pakistan populations qpAdm software produces good fits that include over 50% of BA steppe groups, who have high EHG.

    Then there are these TreeMix results from http://www.unz.com/gnxp/white-people-are-a-homoplasy/. Ten iterations with the larger dataset all look like this:
    http://www.unzcloud.com/wp-content/uploads/2015/08/KalashOut.21.jpg

    Look at how Hazara and Uygur, highly affected by Turkic migrations, are resolved. They're placed on the East Eurasian branch unlike other S-C Asian populations but unlike them get considerable migration edges from North Europe (always either common North-Central European root or Finland). It might seem odd that the edge is not from an actual BA steppe group (Yamnaya) but that never extended so far South, and later steppe groups like Sintashta were more like modern North Europeans than Yamnaya was.

  13. “… as simple as taking candy from a baby.”

    I tremble when I recall that you are the father of very small children, and feel for them when I think about the little weight you give to the long term effects of child-rearing practices on individuals’ outcomes.

    ;-)

    Read More
    • Replies: @iffen
    Don’t drop them on their head, don’t be a dickhead to your children, let them know that no matter what the rest of the world might think, there is at least one person who thinks they are great just because they exist. Razib’s kids are safe.
  14. @Pseudonymic Handle
    Breathtaking tapestry you waved here Razib.

    BTW in the genomic map what are slovaks doing smack between italians, greeks and turks?

    There is just one SK on that dataset. That being said, I think a Slovak sample should not be clustering there unless it is fully Jewish.

    re: European components in S-Asia, at least for some Afghanistan and Pakistan populations qpAdm software produces good fits that include over 50% of BA steppe groups, who have high EHG.

    Then there are these TreeMix results from http://www.unz.com/gnxp/white-people-are-a-homoplasy/. Ten iterations with the larger dataset all look like this:

    http://www.unzcloud.com/wp-content/uploads/2015/08/KalashOut.21.jpg

    Look at how Hazara and Uygur, highly affected by Turkic migrations, are resolved. They’re placed on the East Eurasian branch unlike other S-C Asian populations but unlike them get considerable migration edges from North Europe (always either common North-Central European root or Finland). It might seem odd that the edge is not from an actual BA steppe group (Yamnaya) but that never extended so far South, and later steppe groups like Sintashta were more like modern North Europeans than Yamnaya was.

    Read More
  15. “R1b and R1a transcend a connection to Indo-European ethno-linguistic groups” is a big takeaway from this. Especially in India, R1A is somehow associated with Indo-European languages and religion, whereas, R1A in India may have preceded the language expansion, and have no well-defined relationship to religion.

    Read More
  16. Seeking wealth is the goal of all human activities including education, war, business decision, proffesional sports, hard work, even marriage.

    Conquering lords might levy on native population or replace them with more productive immigrant population which can be from their own ethnic stock or different ethnic groups. European colonial history was good example of that. Winners in acient world were the one who have most wealth that even can recruit enemy soldiers into your own army. Soldiers are looking for wealth too. If your enemy pay you more, not sure how many can resist temptation. Chin, Han and Tang empires can effectively turn enemy soldiers fight their own lords for obvious reason.

    As lords, managment of your human cattle is not same simple task like true cattle. To attact and retain your human cattle or capital on to your territory, tax incentive often was given to new immigrant. Chin kindom did just that befor it could conquer the whole China. Dutch East Indian company did that in Taiwan. Hun invaders did similar thing in Europe to attract European farmers to settle in their land. Simple conquerring and treating your conquered people harshly could hardly be translated into final success. If conquered people are not very productive, then their fate is sealed. If conquered people are more productive than your own stock, it is was their own ethnic kin at risk like numerous sinicization incidences in Chinese history. At end, it is non-productive people at risk of fading away no matther who conquer who. For most farmers, they really don’t care who is the lord which can be ethnic same or different. They are seeking wealth too. They will only settle on the land that they can earn more.

    In today’s world, rich one still wins most time.

    Read More
    • Replies: @Razib Khan
    Seeking wealth is the goal of all human activities including education, war, business decision, proffesional sports, hard work, even marriage.

    If women didn’t exist, all the money in the world would have no meaning. ~Aristotle Onassis
  17. 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.

    Good choice using John Ross as an example. In fact, we can find a lot of recent examples in the New World. In my own part of the US there are many American Indians with surnames such as Anderson and Jensen because many of the local Scandinavian working men married into the tribes. This marriage into the tribe has benefits for both the natives and the newcomers, but mainly the newcomers. If you’re a lower status male such as a soldier, immigrant, or even a younger son of a lesser noble, marrying into the subjugated tribe gives you status you don’t have in your native society. It also allows you to act as an intermediary, and often a defender of your new tribe. In Mexico this seems to have occurred on a massive scale.

    So my guess is that there was some measure of symbiosis between the carriers of these Y chromosomes and the people they merged into. In essence, you give me a wife (or wives) and I defend your ways and culture. One can see the same thing with the Cambro-Normans who conquered much of Ireland following their conquest of England. After a few hundred years, the Cambro-Normans spoke Gaelic, practiced the traditional Celtic Christianity and stood up to the English when they began another colonization push in the 16th century.

    However, I’m not entirely sure patriarchy is the right word for what’s going on here. Real patriarchy, as I understand it, is more of a contract between men of the same tribe but different station; i.e. you serve under me and I leave your family alone.

    Read More
  18. @AG
    Seeking wealth is the goal of all human activities including education, war, business decision, proffesional sports, hard work, even marriage.

    Conquering lords might levy on native population or replace them with more productive immigrant population which can be from their own ethnic stock or different ethnic groups. European colonial history was good example of that. Winners in acient world were the one who have most wealth that even can recruit enemy soldiers into your own army. Soldiers are looking for wealth too. If your enemy pay you more, not sure how many can resist temptation. Chin, Han and Tang empires can effectively turn enemy soldiers fight their own lords for obvious reason.

    As lords, managment of your human cattle is not same simple task like true cattle. To attact and retain your human cattle or capital on to your territory, tax incentive often was given to new immigrant. Chin kindom did just that befor it could conquer the whole China. Dutch East Indian company did that in Taiwan. Hun invaders did similar thing in Europe to attract European farmers to settle in their land. Simple conquerring and treating your conquered people harshly could hardly be translated into final success. If conquered people are not very productive, then their fate is sealed. If conquered people are more productive than your own stock, it is was their own ethnic kin at risk like numerous sinicization incidences in Chinese history. At end, it is non-productive people at risk of fading away no matther who conquer who. For most farmers, they really don't care who is the lord which can be ethnic same or different. They are seeking wealth too. They will only settle on the land that they can earn more.

    In today's world, rich one still wins most time.

    Seeking wealth is the goal of all human activities including education, war, business decision, proffesional sports, hard work, even marriage.

    If women didn’t exist, all the money in the world would have no meaning. ~Aristotle Onassis

    Read More
  19. @Jaydeepsinh Rathod
    Before commenting on the article itself, I would like to put a question.

    Do we know when exactly, the paper by Lazaridis et al is coming out ? And are there any major aDNA papers besides Lazaridis et al, that may be published soon ?

    ----------------

    Coming to the article, I would not comment on the general theme.

    I would like to point out that the Abrahamic/Sumerian flood myth has strong parallels in the Indian tradition as well in the story of Manu Vaivasavata - https://www.academia.edu/9981910/Some_Observations_on_the_Indian_and_the_Mesopotamian_Flood_Myths

    The Indian flood myth is likely a remnant of a common Indo-European myth. And its parallel with the Mesopotamian/Abrahamic myth is worth investigating.

    There is also a lot of word correspondence between Sumerian and the Indo-European languages - http://new-indology.blogspot.in/2015/05/sumerian-and-indo-european-surprising.html

    So, a possibility of a deep shared origin between the Indo-Europeans and the Middle Easterners dating to the early Holocene should be looked into.

    ------------------

    Regarding the absence of ASI into the steppe and elsewhere negating the possibility of an Out of India movement, the EHG (Eastern European Hunter Gatherer) ancestry is nowhere to found in South Asia. Hence, it would have to be argued that a movement from the steppe into South Asia is also not possible. Or else, where is EHG in South Asia ?

    It should also not be forgotten that according to Moorjani et al paper, the ANI-ASI admixture could be dated by them earliest to only 4200 BP. If there was an Out of India movement of Indo-Europeans, it must have already taken place much before 4200 BP because of the early dates we have for Yamnaya. Hence, you are unlikely to find ASI admixture among a migrant population in Europe or Middle East, even if it had come from somewhere in Afghanistan/Pakistan. Now if the assumptions of the Moorjani paper are wrong, thats an entirely different story.

    --------------------

    It may also be worthwhile to note that the West Eurasian mtDNA while not in majority, appears to be very high in South Asia. According to the Palanichamy et al paper of a few months back, mtDNA U alone accounts for 40 % of all mtDNA lineages in India. Besides this, we also have other West Eurasian mtDNA in India such as H, HV, R, T etc. By all indicators this is a very large proportion of mtDNA lineages in India. It is therefore unlikely that only a male-mediated migration took place, whichever direction it was.

    --------------------

    Lastly, it should also be noted that sporadic instances of South Asian mtDNA among ancient Bronze Age (or earlier) samples in the Middle East and in the Tarim Basin have taken place.

    - http://eurogenes.blogspot.in/2015/10/mitochondrial-dna-from-maykop-wolfgang.html

    - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4192148/pdf/pone.0109331.pdf

    - http://www.biomedcentral.com/content/pdf/s12863-015-0237-5.pdf

    This should also be investigated.

    Apologies if I have strayed far off from the subject.

    Flood stories are very widespread. The gods grow angry with humans, send flood waters either from the sky or the earth, almost everyone drowns, but a few survivors, maybe a single family, on a hilltop or a raft survive and repopulate the world: you find this story throughout Eurasia, and in the New World as well. Where these stories come from I don’t think anyone knows. They mostly predate missionary influence. https://logarithmichistory.wordpress.com/2015/09/01/mythopoeia/

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  20. “In short, the phylogenomic history of the continent over the past ~10,000 years has been “solved” more or less.”

    In my view, some of the big “unsolved questions” with regard to the phylogenomic history of the continent are:

    1. What archeological cultures caused Western Europe to develop high levels of Y-DNA R1b, when did this happen, and what linguistic affiliations were involved? This probably overlaps with the story of what drove the rise of the LP gene in Europe.

    2. Did mtDNA H derive from the original expanding R1a/R1b population or was it picked up along the way, and if so, where?

    3. What is the story behind the ethnogenesis of the EEF population? How much European HG ancestry in Europe is attributable to this ethnogenesis and how much introgressed en route?

    4. What caused the dramatic decline of Y-DNA R1b among the people living in what was Yamnaya territory?

    5. Did the R1a/R1b expansion fill a vacuum that had already been created due to climate/crop failure, or was it conquest?

    6. When did Y-DNA E clades present in Europe expand there?

    7. What does the population transect over time in Anatolia look like? What about the Levant or Mesopotamia?

    8. How much ANI is Harappan and how much is Indo-European?

    9. How and when did Y-DNA T come to be so common in a few states of India?

    10. What is the story of Y-DNA R2 in Pakistan and the vicinity?

    11. How much demic impact did Islamic expansion have in the various places it reached?

    12. How much demic impact did Slavic expansion have relative to pre-existing Balto-Slavic people?

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  21. 4. What caused the dramatic decline of Y-DNA R1b among the people living in what was Yamnaya territory?

    we did :-)

    also andrew, i’m talking about europe. the non-european questions are more open.

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  22. Pedantry on a few points:

    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!

    Thinking about this, I could also phrase it that the difference between WHG to EEF (Antolia_Early_Neolithic) was around half the distance between South American Indians and Han Chinese: Karitiana-Han Chinese FST – 0.177, WHG-Antolia_EN 0.097. While French-Han 0.109 (French is closer by FST to Han than Han is to Karitiana..). For another comparison, the EHG-WHG FST is also 0.08, while Motala Scandinavian HG-WHG is 0.052. The Motala-WHG divergence is about the same size as between French and Mala people from South India, so arguably “sub-continental”.

    First, the Srubna have nearly ~20% ancestry from a population related to the EEF.

    In the models in Mathieson’s revised paper Srubna look around around ~15% EEF and ~15% WHG ancestry as well. So appear around 70% Yamnaya, in their ancestry, from how their figures look.

    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.

    On that note, one of the reasons I think the idea did show up is that genetic variation really does decrease in Europe on a north-south basis. If I understand correctly, Europe north to south is not defined so much that the south shares a lot of drift together, while the north a lot of drift together but perhaps also more that the northern populations share drift, while southern share less (with each other, or northern populations).

    Maybe makes sense with today’s knowledge in that populations in the south are more likely to be descended from populations from outside Europe which probably preserved more genetic diversity (less genetic drift). While La Brana from Spain which may have been assumed to be be a reserve of genetic diversity (refugia) did not seem particular diverse, although perhaps we will await more samples from Mesolithic and Paleolithic Europe to say for sure. Ron Pinhasi has a project on this, which is likely to shape our understanding – http://horizon-magazine.eu/article/ice-age-europeans-roamed-small-bands-fewer-30-brink-extinction_en.html

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  23. Is there any reason to think R1b is particularly associated with Indoeuropean languages? We know it reached Iberia and Africa long before the Indoeuropean expansion, so it seems strange to put forward Indoeuropean as the cause for its dominance on the Atlantic coast. I think people are mistaking multiple pulses for one.

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    • Replies: @Paul Ó Duḃṫaiġ
    Most European R1b falls into various clades of R1b-L23 (which is major sub-clade of R1b-M269). The Yamnaya remains that were sequenced were also R1b-L23. One of them was R1b-L23+ (L51-, Z2103-) and 5 of them were R1b-Z2103+ (L23+, L51-). Most modern day European R1b belongs to L51 branch, so it will be interesting when Yamnaya remains from western part of their range are sequenced.

    In comparison the African R1b tends to belong to R1b-V88, this also appears to be case with single case of R1b from Neolithic Spain. This is parallel branch to R1b-M269 parent P297

    eg.
    • • • R1b1 P25_1, P25_2, P25_3, L278, M415/PF6251
    • • • • R1b1a P297/PF6398, L320
    • • • • • R1b1a2 M269
    • • • • • • R1b1a2a L23/PF6534/S141, L49.1/S349.1 -- 1 Yamnaya example
    • • • • • • • R1b1a2a1 L51/M412/PF6536/S167 -- most modern European R1b (~95%)
    • • • • • • • R1b1a2a2 CTS1078/Z2103 -- 5 Yamnaya remains

    • • • • R1b1c PF6279/V88 -- African R1b (Chadic?) + 1 Neolithic/Copper age remains from Iberia -- very rare in modern Europe today.

    If you look at the Reich study I think they put their Scottish sample at about 12-17% ANE when it came to 3-component analsysis (WHG, EEF, ANE)

    Generally Irish people in various calculators come in around the same as well, so considerable ANE into NW Europe. The dominant clade of R1b in NW Europe appears to be R1b-P312 (majority in Ireland via R1b-L21, probably majority in Britain, at least has pluarity status in England), Bell Beaker remains sequenced (aDNA) in Southern Germany were R1b-P312+ (specifically U152+ though)
    , @Razib Khan
    haplgroup R goes back to 20,000 years BP. probably distributed across a range of linguistic groups.
  24. With regard to rapid lineage expansion, one good example that many people often miss is that of Gaelic Ireland up until the Tudor conquest. We have accounts of men from 15th century who were Lords/Kings having up to 15-20 surviving son’s (who reached adulthood) by multiple women (divorce was endemic, no concept of illigimatcy) and sometimes on order of 50-60 grandson’s.

    Result at least from the dawn of Christian period (5th century) is we probably had fairly rapid turnover of male lineages as dominant kin groups expanded rapidly. R1b-M222 for example appears to follow this pattern in Ireland.

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  25. @CupOfCanada
    Is there any reason to think R1b is particularly associated with Indoeuropean languages? We know it reached Iberia and Africa long before the Indoeuropean expansion, so it seems strange to put forward Indoeuropean as the cause for its dominance on the Atlantic coast. I think people are mistaking multiple pulses for one.

    Most European R1b falls into various clades of R1b-L23 (which is major sub-clade of R1b-M269). The Yamnaya remains that were sequenced were also R1b-L23. One of them was R1b-L23+ (L51-, Z2103-) and 5 of them were R1b-Z2103+ (L23+, L51-). Most modern day European R1b belongs to L51 branch, so it will be interesting when Yamnaya remains from western part of their range are sequenced.

    In comparison the African R1b tends to belong to R1b-V88, this also appears to be case with single case of R1b from Neolithic Spain. This is parallel branch to R1b-M269 parent P297

    eg.
    • • • R1b1 P25_1, P25_2, P25_3, L278, M415/PF6251
    • • • • R1b1a P297/PF6398, L320
    • • • • • R1b1a2 M269
    • • • • • • R1b1a2a L23/PF6534/S141, L49.1/S349.1 — 1 Yamnaya example
    • • • • • • • R1b1a2a1 L51/M412/PF6536/S167 — most modern European R1b (~95%)
    • • • • • • • R1b1a2a2 CTS1078/Z2103 — 5 Yamnaya remains

    • • • • R1b1c PF6279/V88 — African R1b (Chadic?) + 1 Neolithic/Copper age remains from Iberia — very rare in modern Europe today.

    If you look at the Reich study I think they put their Scottish sample at about 12-17% ANE when it came to 3-component analsysis (WHG, EEF, ANE)

    Generally Irish people in various calculators come in around the same as well, so considerable ANE into NW Europe. The dominant clade of R1b in NW Europe appears to be R1b-P312 (majority in Ireland via R1b-L21, probably majority in Britain, at least has pluarity status in England), Bell Beaker remains sequenced (aDNA) in Southern Germany were R1b-P312+ (specifically U152+ though)

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  26. Your reference to your European friend having a south Asian ancestor within the last two hundred years at first struck me as surprising because I thought it meant that his R1a Y chromosome derived from that ancestor. Clearly the natural inference would be that more than one generation of Anglo-Indian marriages to European women had occurred after the initial marriage of an Indian man to an Anglo-Indian woman, given the social realities of the time. But I now see that you were merely adding a side note to the basic fact of there being common make ancestry something like 5000 years ago?????

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    • Replies: @Razib Khan
    right. the R1a is from the macarthur lineage. the ancestor was a female who was probably a native bengali who lived ~150 year ago.
  27. Epic post, Razib. Thanks!

    So, the crazy lefty academics — the post-Marxist, post-Structuralist, critical theorists, or whatever the hell they call themselves — are actually on to something!?!? There really is a thread connecting roving bands of patriarchal men to modern multinational corporations!? :-0

    “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.”

    Yup, even a Levantine-descendent like me gets to enjoy the connection to R1a. My maternal grandfather was R1a (while I’m G2a, which I find pretty funny.) The Ashkenazi R1a is likely descended from this same milieu, mediated by the tumult that accompanied the transition from the bronze age to the iron age… the Mitanni collapsed while Semitic tribes expanded… Eventually R1a ended up in the formative Jewish population.

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    • Replies: @Razib Khan
    R1a is found in assyrian christians. i think it's probably mitanni derived if it is z93 (there are other forms of R1a in the middle east though...perhaps not IE related).
  28. [. 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).]
    Where is Neanderthal in this picture?

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  29. This brief gloss on the OT Saul/Agag/Samuel story is not totally OT: It has always struck me that this story may have been redacted to remove some aspects of late Bronze Age/early Iron Age warfare that might not have fit in well with practices of the later Jerusalem-Temple-centered cult. In Saul’s time only the most skilled and/or attractive captives were worth enslaving. Probably many residents of besieged and conquered cities were able to escape slaughter but most of the rest were captured and killed, often in sacrificial rituals. It’s intriguing that Saul saved only the Amalekite king and the best, most spotless livestock. This suggests to me that Saul may have been planning a regressive move back to human sacrifice; recall for example Jeptha’s daughter in Judges. Perhaps Samuel’s anger with Saul had as much or more to do with Saul planning to reintroduce human sacrifice than with any affront to Samuel or the Lord.

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  30. You might consider putting out an E book that is a collection of your best articles. That way 1) the links would work 2) no stinking middleman 3) the readers could wander to areas of their specific interest because similar articles would link to each other and 4) the scientific area you report on is changing so fast that a printed book is quickly outdated. With an E book you would not have to go back and rewrite constantly just add a link to more recent developments.

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  31. @CupOfCanada
    Is there any reason to think R1b is particularly associated with Indoeuropean languages? We know it reached Iberia and Africa long before the Indoeuropean expansion, so it seems strange to put forward Indoeuropean as the cause for its dominance on the Atlantic coast. I think people are mistaking multiple pulses for one.

    haplgroup R goes back to 20,000 years BP. probably distributed across a range of linguistic groups.

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  32. @Wizard of Oz
    Your reference to your European friend having a south Asian ancestor within the last two hundred years at first struck me as surprising because I thought it meant that his R1a Y chromosome derived from that ancestor. Clearly the natural inference would be that more than one generation of Anglo-Indian marriages to European women had occurred after the initial marriage of an Indian man to an Anglo-Indian woman, given the social realities of the time. But I now see that you were merely adding a side note to the basic fact of there being common make ancestry something like 5000 years ago?????

    right. the R1a is from the macarthur lineage. the ancestor was a female who was probably a native bengali who lived ~150 year ago.

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  33. @sprfls
    Epic post, Razib. Thanks!

    So, the crazy lefty academics -- the post-Marxist, post-Structuralist, critical theorists, or whatever the hell they call themselves -- are actually on to something!?!? There really is a thread connecting roving bands of patriarchal men to modern multinational corporations!? :-0

    "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."
     
    Yup, even a Levantine-descendent like me gets to enjoy the connection to R1a. My maternal grandfather was R1a (while I'm G2a, which I find pretty funny.) The Ashkenazi R1a is likely descended from this same milieu, mediated by the tumult that accompanied the transition from the bronze age to the iron age... the Mitanni collapsed while Semitic tribes expanded... Eventually R1a ended up in the formative Jewish population.

    R1a is found in assyrian christians. i think it’s probably mitanni derived if it is z93 (there are other forms of R1a in the middle east though…perhaps not IE related).

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  34. […] Fires in the Forest: The Revolution in Human Evolution – “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.” – also from razib. […]

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  35. @marcel proust
    "... as simple as taking candy from a baby."

    I tremble when I recall that you are the father of very small children, and feel for them when I think about the little weight you give to the long term effects of child-rearing practices on individuals' outcomes.

    ;-)

    Don’t drop them on their head, don’t be a dickhead to your children, let them know that no matter what the rest of the world might think, there is at least one person who thinks they are great just because they exist. Razib’s kids are safe.

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