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

August 15, 2012

The Age of Heroes

Filed under: Culture,Genetic History,Genetics,History — Razib Khan @ 5:42 pm

Sometimes when you read reviews or papers you need to look very closely at what people say in a tentative speculative fashion. That’s because though the prose may be as such when read plainly and without context, you often have more prior information as to the background of the authors. In other words, assertions which literally seem cautious are actually foreshadowing likely probabilities down the pipeline, because the authors are not distant third-party observers, but active participants in the production of new insights. I think that’s what’s going on in a new paper in Trends in Genetics, The genetic history of Europeans:

Future research should also reveal the effects of post-Neolithic demographic processes, including migration events, which preliminary data suggest had a major impact upon the distribution of genetic variation. These include events associated with Bronze Age civilizations, Iron Age cultures, and later migrations, including those triggered by the rise and fall of Empires. Challenges remain in being able to sequence aDNA routinely from serial samples in the range of megabases, and in the development of software that allows spatially-explicit simulation of genome-scale data, but advances in these areas are now a weekly occurrence and the stage is set for ...

December 17, 2010

South Asians too are sons of the farmers?

Filed under: Aryans,Genetic History,Genetics,Genomics,India,India Genetics,Indo-Aryans — Razib Khan @ 2:58 pm

I mentioned a few days ago that a friend was trying to get together some data to analyze the genetic variation of South Asians. By a strange coincidence Dienekes just published a more detailed analysis of South Asians…and uncovered something very interesting, though not that surprising. Some technical preliminaries:

A note of caution: The reduced marker set (~30k) means that a lot of noise is added in the admixture estimates. In particular, many individuals are likely to get low-level admixture from population sources that can be attributed to noise. But, as we will see, the small marker set does not really affect either the power of the GALORE approach, or of ADMIXTURE to infer meaningful clusters.

In addition to the various online sources of public data Dienekes got about a dozen South Asians. I was one of those South Asians, DOD075. In many ways I’m a rather standard issue South Asian, similar to Gujaratis, except that I have a substantial ‘East Asian’ component. More concretely, between 1/6 and 1/7 of my ancestry seems to be of eastern origin, far higher than the norm among South Asians. The rest of my ancestry was mostly South Asian specific, with a minor, but significant ‘West Asian’ component common across northern India.

Rerunning with more data with different samples Dienekes came out with a different set of ancestral components. Of particular interest to me he broke down the East Asian between East Asian proper and Southeast Asian. Below are a selection of populations with ancestral components + me. I’ve also renamed a few components. North Kannadi = Dravidian and Irula = Indian tribal. Indian = Generic Indian. Looking at the Fst it seems that Indian endogamy and population bottlenecks has had an effect…look at the North Kannadi distance from everyone else.


Remember that in the previous analysis I was very similar to a Gujarati, except with an East Asian element. My supposition that my ancestry has some connection to Burma seems to be supported by these results. Looking at my balanced ratio between East Asian and Southeast Asian, that is what one might expect from someone of a Burman ethnicity. I am not saying that I have recent Burman ancestry per se. Rather, Ahom, Mizo, Chakma, and a range of tribal populations from the liminal zone between South and Southeast Asia may suffice. The main other option is that I have a great deal of Munda ancestry. Not implausible in light of the likelihood that Munda brought rice agriculture to northeast South Asia, and pre-date Indo-Aryans, and possibly Dravidians, in Bengal. How would I distinguish these possibilities? I’ve ordered 23andMe kits for both my parents. The most likely candidate for recent Southeast Asian ancestry is my paternal grandfather. If the admixture event was recent, if I have a recent ancestor(s) of “hill tribe” origin, I would expect to see more linked regions of East/Southeast Asian origin than if the admixture was ancient (and so distributed more equitably across DNA strands due to recombination).

But the bigger point of Dienekes’ post is what he terms “Dagestani” ancestry across much of Eurasia. I’ll quote him:

The most exciting thing, however, is the fact that the origins of a part of the West Asian component of my previous analyses can be partially located: it is the purple component centered in Dagestan, i.e., among Northeast Caucasian speakers such as Lezgins, and the Dargins who inhabit Urkarah.

Readers of this blog may remember the surprising appearance of this Lezgin-specific component in the Balkans (but not Greeks) a few weeks ago. Now it has turned up as a substantial component in India as well.

Back then, I speculated that this component may derive from a prehistoric population that was spread in (but not limited to) the northern arc of the Black Sea from the Balkans to the Caucasus. Even in this analysis, you can see that both Romanians and Hungarians have some of it, and so do Lithuanians and Belorussians, while Tuscans (like the Greeks of my previous experiment) do not.

Hence, this component stretches from at least the Baltic to India, but is largely absent in southern Europe. I will go out on a limb and propose that this component is representative of a non-Indo-European component in the ancestors of the Indo-Iranians.

Paul Conroy observes that on this finer-grained analysis I don’t have any “West Asian” at all. What had previously been West Asian terms out to have been, in my case, a compound of Dagestani + European. I can’t say that I’m that surprised by this. Years ago I noticed that HGDP STRUCTURE analyses were always giving suggestive signs of a connection between West-Central Eurasia and South Asia.

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

Back to farming:

As I’ve remarked in the past, Eurasia can be broadly seen as the playground of three major groups of people: the Caucasoids of the West, the Mongoloids of the East, and a southern group of people which is most strongly represented in South Asia, but whose presence can be detected in Southeast Asia as well, although in the latter case it has been marginalized and/or absorbed by the arrival of Mongoloids.

This southern group of people has sometimes been called “Australoid” because of its perceived resemblance to Australo-Melanesians. Indeed, in my K=5 mega-analysis an affinity between Papuans/Melanesians and people of South and Southeast Asia is apparent. These “Australoids” are very old populations, probably stemming from the early Out-of-Africa coastal dispersal route, and we shouldn’t be tricked by their phenotypic similarity into thinking that different groups of them are particularly close genetically. Just as “black Africans” are not the same, neither are the “Australoids” and mixed-”Australoids” at the shores of the Indian Ocean.

It is probably the invention of agriculture that is responsible for their marginalization. In Africa, the Pygmies and Bushmen have been absorbed or pushed aside by the demographic Bantu juggernaut, with a few other language groups also hitching a ride on the agriculture/pastoralism economy. In West Eurasia, where agriculture was invented earliest, pre-agricultural populations left no traces. In East Eurasia, the agriculturalists could not expand to the far north where many relic populations exist, but they could (and did) move to the south where they assimilated or drove away pre-existing populations, leaving a few of thems, like the Taiwanese Atayal as partial remnants of the older population stratum.

The Irula are South Indian tribals, so they are the the closest one can get to South Asian autochthons, and yet even they presumably have a large minor component of “Ancestral North Indian.” The tribal groups in Reconstructing Indian Population History all exhibited proportions on the order of ~40% ANI. It seems that agriculture “stalled” in the Indus valley and the highlands to the west for thousands of years in South Asia. During this period of stalling I believe that the farmers absorbed a great deal of genetic material from the indigenous hunter-gatherers, and so produced a “distinctive” Indian genetic profile. More West Eurasian than not, but with a very large dollop of the ancient substrate of southern Eurasia which had a distant, but closer, affinity with that of East Asia. Once social and cultural forces allowed for the rapid expansion of farmers there was a wave of advance from the Indus valley east and south. In the east the proto-Indians would have encountered Mundari speaking groups drifting who practiced rice agriculture, which they also adopted. In the south the proto-Indians would have encountered more hunter-gatherers. Many of the tribal people in India are today facultative hunter-gatherers, herders, and extensive farmers. I believe that these marginal proto-Indian groups assimilated hunter-gatherers more easily than would have otherwise been the case because some of the proto-Indians reverted to a hunter-gatherer lifestyle in the agriculturally unsuitable highlands of the Deccan and Chota Nagpur. The social boundaries in the uplands of South India were such that the line between hunter-gatherer and farmer was more fluid than elsewhere, explaining the former’s greater genetic impact through intermarriage and assimilation.

This sort of general dynamic probably applies to Indo-Europeans. There is no reason why the original Indo-European tribes could not have been compounds who picked up different ancestral components in their peregrinations. Compare the various Turkic people, Anatolian Turks, Chuvash, and Yakut. All of them have affinities with nearby peoples, despite having a common Turkic culture and genetic component. One notable trend in Europe is that while the French have a minor, but significant West Asian component, the Basque have none of it. Dienekes’ sample is small, but it looks as if Scandinavians have more of this than the Finns. This West Asian component may not have been the dominant one among the Indo-Europeans, but I suspect it was a significant one. If the original speakers of proto-Indo-European did not have it, they likely absorbed early on, just as the West Asians absorbed a native South Asian element in the Indus valley.

Finally, as a general rule of thumb, I would now suggest that the primary way in which hunter-gatherer genes can persist is through an ecological stall on the part of farmers. During the stall gene flow naturally occurs, probably through exchange of females (coercive or not), or the integration of hunter-gatherer males into war-bands or as slaves. Over time the farmers on the frontier have changed genetically, so that when they start expanding rapidly due to a technological or cultural innovation, they share more with the hunter-gatherers whom they supersede than they otherwise would have.

November 22, 2010

The flux of genes on the South Seas

Filed under: Genetic History,Genetics,Genomics,Melanesia,Oceania,Papua,Polynesia — Razib Khan @ 12:29 am

Huli Wigman from the Southern Highlands, Painting of Tahitian Women on the Beach by Paul Gauguin

ResearchBlogging.orgMany demographic models utilized in genetics are rather simple. Yet the expansion and retreat of various demes in post-Ice Age Europe seems to be far more complex than had previously been assumed, though I suspect part of the rationale for the original simplicity was a preference for theoretical parsimony in the face of a paucity of data. The landscapes traversed by our species are rich and topographically convoluted. Not only does the land vary, from plains, to deserts, to mountains, but the climate shifts radically over time and space. In the pre-modern age when humans were more dependent on environmental exigencies these fluxes in ecological and climatic parameters were essential in sharping the arc of human demographic expansion and contraction.

Oceanias_RegionsThis is why a closer examination of the prehistory of Oceania is so appealing: here you have a physical geography which is radically constrained and so reduces the degrees of freedom of human movement and habitation. Unlike Europe, South Asia, or much of Africa, the time depth of the residence of the current indigenous inhabitants of Australia is on the order of 40 – 50,000 years. It seems likely that the indigenous people of the island of New Guinea to the north are from the same original settlement of Sahul, the ancient super-continent which consisted of New Guinea, Australia, and Tasmania. After the initial sweep out to the farthest reaches of what became Tasmania, there was a later push to the east of New Guinea, to the Solomon Islands,~30,000 years before the present. Then nothing for tens of thousands of years. The march of humanity seemed to stand still on the shores of the Solomons, just as the hominin lineage had once been cordoned off from Sahul by the forbidding seas between it and Sundaland, the Ice Age peninsula of Southeast Asia which was later submerged and became the western portion of Indonesia and Malaysia. The stasis was shocked by the Austronesians, a seafaring peoples who seem to have exploded out from somewhere between Borneo and Taiwan within the last 10,000 years, likely just on the margins of written history. The most famous of th Austronesian peoples are the Polynesians, who pushed across the Pacific, and likely even had some tentative contact with the New World. A less well known case is Madagascar, whose inhabitants speak an Austronesian language with clear affinities to a dialect of Borneo. The map below shows rough distribution of Austronesian peoples:

Austronesian expansion

Of particular interest for the purposes of this post is the expanse to the east: Melanesia and Polynesia, Near Oceania and Far Oceania. A new paper in Current Biology , Demographic History of Oceania Inferred from Genome-wide Data, examines the genetics of this region of the world in light of history utilizing a ~1 million marker SNP-chip:

We developed a new approach to account for SNP ascertainment bias, used approximate Bayesian computation simulations to choose the best-fitting model of population history, and estimated demographic parameters. We find that the ancestors of Near Oceanians diverged from ancestral Eurasians 27 thousand years ago (kya), suggesting separate initial occupations of both territories. The genetic admixture in Polynesian history between East Asians (87%) and Near Oceanians (13%) occurred 3 kya, prior to the colonization of Polynesia. Fijians are of Polynesian (65%) and additional Near Oceanian (35%) ancestry not found in Polynesians, with this admixture occurring considerably after the initial settlement of Remote Oceania. Our data support a greater contribution of East Asian women than men in the admixture history of Remote Oceania and highlight population substructure in Polynesia and New Guinea.

Like Dienekes I think there’s something off with the dates they’re generating here. The archeology tells us New Guinea was settled by humans 15-20,000 years before this paper finds that they diverged from other Eurasians! We know that Aborigines are the closest to Papuans genetically, so if they separated from Eurasians less than 30,000 years ago, that would mean that the original inhabitants of Sahul were replaced after that period by the current groups. Far simpler I think to assume that something is off with their timing. Below are the primary figures, a frappe bar plot, PCA, and tree 7b which illustrates the most supported pattern of population branching and admixture.

There’s nothing too revolutionary in this paper. Rather, it seems to be an exploratory analysis of Oceanian genetics, a precursor to what may come soon. They can not, it seems, differentiate between the slow-boat and express-train models of the settlement of Polynesia, though the consistent pattern of Melanesian admixture seems to lean toward some form of slow-boat, because that is the theory which emphasizes a longer interaction with Melanesian populations.

800px-Area_of_Papuan_languages.svgI know I emphasized the relative simplicity of Oceania in relation to other parts of the world in terms of interpretation because of the geographical constraints, but even here there are layers and twists in the genetic and cultural bedrock. To the left is a map of the Papuan languages. From what I can tell Papuan languages are actually a negation of Austronesian and other well supported language families. The key is to notice that some parts of Near Oceania, Melanesia, have been shifted toward Austronesian languages, though New Guinea is a general exception to this pattern. Remember that humans did not move past the Solomons for ~30,000 years. Large scale settlement of Madagascar seems to have occurred only with the arrival of the Austronesians within the last 2,000 years (after a likely sojourn in East Africa!). This was a genuine cultural revolution which radically shifted the terrain of the possible. And yet by and large the Papuans resisted assimilation to the Austronesian cultural toolkit, which seems to have been otherwise so successful. Why? The Papuans were well equilibrated to their own local ecology, and the Austronesians had no comparative advantage. Rather, the Austronesians, in the form of the Polynesians, struck out into unknown waters and innovated. They found low hanging fruit by discovering trees which had been neglected.

The second interesting point is the bias toward Austronesian mtDNA, and substantial admixture on the Y lineages from Papuans even among Polynesians. The standard explanation of this is that the Austronesians had some aspect of matrilineal descent and matrilocality in terms of communal fission. I think that the Austronesians are arguably a perfect example of the leap-frog pattern of migration, and yet unlike most continental leap-frogs the genetic signal seems to be stronger on the female than male side. There is some evidence of the same in Madagascar. This indicates to me that the Austronesian maritime expansions were qualitatively different from continental leap-frogs, which often were based on the mobility of men on horses.

As I said, the picture remains broadly the same. But there are some touch ups and clarifications on the margins, and that is worthwhile. And definitely an appetizer for what is to come.

Citation: Wollstein A, Lao O, Becker C, Brauer S, Trent RJ, Nürnberg P, Stoneking M, & Kayser M (2010). Demographic History of Oceania Inferred from Genome-wide Data. Current biology : CB PMID: 21074440

Image Credit: Nomadtales, Wikimedia

November 8, 2010

What intra- & inter- population genetic variance tells us

Filed under: Admixture,Dodecad,Genetic History,Genetics,Genomics,History,Select Post — Razib Khan @ 2:30 pm

uyafrThe figure to the left is a composite merged from two different papers. One analyzes the patterns of genetic variation within African Americans, and the other the patterns within the East Turkic ethnic group, the Uyghurs. The bar plots show the ancestral element which is similar to two parent populations which resemble Europeans and Africans or East Asians. Looking at total aggregate ancestral quanta we infer that African Americans are on the order of 15-25% European in ancestry, and 75-85% African. Uyghurs seem to be a composite in even measure of a European-like group, and an East Asian-like group. This makes total sense phenotypically; most African Americans look more African, while Uyghurs seem to exhibit a phenotype on average which spans the middle-range between West and East Eurasians.

Central_Asian_Buddhist_MonkBut we’re clearly missing something when we focus purely on a population level statistic. Each “slice” of the bar plot actually represents an individual. Note the contrast between African Americans and Uyghurs. There is relatively little intra-individual variation among Uyghurs, while there is a great deal of such variation among African Americans. Why? Population geneticists have looked at linkage disequilibrium in both African Americans and Uyghurs, and inferred that the former went through an admixture phase much more recently than the latter. Though you don’t really have to be a population geneticist to have known that about African Americans. The ethnogenesis of the group African Americans as a cultural entity occurred in the period between 1650 and 1850. Genetically they are a compound of African, European, to some extent Native American, ancestry. For the Uyghurs we have thinner textual evidence, but the visual and genetic data point to a “western” Indo-European speaking population in the Tarim basin before the arrival of the Turks sometime in the second half of the first millenium A.D. The assumption is that after the initial admixture event and the absorption of the pre-Turkic substrate there was no population substructure. Over time the two components distributed themselves evenly across the population over a period of 1,000-1,500 years.

From this we can infer that patterns of individual variation within populations, as well as between closely related populations, can tell us a great deal. Today the Dodecad Ancestry Project posted a file with the population ancestries broken down by individuals. Looking at this sort of fine-grained data patterns can jump out based on what you already know. Below is a slide show I created which highlights some patterns of interest.

The first slide is confirmation of what we already know, or should expect. The Burusho are a linguistic isolate in the mountains of northern Pakistan. Their lack of inter-individual variation within the population is suggestive of long term isolation, as is common in mountainous regions. The very fact that they speak a linguistic isolate should lead us to expect this, as the flow of culture and genes often correlate. The Sindhi are the dominant Indo-Aryan speaking ethnic group of the lower Indus watershed. Because of their geographic position they have been conquered many times, being under Persian, Arab, and Turkic rule. Genetically they’re very similar to the Burusho, but observe that there are two individuals with substantial West African ancestry. The presence of black Africans in the armies of the Muslims who conquered the subcontinent is well known, and the origin of the Indian Siddi community. Some of the Sindhis also have appreciable ancestral components which are probably derived from Muslims from West Asia, the “Southern European” and “Southwest Asian” ancestral element which the Burusho lack.

418px-Kim_Kardashian_6Next you see a comparison between Assyrians and Armenians. These two groups seem very similar, and both have deep textually attested roots in the Middle East. The Armenians date to the Persian Empire, at least, while the Assyrians are clearly the descendants of the indigenous Semitic population of Mesopotamia before the arrival of the Arabs. In the Muslim period many of them retreated to mountainous areas of northern Iraq, before emigrating to the cities of modern Iraq with the relaxation of their status as marginalized dhimmis. Today the Assyrian community is scattered across the world. The portion which adheres to the Church of the East was nearly totally extirpated from Iraq early in the 20th century, while that which is in union with the Roman Catholic Church, the Chaldeas, is currently leaving Iraq en masse.

But the Armenians are a far different case in terms of their interactions with the rest of the world. They have been present as “middlemen minorities” as far east as Southeast Asia, and north into the Russian Empire, and south into the Muslim world. The most parsimonious explanation for the individuals with Northern European ancestry is that like Kim Kardashian they are products of mixed-marriages, but I wonder if the centuries of the Armenian Diaspora has resulted in a change in the gene frequencies in the Armenian homeland in part because of back-migration. With larger data sets this will be testable, as well as the hypothesis that Diaspora communities are admixed while the Armenians in Armenia proper are not.

The third slide compares Scandinavians, Finns, and Lithuanians. Scandinavia refers to the Germanic speaking lands of Norden. Lithuania has historically been just outside the arc of Nordic influence (in contrast to Estonia and Latvia), so it can serve as a Northern European control. I believe some of the Finnish samples in Dodecad are related, so one shouldn’t make too much of them. But, contrast the relatively constant level of Southern European in the Scandinavian samples, and their variance in the Finnish ones. Inversely, the Finns show relative constancy of the “Northeast Asian” proportion, while the Scandinavians vary, with some lacking it. This is likely evidence of recent population exchange, and cultural switching. Finland was under Swedish rule for most of the past 1,000 years, and there still remains a large ethnic Swedish population in Finland, and an ethnic Finnish population in Sweden. Some families in Finland likely switched from Finnish to Swedish to Finnish within the last 500 years. The Southern European and West Asian elements more prominent in the Scandinavians tend to increase as one goes south in Europe, with the former modal in Sardinia (in fact, Sardinians are nearly fixed for the Southern European component), and the latter more prominent among southeast European groups. Geography may then explain why the Lithuanians have similar amounts of the West Asian, but less of the Southern European.

UygurFinally we compare Turks, Greeks, and Cypriots. The historical ethnography strongly implies that the major component of Anatolian Turkish ancestry is Greek and Armenian. A broad similarity to the Greeks here is rather clear (with an elevated West Asian component probably from the Armenian ancestry). But notice the differences. There is a consistent East and Northeast Asian component of ancestry among Turks which is lacking in the Greeks. Since the origin of the Turks is in what would today be termed Greater Mongolia, this makes sense. What surprised me though is the presence of a South Asian component among the Turks. This is where looking at individual level results yields results; I’d assumed that like the Romanians the South Asian element was due to a few assimilated Roma. That seems unlikely now, it’s too evenly distributed. So what then? I think here looking at the Uyghur plot illuminates this for us. I don’t know what to make of the South Asian component which you can find in the Uyghur, and even to a trace extent, but again consistent, among the Chuvash, who inhabit the South Urals. Some readers have long claimed that some of the West Eurasian Uyghur ancestry was somehow connected to South Asia, and to be honest I’ve kind of seen that in other HGDP bar plots, but ignored it as of secondary importance. The Turkic group to the north and east of the Uyghurs, the Yakut, totally lack it. From what little we know it seems that the Turks pushed west to Europe, the Middle East, and South Asia, via what is today Xinjiang and Kazakhstan. The existence of this South Asian element in the Turks of Anatolia may be because of their sojourn in this region. There were Iranian speaking Indo-Europeans in Xinjiang, and certainly in Central Asia. Additionally we know historically that northwest India was connected to Xinjiang culturally, as some Indians arrived in China after a period of residence in Xinjiang. But instead of an “Out of South Asia” event I think what we may be looking at is part of the old “Ancient North Indian” genetic variation which pushed into South Asia from the north, and was eventually overlain in Central Asia with other components. I had assumed that the South Asian component among the Finns was noise or Kale, but perhaps it could be that.

Then there is Cyprus. Today the island is ethnically divided between Greek Cypriots and Turkish Cypriots. But in the Bronze Age Cyprus seems to have had a civilization with a close connection with the Near East, in particular Egypt. Sometime between the Bronze Age and the Classical Era it became an outpost of Greece. But notice the near total absence of Northern European among the Cypriots. Like the people of Sardinia, but unlike Sicily, Cyprus is relatively far from the Eurasian mainland. So how did Cyprus become Greek? If the Greeks always had a noticeable Northern European component, or at least during the Bronze Age, that would indicate that the Cypriots are a case of cultural diffusion and emulation of a small Greek elite which arrived during the migrations of the Sea Peoples. Or, the Northern European element could be due to admixture with the Slavic peoples who arrived in Greece after the collapse of East Roman frontier in the 6th century. Or it could be a combination of both. In any case, the Cypriots look most like the Syrians genetically, though the Syrians seem to have a lot more trace exogenous components.

There’s a lot more one could say. I invite readers to download the RAR file with the bar plots. I will leave you with one last comparison, without comment:


Image Credit: Tocharian Buddhist monk of European appearance, and Kim Kardashian, by Luke Ford

November 4, 2010

Assyrians & Finns in a worldwide genetic context

Filed under: Dodecad,Genetic History,Genetics,Genomics,History — Razib Khan @ 4:45 pm

Dienekes is now allowing people to “out” themselves in terms of their ancestry on a comment thread over at the Dodecad Ancestry Project. One of the major purposes of the project has been to survey variation in under-sampled groups which could give us insights into human genetic history. Yesterday I pointed to an analysis of Europeans from the British Isles to Russia. Basically Northern Europeans. There wasn’t anything too revolutionary about the nature of the results; rather, it confirmed some patterns we’d seen. Additionally it obviously didn’t resolve issues of timing, though it clarified hypotheses on the margin.

The main benefit of the ADMIXTURE bar plots is that it gives you a gestalt sense of relationships in a quantitative fashion. This is especially important for groups in the Eurasian Heartland, who are in some ways at the center of both genetic and cultural exchange. In the comments above some information was divulged as the provenance of two clusters of samples, Finns and Assyrians. The Assyrians here presumably represents the remnants of Mesopotamia’s Christian majority at the time of the Arab conquests in the 7th century. Prior to the Arab conquests Mesopotamia had been under the rule of the Sassanid Persian dynasty for nearly four centuries, but by early 7th century the Syriac speaking majority by and large adhered to a range of Christian sects (the balance seem to have been heterodox non-Christian Gnostics and Jews), with the ancient Church of the East dominant. Because of the social constraints which Christians were placed under within the Muslim Middle East prior to the modern era these communities may be particular informative as to the demographic impact of the Arab conquests, and the cosmopolitan and international nature of the Muslim polities and how they reshaped the genetics of the Middle East. A good approximation is that the Christian minorities are the dominant parent population of the Muslim majority, but that because of their tendency to withdraw into more isolated regions and their enforced economic marginality they would have not intermixed so much with the influx of slaves, both northern (Turk and Slav), Indian, and African, which characterized much of Mesopotamia over the past 1,400 years.

Below the fold is a slide show. I’ve reedited just a touch (removed a few populations, put the labels in larger fonts, etc.). First the total population set. Then I’ve dropped the Finns and Assyrians, respectively, into the global population set (obscure some which are less relevant).

First things first: the different ancestral components are popping out of ADMIXTURE and are suggestive inferences base on the data input. They do not necessarily represent real concrete ancestral populations! As I keep pointing out, the purple South Asian element is probably a compound of at least two very genetically distinct ancient groups in about equal measures, one with strong West Eurasian/European affinities, and another a long resident indigenous South Asian group with distant, but definite, affinities to East Eurasians (it may be that the latter South Asian element gave rise to the various branches of East Eurasians and Amerindians further back in prehistory).

The “Northeast Asian” element in the ancestry of the four Finns is not that surprising (though I believe some of these are related). In 23andMe Finns often seem to show trace “Asian” ancestry, on the order of ~1%.  Uniparental markers, especially Y chromosomal lineages, have long indicated ancient affinities between the Finnic peoples of Europe and various groups in Siberia. The major question has been whether the migration has been from the west to the east, or the east to the west. And yet perhaps this is the wrong way of looking at it, perhaps both these groups derive from an expansion south of the margins of the glaciers in the wake of the last Ice Age? The Finns clearly physically resemble their fellow Nordics more than the Yakuts. But perhaps this is not to be unexpected when you have mobile low density populations on the margins of more numerous conventional agriculturalists? I believe that the Mercator projection has also caused problems in assessing the plausibilities of connections between circumpolar peoples.

Next let’s move to the Assyrians. As with other such surveys the lack of African ancestry in relation to similar Muslim populations is striking. The Syrian set is probably the best point of comparison. Note the small slices from other populations in the Syrians. I would normally ignore that, but their absence in the Assyrians may be informative. This may be a function of close relatedness of the Assyrians, but I’d give it even odds that a low fraction of exogenous post-Islamic ancestry which is associated with travel within the Muslim lands explains some of the difference between the majority and minority populations (above and beyond the clear African element).

Finally, I’m going make up stories on the fly to generate some discussion (I think the stories correspond to reality more than expectation, but I have very weak confidence in them myself).

- The “Southern European” element which is maximal in Sardinia indicates the very first wave of agriculturalists. The Sardinians may not be purely descended from agriculturalists, but like the composite “South Asian” quantum this represents possibly the very first hybridization due to a rapid demographic pulse driven by agriculture which synthesized with the hunter-gatherers of Western Europe. Like the “Ancient South Indians” I doubt that the Ice Age Europeans of Western Europe are present in “pure” form anymore. The influence of this component can be found far to the east among the Assyrians, but it almost disappears in Afghanistan and Pakistan. I think this may have something to do with R1b1b2.

- The “Northern European” element which is maximal in the Lithuanians is found among the Pashtuns and non-Arab Middle Easterners, but not Arab speakers. It drops off in India very quickly. I don’t think the Lithuanians are the “purest” Indo-Europeans, and I don’t think that this element was necessarily exclusive to Indo-Europeans. But there has to have been some leap-frogging going on, because on average Semitic Middle Eastern groups are more like Europeans than Gujaratis are in total genetic distance, but Gujaratis seem to have a higher fraction of this quantum. And suggestively Punjabis seem to carry the Central Eurasian lactase persistence alleles (I know this from the literature and genome sharing on 23andMe). Again, because these ancestral quanta don’t represent real populations, but are proportions popping out of ADMIXTURE, we shouldn’t take the orange fraction as the “Aryan” ancestry in South Asia. But that seems the most plausible explanation for why it seems at  far higher frequency in Indo-European speaking northwest India than it does in the Semitic speaking Fertile Crescent.

- The light-blue “West Asian” fraction gets around. It’s found at the same proportions in Tuscans as Uyghurs, and, you can find it pretty far south and east in South Asia (I have a fair amount of it, as does a Reddy from South India, and the Kannada speakers in the global Dodecad set have some of it too, though less). I assume that it is present at high frequency among the Uyghurs because of the Indo-European speakers. But it clearly doesn’t have an Indo-European origin as such. It has a high frequency among the Cypriots, but not the Sardinians, with modal proportions among various Caucasian groups. I assume it has something to do with agriculture, but seems to have less of an influence in Western Europe than further to the east. The Finns and Lithuanians have a little bit, about the same as South Indians. So again, something which probably hitch-hiked with population movements in the center of Eurasia, but I assume pre-dating the Indo-Europeans.

October 14, 2010

The blood of kings

Filed under: Genetic History,Genetics — Razib Khan @ 1:33 pm

429px-Ludvig_XVI_av_Frankrike_porträtterad_av_AF_CalletOne of the more fertile grounds of modern genetics with all its various tools is that it makes for some interesting possibilities of inquiry in relation to the genealogy of aristocratic elites. The vast majority of us have very shallow roots in terms of genealogy. Some of this ignorance can be compensated if you have a clear and distinct group identity. If you are a Cohen or a Levite you have some notional conception of your line of ancestry. If you are a member of a Chinese patrilineage your genealogy likely can be traced at least hundreds of years, and possibly nearly one thousand years. Many European nations, in particular in the Nordic nations, have excellent church records which go back centuries.

High aristocratic elites are different in the scope of what we know. For most of history marriage for them was a matter of politics, not war, and the details of their lives were often recorded punctiliously. The births of royal children may have been attended by most of the court at some point to certify legitimacy. Some European lines have deep histories indeed. There are two direct male line descendants of Hugh Capet who reign today, Juan Carlos of Spain and Henri of Luxembourg. Hugh was a Robertian, a descendant of Robert of Hesbaye, who was a ruler of a region in modern Belgium. Robert of Hesbaye was derived from the Frankish elite, but the details seem to be unclear. But it seems then that Juan Carlos of Spain and Henri of Luxembourg should be of Robert of Hesbaye’s lineage, and so have a paternal line going back 1,200 years.

I began to think of this when a friend with a strong interest in genealogy pointed me to this short article, Genetic analysis of the presumptive blood from Louis XVI, king of France:

A text on a pyrographically decorated gourd dated to 1793 explains that it contains a handkerchief dipped with the blood of Louis XVI, king of France, after his execution. Biochemical analyses confirmed that the material contained within the gourd was blood. The mitochondrial DNA (mtDNA) hypervariable region 1 (HVR1) and 2 (HVR2), the Y-chromosome STR profile, some autosomal STR markers and a SNP in HERC2 gene associated to blue eyes, were retrieved, and some results independently replicated in two different laboratories. The uncommon mtDNA sequence retrieved can be attributed to a N1b haplotype, while the novel Y-chromosome haplotype belongs to haplogroup G2a. The HERC2 gene showed that the subject analyzed was a heterozygote, which is compatible with a blue-eyed person, as king Louis XVI was. To confirm the identity of the subject, an analysis of the dried heart of his son, Louis XVII, could be undertaken.

Let’s assume that the results are of Louis XVI. My friend was very interested in the fact that Louis XVI’s uniparental lineages were atypical; the direct male and female lines. I don’t know much about this area, but his maternal lineage was an undocumented branch of N1b. More common among Central Eurasian peoples than Western Europeans. His paternal lineage, of more interest because of our genealogical depth in the form of the remaining Bourbons, was a variant of G2a, again, of a branch or type which does not exist in current databases, though more common in the east of Europe than in the west. These data as to the distinctiveness of Louis XVI’s uniparental lineages need to be framed in light of the recent history of attempting to divide the French populace by class and ancestry; some theorists modeled the French elite as descendants of German Franks, while the commoners were Gallo-Romans. This narrative has long been out of fashion, but the cosmopolitan nature of the high nobility of Europe does mean that they will be distinctive and atypical (ergo, the tension between the nationalist and aristocratic ethos).

Of more interest for me is the discussion about the genetics of eye color and Louis XVI:

The amplification of the HERC2 gene provides controversial evidence on the physical appearance of the subject studied. Of course, lack of the rs12913832G allele would immediately imply that the subject is not Louis XVI because the presence of this variant is required for blue eyes. However, while most of the rs12913832 heterozygotes have hazel, brown or black eye colour, still about 15.8% of them (in a total sample of 388) have blue eyes The fact that both his parents, the Dauphin Louis-Ferdinand and Marie-Josephe of Saxony had brown eyes, as shown in their respective portraits available, makes slightly more probable that Louis XVI was heterozygous at rs12913832, despite having blue eyes….

They moot the real possibility that this isn’t Louis XVI’s sample. But what about issues of paternity? The probability is low for elite lineages, especially royal ones, but certainly not zero. More importantly, surveying the Y chromosomal lineages of aristocratic families would be very informative in getting a better grasp of the nature of human fidelity at the commanding heights. From what I have seen in the literature all things being equal culturally it is in low status lineages that paternity uncertainty looms largest in a concrete manner. This is balanced against the fact that the consequences of paternity uncertainty are graver in high status lineages, since paternity and property have a stronger relevance in kin-groups which have substantial levels of intergenerational wealth transfer.

Balanced against this is the dynamic of skew toward elites in demographics. In pre-modern times it seems likely that the top half, and especially top ten percent, of a society would contribute more to the next generation. Because of social (primogeniture) and economic (Malthusian era growth rates) pressures many of these offsprings of elites would descend down the ladder of status, presumably taking up the slots of commoners who did not reproduce above replacement. Oliver Cromwell is a classic case of a man born into the lower gentry whose ancestors were far wealthier and illustrious.

We don’t have the records of low status people for most of history. Additionally, we are unlikely to have marked graves from which DNA can extracted. But sometimes getting half the picture can allow you to construct the whole. A better map of the genes of the European nobility, their patterns of relationship, as well as extractions from tombs and mausoleums, would give us a very fine-grained understanding of the demographic parameters of this population. Though I’m not sure that some of the European nobility would be totally open to finding out the facts, as opposed to the myths.

August 16, 2010

Where writing is silent

In my post on Empires of the Word I observed that quite often the written record is silent on many matters which only language or genes tell us must have occurred. The Indo-Aryan character of the dominant language on the island of Sri Lanka seems to be a geographical anomaly in the least, but perhaps most strange of all is the existence of a language and ethnic group of clear Southeast Asian provenance on the island of Madagascar. To my knowledge Arab, Persian and South Asian sources do not record the existence of a prominent Southeast Asian maritime diaspora which spanned the Indian ocean in the years before 1000 A.D., but we know that it did exist. A new paper on the genetics of the island of Comoros fleshes out another piece of the puzzle, Genetic diversity on the Comoros Islands shows early seafaring as major determinant of human biocultural evolution in the Western Indian Ocean:

The Comoros Islands are situated off the coast of East Africa, at the northern entrance of the channel of Mozambique. Contemporary Comoros society displays linguistic, cultural and religious features that are indicators of interactions between African, Middle Eastern and Southeast Asian (SEA) populations. Influences came from the north, brought by the Arab and Persian traders whose maritime routes extended to Madagascar by 700–900 AD. Influences also came from the Far East, with the long-distance colonisation by Austronesian seafarers that reached Madagascar 1500 years ago. Indeed, strong genetic evidence for a SEA, but not a Middle Eastern, contribution has been found on Madagascar, but no genetic trace of either migration has been shown to exist in mainland Africa. Studying genetic diversity on the Comoros Islands could therefore provide new insights into human movement in the Indian Ocean. Here, we describe Y chromosomal and mitochondrial genetic variation in 577 Comorian islanders. We have defined 28 Y chromosomal and 9 mitochondrial lineages. We show the Comoros population to be a genetic mosaic, the result of tripartite gene flow from Africa, the Middle East and Southeast Asia. A distinctive profile of African haplogroups, shared with Madagascar, may be characteristic of coastal sub-Saharan East Africa. Finally, the absence of any maternal contribution from Western Eurasia strongly implicates male-dominated trade and religion as the drivers of gene flow from the North. The Comoros provides a first view of the genetic makeup of coastal East Africa.

In the paper they note that ~6% of the Y chromosomal lineages were Southeast Asian, while ~15% of mtDNA lineages were. That indicates that the Southeast Asian presence on the Indian ocean was a case of folk migration, men, women and children on the move. The data from Madagascar indicate something similar, both male and female lineages show Southeast Asian imprint among the highland Malagasy (I don’t make much of the proportional difference because this is just one sample). In contrast, they show in this paper that there’s a substantial West Eurasian (probably Arab, Indian and Persian) Y chromosomal gene flow into the population of Comoros, but no West Eurasian mtDNA. So in this case you have a clear contrast with that of the Southeast Asian seafarers, the Muslim merchants who settled on the Comoros did not bring their children or womenfolk. It was not a folk migration, but a mercantile network. Because of the nature of the sources, and the cultural influence of the West Asians, we know of their presence from the historical record. In contrast, the arguably more substantial folk migration of Southeast Asian seafarers from Borneo is hidden in the text. They may have been of no concern or beneath mention from the perspective of the Muslim merchant princes, but the fact that they were no longer on the high seas by the time the Portuguese arrive may also indicate that they were driven off by the same Muslim merchant princes in the years after 1000. If the latter is the case the silence may be due to the inclination to forget an unpleasant rivalry.

All this goes to show that history’s reliance on text can mislead and obscure real dynamics. Even social and economic history which attempts to tunnel-down to the level of the populace is still heavily reliant on written records. In the case of seafarers it seems likely that even archaeologists would be unable to detect their movements because of the liminal nature of their settlements. The linguistic and cultural influences in Madagascar and in East Africa indicate a sojourn by Austronesians in that coast, but there is no physical or textual record. There is the “dark history” which we ignore because of current ideological preferences, and then there is the dark history which has fallen outside of our methodological window.

Dienekes has more on this paper.

April 30, 2010

Men & ideas on the move: settled lands & colonized minds

Filed under: Genetic History,Historical Genetics,History — Razib Khan @ 8:15 am

I am currently reading Peter Heather’s Empires and Barbarians: The Fall of Rome and the Birth of Europe. This is a substantially more hefty volume in terms of density than The Fall of the Roman Empire: A New History of Rome and the Barbarians . It is also somewhat of a page turner. One aspect of Heather’s argument so far is his attempt to navigate a path between the historically tinged fantasy of what its critics label the “Grand Narrative” of mass migration of barbarian tribes such as the Goths, Vandals and Saxons during the 4th to 6th centuries, dominant before World War II, and its post-World World II counterpoint. As a reaction against this idea archaeologists have taken to a model of pots-not-people, whereby cultural forms flow between populations, and identities are fluid and often created de novo. This model would suggest that only a tiny core cadre of “German” “barbarians” (and yes, often in this area of scholarship the most banal terms are problematized and placed in quotations!) entered the Roman Empire, and the development of a Frankish ruling class in the former Gaul, for example, was a process whereby Romans assimilated to the Germanic identity (with the shift from togas to trousers being the most widespread obvious illustration of Germanization of norms). I believe that liberally applied this model is fantasy as well. Being a weblog where genetics is important, my skepticism of both extreme scenarios is rooted in new scientific data.

There are cases, such as the Etruscans, where the migration is clear from the genetics, both human and their domesticates. The peopling of Europe after the last Ice Age is now very much an open question. The likelihood that the present population of India is the product of an ancient hybridization event between an European-like population and an indigenous group with more affinity with eastern, than western, Eurasian groups, is now a rather peculiar prehistoric conundrum. It also seems likely that the spread of rice farming in Japan was concomitant with the expansion of a Korea-derived group, the Yayoi, at the expense of the ancient Jomon people. And yet there are plenty of inverse cases. The spread of Latinate languages and Romanitas did not seem to perturb the basic patterns of genetic relationship among the peoples of Europe. The emergence of the Magyar nation on the plains of Roman Pannonia seems to have involved mostly the Magyarization of the local population. In contrast, the Bulgars were totally absorbed by their Slavic subjects culturally, leaving only their name. The spread of the Arabic language and culture was predominantly one of memes, not genes (clearly evident in the current dynamic of Arabization in parts of the Maghreb).

And yet you will note that there is a slight difference between the few examples I’ve cited: population replacement seems to have occurred in the more antique cases, rather than the more recent ones. This would naturally bias the perspectives of historians, who have much more data on more recent events (no offense, but archaeologists seem to be able to say whatever they want!). The Etruscan language itself is known only from fragments, while the happenings in prehistoric Europe and India can only be inferred very indirectly. I now offer a modest hypothesis for the distinction, why in some cases is it just the “pots” which move (Arabs), and in other cases it is the people who move (the Japanese). In cases of population replacement there is often a shift in mode of production. In cases where there is the diffusion of culture it is often a system or set of ideas which rent-seeking elites can exploit to maintain their position, or perpetuate it, flow across space. Islam was not only a potent ideology which bound the tribes of Arabia together so that they could engage in collective action, local elites across the new Muslim-dominated world found it a congenial international system whereby they could integrate themselves into a civilization of elite peers, as well as justify their god-given position at the apex of the status hierarchy (granted, many had this in the form of Christianity or Zoroastrianism, but once the old top dogs were overthrown the benefit of these systems was considerably less). The spread of Yayoi culture in Japan involved a shift from more extensive, toward more intensive, forms of agriculture. Their population base was greater, and the domains of the Jomon were left “underexploited” from the perspective of the more productive mode of agriculture which the Yayoi were engaged in. It need not be an issue of mass slaughter or extermination, a high endogenous rate of natural increase as well as disease, combined with assimilation and co-option of local elites, could result in the swallowing up of a population engaged in a less intensive mode of production. This sort of hybrid aspect of cultural and genetic expansion, whereby the local substrate is assimilated and synthesized with the expanding ethnic group, seems to be a good fit to the pattern that we see among the Han of China.

But shifts from modes of production exhibit some level of discontinuity, insofar as there are diminishing returns once all the land appropriate for that mode of production has been taken over. Farmers who are expanding into land held by hunter-gatherers or those practicing less intensive forms of agriculture can have enormous rates of natural increase because they’re not bound by Malthusian constraints. This is evident in the United States, until the late 20th century the majority of the ancestry of the white population of the republic descended from those who were counted in the 1790 census. The reason had to do with the extremely high birthrates among white Americans. When regions such as New England were “filled up,” they pushed out to the “frontier,” to northern Ohio, then to the Upper Midwest, and finally the Pacific Northwest. And in the process there was a radical change in the genetic variation of North America, as the indigenous populations died from disease, were numerically overwhelmed, or genetically absorbed. This is an extreme case scenario, but I think it illustrates what occurs when modes of production collide, so to speak. The pattern in Latin America was somewhat different, though an amalgamated Mestizo population did emerge over time, there was not the wholesale demographic replacement in many regions. And I believe that the reason is that the Iberians did not bring a superior mode of production, rather, the large local population base engaged in agriculture presented an opportunity for rent-seekers to place themselves atop the status hierarchy. Sometimes this involved intermarriage with local elites, as was the case in Peru where the nobility of the Inca intermarried with the Spanish conquistadors for the first few generations (the whiteness of the Peruvian elite despite the fact that the old families have Inca ancestry is simply due to dilution as successive generations of lower Spanish nobility set off to the New World and married into Creole families).

By the Roman period I believe that much of the core Old World was “filled up” in terms of intensive agricultural production. So most, though not all, of the changes in ethnicity or identity are biased toward elite emulation and novel identity formation. The Turks did not bring an innovative new economic system whereby they replaced the Greek and Armenian peasantry in Anatolia, rather, on the contrary peculiarities in the Turkish Ottoman system of rule produced a situation where the old families were usually replaced in positions of power by converts from the Christian groups who assimilated to a Turkish identity. When the economic arrangements reach stasis and the population is at Malthusian equilibrium change is a matter of shifting identities and affinities of the rent-seekers. When radically new economic systems emerge, opportunities for disparate population growth present themselves. Ergo, England went from being demographically dwarfed by France in the 17th century, to surpassing it in population in the 19th. England was of course the first nation to break into a new mode of production since the agricultural revolution.

Credit: Thanks to Michael Vassar for triggering this line of reasoning after a conversation we had about the Neolithic revolution.

March 27, 2010

The science of human history as written by Herodotus

The following passage is from the epilogue of The Real Eve: Modern Man’s Journey Out of Africa by Stephen Oppenheimer:

In this book I have offered a synthesis of genetic and other evidence. Everything points to a single southern exodus from Eritrea to the Yemen, and to all the non-African male and female gene lines having arisen from their respective single out-of-Africa founder lines in South Asian (or at least near the southern exit). I regard the genetic logic for this synthesis as a solid foundation, and I have based the rest of my reconstruction of the human diaspora upon it. Obviously, the ‘choice’ of starting point (mine or theirs) determined all the subsequent routes our ancestors and cousins took. Tracing the onward trails is only possible as a result of marked specificity in regional distribution of the genetic branches The geographic clarity of both male and female gene trees is a big departure from the fuzzy inter-regional picture shown by older genetic studies. The degree of segregation of lines into different countries and continents is in itself good evidence that once they got to their chosen new homes, the pioneers generally stayed put, at least until the Last Glacial maximum forced some of them to move. This conservative aspect of our genetic prehistory also provides a partial explanation for the fact that when we look at a person, we can usually tell, to the continent, where their immediate ancestors came from, and underlies differences that some of us still call ‘race.’

Oppenheimer wrote the above in the early aughts, as his book was published in 2003. Much of this is generally in line with the ‘orthodoxy’ of the day. I believe that Oppenheimer’s assertion that there was one southern migration out of Africa by anatomically modern humans has gained some advantage over the alternative model of two routes, northern and southern, over the past ten years (Spencer Wells’ The Journey of Man sketches out the two wave model). Other assertions and assumptions have not stood the test of time. In particular, I would contend that generally the ‘conservative aspect of our genetic prehistory’ can no longer be taken for granted. Specifically, it seems likely now that much occurred after the Ice Age and during the Neolithic.

420px-AGMA_HérodoteThe false inferences of the early aughts were due to two primary problems. First, they relied heavily on the powerful new techniques of extraction and analysis of uniparental ineages; the male and female direct line of descent. Concretely, mtDNA and the nonrecombintant portion of the Y chromosome. The lack of recombination allows for relatively easy reconstruction of phylogenies assuming a coalescent model. Second, the inferences attempt to make connections between the patterns of variation in modern populations, and what one may infer about the past from those patterns. Obviously constructing a phylogeny, or plotting haplogroup frequencies as a function of geography, is rather straightforward science. But using these results to generate inferences of the past is often more of an art than a science, and implicit assumptions lurk behind the causal chains. Consider for example the utilization of modern Anatolian (i.e., Turkish) genetic variation as a reference for the expansion into Europe of Neolithic farmers from the Near East. This of course presumes that modern Anatolians are a good proxy for ancient Anatolians. There are various suggestive reasons for why this is a plausible assumption, but assemble enough plausible assumptions, and rely on their joint likelihood, and you construct a very rickety machinery of possibility.

In early 2007 I began to have serious doubts about the orthodoxy of genetic conservatism. The primary trigger was the story of the Etruscans. Here is the crux of the issue: there are two models for the origins of the Etruscans, first, that they were the pre-Indo-European autochthons of Italy, or, that they were the migrants from the eastern Mediterranean, in particular Anatolia. The second may seem an outlandish hypothesis, but there were several tendrils of evidence to support it. But perhaps the ’support’ which weighed most against it is that the fact that the Anatolian model has an ancient source, the Greek historian Herodotus. I should perhaps put historian in quotes as well, because Herodotus is often viewed more as a repeater of myths, and derided by some as the ‘father of lies’ (in this he stands in sharp contrast to contemporary perceptions of the ‘modern’ Thucydides, though revisionists have begun to challenge this narrative). In contrast, the model that Etruscans are indigenous to Italy, and that their ‘exotic’ foreign traits were simply acquired through trade and cultural diffusion, dovetailed well with the post-World War II ‘pots not peoples’ paradigm. That cultural change was ubiquitous, while at the same time populations were immobile. It was boring, prosaic, and conservative, and so an ideal null hypothesis.

But here it turns out that Herodotus was right, and archaeologists were wrong. Genetic analysis of modern Tuscans from isolated villages shows that some are surprisingly closely related to extant eastern Mediterranean lineages. Genetic analysis of Tuscan cattle showed that they were surprisingly closely related to extant eastern Mediterranean lineages of cattle. Finally, extraction of ancient Etruscan DNA showed that they were closely related to extant eastern Mediterranean lineages. The overlap was often with Anatolia, and combined with fragmentary linguistic and archaeological data, the evidence clearly points to an exogenous origin for the Etruscans. The boring null hypothesis was wrong. After these genetic stories gained prominence I went and reread recent archaeological texts on the Etruscans, and there were many models which showed exactly how Etruscan cultural uniqueness derived back to prehistoric Italy. It seems in hindsight that the prior assumption served as an interpretative filter, and people saw patterns that they were primed to see based on what they ‘knew’ to be the history of prehistoric and early Iron Age Tuscany.

Of course to refute the primacy of Oppenheimer’s conservative model of genetics one has to offer more examples than that of the Etruscans, and in particular, examples which are of greater scope and weight. I believe those examples exist. In the early aughts based on the mtDNA evidence the likelihood was that South Asian genetic variation is by and large a product of changes wrought upon the basic elements extant in the region around the end of the last Ice Age. The Y chromosomal data was more confused, though it did imply a closer relationship to groups in western Eurasia. But based on the mtDNA Oppenheimer posited a model whereby India was the mother of all non-Africans, that is, all non-African lineages derived from roots within the Indian subcontinent before the Last Glacial Maximum. This is at sharp variance with colonialist narratives of an Aryan invasion of the subcontinent, and the subjugation of the natives by quasi-European overlords, who are the ancestors of the moder upper castes. The charged ideological import of this model is transparently obvious.

Unfortunately the reality is likely more complex. I suspect that some form of Oppenheimer’s model is correct, insofar as South Asia was likely an important way station for modern humans as they left Africa, and pushed into other regions of Eurasia, on to Australasia and the New World. This interpretation does gain support from mtDNA, the direct maternal lineage. But a new analysis of South Asian genetic variation using a substantial proportion of the autosomal genome implies in fact that South Asians are possibly descendants of an ancient hybridization event between a native population with deep roots in the subcontinent, and a quasi-European population which was exogenous to the subcontinent.* Genetically the quasi-European population is quite close to northern Europeans, similar to the genetic distance between modern Finns and Italians, not trivial, but far closer than that between modern South Asians and Europeans. Was this the ancient Aryan invasion? I remain skeptical of this particular detail for various reasons, as I suspect that the history of the Indian subcontinent is in fact even more complex than has been assumed before (I think it is more likely that the quasi-Europeans came before the Indo-Aryans, who arrived late, and had a stronger cultural than genetic influence).

Finally, there is another region of the world where it seems likely that the old orthodoxies of genetic conservatism will be overthrown. That region is Europe. The scientific orthodoxy of deep time continuity is strong enough that it has percolated into the public consciousness, the leader of the British National Party even referred to the deep roots of white British in demarcating who he believed ‘indigenous people’ of the Isles were. But newer data is more supportive of the hypothesis that in fact Neolithic farmers who arrived from elsewhere are the likely ancestors of most Europeans, not the hunter-gatherers who remained after the Ice Age. Extraction of ancient DNA has yielded a set of results which simply are not explicable assuming the older models of genetic continuity, which were based on inferences made from modern population variation. If I had to hazard a guess, I would have some, though not high, confidence in the following story. First, the indigenous hunter-gatherers are assimilated or marginalized by waves of Neolithic farmers pushing out from the eastern Mediterranean. The demographic expansion does not necessarily sweep outward along a southeast-northwest axis, rather, it follows the Mediterranean and Atlantic fringes, as well as along river systems in the interior. Its impact is weakest in the northeast of Europe, where Middle Eastern crops are least suitable, and the natives have the most time to absorb the cultural toolkit of the newcomers so as to resist their advance. Second, and far later, there was another wave pushing out from the region of the Ukraine to the Volga, likely the ancestors of the Indo-Europeans. Tentatively I would contend that these were the carriers of the Kurgan culture, and also brought the allele for lactase persistence. Again, for ecological reasons the populations of the northeast Baltic and into the forests of northern Russia were most insulated from this push (and non-Indo-European languages persisted in Iberia down to Roman times, and specifically in the Basque-country down to modern times, though I suspect this is a function of distance). So modern European populations may be assumed to be tri-hybrid, first a synthesis of Middle Eastern farmers overlain upon the Paleolithic substrate, and second a synthesis of Indo-Europeans from the east overlain upon pre-Indo-European substrate. Unlike the case of India I suspect teasing out these patterns in modern populations is more difficult because the genetic distance between the three ancestral populations is far smaller than between the indigenous peoples of India before the quasi-Europeans arrived.

This leaves much of the world untouched by my speculations, but I believe showing that the genetically conservative null hypothesis is now in serious doubt in South Asia and Europe is sufficient to knock it from being a necessarily default assumption through which we must filter our interpretations. I do not believe that the reordering of human variation and the welter of population movement after the Ice Age was equivalent in effect to the Out of Africa migration, but I do believe that it was important enough to make the world of 2000 BCE very different from that of 15000 BCE in regards to genetic variation. In some cases, such as Central Asia from the Caspian to the Taklamakan the world of 2000 CE is fundamentally different from the world of 0 CE.

I will then end with a prediction, one in which I do not have much confidence, but which may no longer be wrong on the face of it with these new data in mind. Here is a passage from page 7 of Jared Diamond’s Guns, Germs, and Steel:

Initially, archaeologists considered the possibility that the colonization of Australia/New Guinea was achieved accidentally by just a few people swept to sea while fishing on a raft near an Indonesian island. In an extreme scenario the first settlers are pictured as having consisted of a single pregnant young woman carrying a male fetus…..

Let me stipulate that Diamond seems skeptical of the extreme model, but it illustrates the consensus that Australian Aboriginal populations are descended from the first settlers. That is, the modern populations of indigenous Australians are the direct descendants of those who swept Out of Africa along the fringe of the Indian ocean, through Southeast Asia, and arrived in Australia (more specifically, Sahul), on the order of 40 to 60 thousand years ago. From what genetic data I have seen this may be true. But I do not know of any extractions of ancient DNA, and it seems to me that the analysis of the phylogenetics of Australian Aboriginals is relatively sketchy. Therefore, I will suggest that within the last 10,000 years there has been a major new migration of people into Australia, and the modern range of genetic variation of Australian Aboriginals is significantly different from that of the populations of the Ice Age. I suggest this primarily because the dingo arrived within the last 10,000 years, more likely as recently as 4,000 years ago. With the expansion of the utility of ancient DNA extraction and analysis this question may be answered in the near future. I would still bet I’m wrong with the hypothesis I just offered, but I’m far less sure than I would have been 2 years ago.

Note: This post emerged from a conversation I had with Kevin Zelnio and Dave Munger.

* I say ‘quasi-European’ because the population may have origins outside of the boundaries of modern Europe at the Urals. Perhaps in western Siberia. Additionally, the idea of ‘Europe’ is relatively new, and exhibits little ancient cultural coherency.

Image source: Wikipedia

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