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Demic Diffusion

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As many of you know when you have two adjacent demes, breeding populations, they often rapidly equilibrate in gene frequencies if they were originally distinct. There are plenty of good concrete examples of this. The Hui of China are Muslims who speak local Chinese dialects. The most probable root of this community goes back to the enormous population of Central Asia Muslims brought by the Mongol Yuan dynasty that ruled ruled China for over a century from the late 1200s to 1300s. Genetic studies of this group that I’ve seen indicate that a high bound estimate for West Eurasian ancestry is ~10%. The other ~90% is interchangeable with the Han Chinese. So let’s assume that the Hui are ~10% West Asian. If you assume that in the year 1400 the Hui were “pure,” you have 24 generations (25 years per generation). The original population of “Central Asian Muslims” were heterogeneous, including Iranians and Turks. But let’s take it granted that they were 50% East Eurasian and 50% West Eurasian in ancestry at the time of their arrival. What would the intermarriage rate per generation have to be so that the Hui are ~10% West Eurasian at t = 24 (24 generations after the beginning of intermarriage assuming 50/50 West vs. East Eurasian splits)? Turns out all you need is a constant 7% intermarriage rate per generation (the Han Chinese population is so large in relation to the Hui that you can model it as infinite in size).

The situation gets even simpler when you have one population which divides into two. For example, imagine that the Serbs and Croats fissioned from a set of unstructured South Slavic tribes which filtered into ancient Illyria ~600 A.D. Soon enough there was a cultural division between the two in terms of religion (Western vs. Eastern Christian) which threw up a population genetic barrier. If you assume that genetically the two groups were totally similar at t = 0, and you separated them perfectly, over time they would diverge due to drift in their allele frequencies. But the reality is that barriers between geographically close groups do not prevent all intermarriage. Even extremely insular groups in a cultural sense such as the Roma of Eastern Europe are clearly heavily admixed with their surrounding populations, as they seem to be no more than ~50% South Asian in total genome content. Going back to the South Slavs, who start out very similar in our putative scenario, how much intermarriage will be necessary for them to not diverge? The issue is not the rate of intermarriage, rather, one migrant per generation across the two demes will be sufficient to equilibrate allele frequencies. On the face of it this seems implausible, but recall that divergence is driven mostly by drifting of genes as well as new variation (whether through other exogenous migratory sources or mutation). Very small populations are subject to a lot of drift, and so diverge rapidly, but only very few migrants are needed to bring it back into alignment, because they are proportionally significant. In contrast, the frequencies of large populations are less buffeted by generation-to-generation sample variance (e.g., 10 tosses of a coin will deviate more from 50/50 proportionally than 100 tosses), requiring less gene flow proportionally to maintain parity.


These models of how genes flow between populations and how they diverge are analytically very useful. They allow us to conceptualize how gene flow and population substructure could work to generate allele frequency clines on a large geographical scale. Aggregating and averaging allele frequencies in deme-by-deme bins you can perceive the changes as a function of space as smooth continuities. This is certainly the take away from the synthetic maps derived from PCA results in L. L. Cavalli-Sforza’s History and Geography of Human Genes. This gradualistic space of variation can be well accounted for by a few rapid expansion events and bottlenecks as well as geographic isolation building up variation, which eventually “smooths” over through gene flow (with a few exceptions such as Oceania and the New World). Imagine for example the New World. From what I have read the shortest time frame for the push of modern humans from north to the very far south is on the order of ~1,000 years. That’s 40 generations. Depending on how you look at it, that’s very short, or very long. If our understanding of pre-agricultural populations is correct, this would have occurred via a demic fission where tribes would rapidly expand demographically to fill the “empty space,” and move the frontier forward due to classic Malthusian pressures which would manifest in tribal fissioning.

To a great extent this model of small-scale demic diffusion can be projected into the future, and down to the recent past. From what I can gather L. L. Cavalli-Sforza and Albert Ammerman seem to be positing a shift in terms of quantity and not quality when it came to agriculture and demographics. Because agriculturalists could extract more per unit calories out of the same amount of land their population would surpass that of hunter-gatherers, and they would expand into a relatively “empty” land of hunter-gatherers through the bottom-up force of numbers, admixing with the indigenes as the wave of advance pushed on. As an American this aligns with some of the narrative of the recent history of our own nation, with the myth of pioneer families moving to the frontier drawn by the fruit which could be won by mixing of their labor with their land. But the reality is that such a narrative is mythic in that it focuses too exclusively on individuals. The settling of the frontier was not simply a matter of mass action and demographic pressure, as individuals or families expanded into new territory. It was rather a complex of individual, subcultural, cultural, and governmental dynamics which operated in concert to expand the frontier of settlement! The national, and to a lesser extent in the earlier years state, government set the institutional parameters by which Amerindian populations were cleared off the land and white settlers were allowed to start up their frontier homesteads with relative security. Additionally, there were pulses of settlement which followed broader cyclical dynamics in American and European society. Not only is reducing the expansion to purely individual level natural increase writ large probably not accurate, but it has little inferential power to explain the true arc of the phenomenon of how the West was won.

I believe this institutional parameter in the prehistoric past is far too often ignored. We we can not see, we can not imagine. In particular, I suspect that complex institutions between the level of the tribe and the state came to the fore with the rise of agriculture. The map at the beginning of the post shows the migrations of several historically attested people. You see where they start, and where they end, and you see how long they took. And importantly, these were folk wanderings, not just small bands of mobile males. Because all of these were nomadic populations heavily dependent on the horse it would be easy to fall into technological determinism. That is, we attribute the mobility to the horse (or camel) which these groups had access to. But the difference between the time taken by the Banu Hilal and the Alans was not the speed of their mount, but historical contingency. Rapid population movements of whole people require technologically necessary preconditions, but these are not sufficient. The 200 years that it took the Alans to sweep from the plains of Eurasian heartland to the North African Maghreb occurred in starts and stops. In Spain the Alans were decimated by Roman armies in the 5th century, and were absorbed into the confederacy of the Vandals, who eventually conquered North Africa. All this was possible due to institutional collapse on the part of the Romans. Similarly, the rapidity of the Banu Hilal transfer from Arabia to North Africa had to do with the facilitation on the part of the Fatimids of Egypt. The historical details of this folk wandering need not concern us, suffice it to say that without knowing the specifics one would be at a loss to understand this mass translocation of a whole society.

And it is the issue of translocation which I think is critical. A mass-action and bottom-up model usually entails some synthesis across the source population expanding, and the target population being absorbed. But the Banu Hilal were simply Bedouin who had relocated, pure and simple. They had not had a long sojourn in Egypt, or been influenced by the cities of Cyrenaica. It is as if they had taken a worm-hole from point A to point E without encountering B, C, and D. They were a literal “culture shock” to the Maghreb, as well as a genetic shock. The Banu Hilal, and nomadic peoples in general, are perfectly suited to “leapfrog” in nearly an instant from position A to position D.

But not just the Banu Hilal. The expansion of Europeans during the Age of Discovery to all suitable points across the globe is viewed to a great extent as sui generis. I do not think it we should see it as so exceptional in quality. Rather, it is an extension of an ancient pattern. Water transport is cheap, and one can shift matériel in bulk. In antiquity Egypt fed both Rome and Constantinople in turn because its surplus was easily accessible via river and sea. It seems entirely possible that the expansion of farming across the Mediterranean also occurred to a large extent through jumps from fertile locale to locale, facilitated by the ease of water transport. Instead of a demic diffusion one can model this as a series demic of pulses, which eventually filled in. Our perception of diffusion has to do with the coarseness of our measurements.

This sort of translocation process en masse could not have occurred simply through the ingenuity of groups of a few families. Ancient hunter-gatherers were resident on far more fertile territory than modern ones, and so they were likely more well organized and numerous than we might think. Just as the Russian Empire had to pacify the black lands of Ukraine before peasants could farm without being molested by Cossack or Turk, perhaps military expeditions of some sort cleared out the way for the ancient farmers?

But the power of institutions is not just military. One of the peculiar aspects of agriculture is that the regions which we perceive as rich and fertile today were often settled later than more marginal territories in terms of peak production. To give an example, farming began in the marginal uplands of the Fertile Crescent, only later to expand to the lowland territories of Mesopotamia. A more recent case is Thailand, where the uplands were the center of gravity before the shift began to the modern rice-basket of the lower Chao Phraya. Why? Because small-scale farming is far easier in drylands with easily tillable soil. The more potentially productive territory is often more intensive in capital and requires greater coordination of resources and population. In other words, without institutional scaffolding the frontiers of the production possibility are not exploited. One family or set of families can only do so much. One requires more elaborated structure to leverage the technology to its full range of possibilities.

What does all this have to do with genetics? I believe that a relatively simple isolation-by-distance model re-equilibrating after a few major human population genetic fissions (e.g., “Out-of-Africa”) is a very good first approximation to the patterns of variation we see around us. There’s well over a generation of research in this area. But there are details and deviations on the margins which I think need a more complex model to explain. Some of these are in deep prehistory, such as the possibility of admixture between very divergent human lineages (Neo-Africans and Denisovans). But many of them are very recent. We are only ~10 years into the post-genomic era. I suspect that in a few years we’ll feel that the coverage geographically given by data sets such as the HGDP are coarse indeed. As we drill-down to a finer-grain I suspect we’ll get a better sense of the deviation of human genetic variation from the null, the tortoise of constant and continuous genetic exchange and banal fission of tribe upon tribe, buffeted by animal Malthusian pressures. Into the landscape of the tortoise ~10,000 years ago arose the dynamic of the frog, protean, leaping to and fro, exploring the ecological niches on the margins, and creating them anew. Whereas behavioral modernity ~40,000 years B.P. is termed the “Great Leap Forward,” the past ~10,000 years have been an ever more rapid succession of leaps and lunges. Most of this is clearly cultural, due to the flexibility and plasticity of memes. But some of this has almost certainly has been genetic, as the gentle accumulation of thousands of years of genetic variation upon a demographic palimpsest is torn to shreds by cultural revolutions which have genetic import.

In short, the distance between 8,000 B.C. and 12,000 B.C. in terms of the range of potential possibilities may have been far greater than that between today and 8,000 B.C. Agriculture may have heralded the era of morbid misery, but it also unlocked the keys to startling possibilities.

Image credit: Francois Marchal

(Republished from Discover/GNXP by permission of author or representative)
 
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The image above is adapted from the 2010 paper A Predominantly Neolithic Origin for European Paternal Lineages, and it shows the frequencies of Y chromosomal haplogroup R1b1b2 across Europe. As you can see as you approach the Atlantic the frequency converges upon ~100%. Interestingly the fraction of R1b1b2 is highest among populations such as the Basque and the Welsh. This was taken by some researchers in the late 1990s and early 2000s as evidence that the Welsh adopted a Celtic language, prior to which they spoke a dialect distantly related to Basque. Additionally, the assumption was that the Basques were the ur-Europeans. Descendants of the Paleolithic populations of the continent both biologically and culturally, so that the peculiar aspects of the Basque language were attributed by some to its ancient Stone Age origins.

As indicated by the title the above paper overturned such assumptions, and rather implied that the origin of R1b1b2 haplogroup was in the Near East, and associated with the expansion of Middle Eastern farmers from the eastern Mediterranean toward western Europe ~10,000 years ago. Instead of the high frequency of R1b1b2 being a confident peg for the dominance of Paleolithic rootedness of contemporary Europeans, as well as the spread of farming mostly though cultural diffusion, now it had become a lynch pin for the case that Europe had seen one, and perhaps more than one, demographic revolutions over the past 10,000 years.

This is made very evident in the results from ancient DNA, which are hard to superimpose upon a simplistic model of a two way admixture between a Paleolithic substrate and a Neolithic overlay. Rather, it may be that there were multiple pulses into a European cul-de-sac since the rise of agriculture from different starting points. We need to be careful of overly broad pronouncements at this point, because as they say this is a “developing” area. But, I want to go back to the western European fringe for a moment.


As I stated above the Basques were long used as a Paleolithic “reference” by historical geneticists. That is, the deviation of a population from the Basques would be a good measure of how much admixture there had been from post-Paleolithic sources. Connections between Iberian populations and those of western and northern Europe were used to trace expansions out of the ecological refuges of modern humans during the Last Glacial Maximum ~20,000 years ago. Just goes to show how reliant we are on axioms which are squishier than we’d like to think.

Last fall I posted a result from Dodecad on the difference between French and French Basques (both from the HGDP). I’ve replicated this myself a few times now too:

The striking aspect is that the Basque are less cosmopolitan than the other French. This is evident in most of the runs of the HGDP Basque; they just have a “simpler” genetic heritage than other Western Europeans. Today Dienekes posted some results from the IBS Spanish data set in the 1000 Genomes. He suggests there are clearly a few Spanish Basques in there (I’ve highlighted them):

Recall that the Basques were exempt from inspection for “cleanliness of blood”, because they were presumed to lack Jewish or Moorish ancestry by virtue of being Basque. It seems that the Spanish IBS sample, like the Behar et al. Spaniards and Portuguese, do have some Moorish genetic imprint. This is not too surprising. The Moriscos might have been expelled in the early 17th century, but not before the majority had converted to Christianity over the centuries (in fact, some of the most virulent anti-Morisco partisans had Moorish ancestry themselves, and were particularly tainted by association with the remaining culturally unassimilated crypto-Muslims). All that being said, I suspect that the “West Asian” ancestry amongst the majority of the Spaniards is not due mostly to the Arab period (when of the majority of the settlers probably were Berbers or Arabicized Berbers), but to population impacts prior to that. By the time of the Roman conquest much of Spain was Celtiberian. I have low confidence in this assertion, but I am coming to believe that the Indo-Europeans brought a mix of East European and West Asian ancestry (or at least those two distinct strands which tend to shake out of ADMIXTURE in a broad array of European samples) to western Europe.

On a related note, Wave-of-Advance Models of the Diffusion of the Y Chromosome Haplogroup R1b1b2 in Europe:

Whether or not the spread of agriculture in Europe was accompanied by movements of people is a long-standing question in archeology and anthropology, which has been frequently addressed with the help of population genetic data. Estimates on dates of expansion and geographic origins obtained from genetic data are however sensitive to the calibration of mutation rates and to the mathematical models used to perform inference. For instance, recent data on the Y chromosome haplogroup R1b1b2 (M269) have either suggested a Neolithic origin for European paternal lineages or a more ancient Paleolithic origin depending on the calibration of Y-STR mutation rates. Here we examine the date of expansion and the geographic origin of hgR1b1b2 considering two current estimates of mutation rates in a total of fourteen realistic wave-of-advance models. We report that a range expansion dating to the Paleolithic is unlikely to explain the observed geographical distribution of microsatellite diversity, and that whether the data is informative with respect to the spread of agriculture in Europe depends on the mutation rate assumption in a critical way.

Really I’m waiting for more ancient DNA. These sorts of studies are starting to feel like rewarming cold pizza. Edible, but suboptimal. Next, Phylogeography of a Land Snail Suggests Trans-Mediterranean Neolithic Transport:

Background
Fragmented distribution ranges of species with little active dispersal capacity raise the question about their place of origin and the processes and timing of either range fragmentation or dispersal. The peculiar distribution of the land snail Tudorella sulcata s. str. in Southern France, Sardinia and Algeria is such a challenging case.

Methodology
Statistical phylogeographic analyses with mitochondrial COI and nuclear hsp70 haplotypes were used to answer the questions of the species’ origin, sequence and timing of dispersal. The origin of the species was on Sardinia. Starting from there, a first expansion to Algeria and then to France took place. Abiotic and zoochorous dispersal could be excluded by considering the species’ life style, leaving only anthropogenic translocation as parsimonious explanation. The geographic expansion could be dated to approximately 8,000 years before present with a 95% confidence interval of 10,000 to 3,000 years before present.

Conclusions
This period coincides with the Neolithic expansion in the Western Mediterranean, suggesting a role of these settlers as vectors. Our findings thus propose that non-domesticated animals and plants may give hints on the direction and timing of early human expansion routes.

So basically the snail hitched a ride from Sardinia to Algeria to France. I don’t think this is that surprising. First, it seems pretty obvious that a lot of the cultural expansion in the prehistoric period did not consist of the fission of villages along a continuous wave of advance, but involved leap-frogging to suitable nuclei from which the populations expanded. Imagine a rising flood where the lowest zones are inundated first, and then the higher peaks. Additionally, we shouldn’t presume that these expansion events were without conflict and institutional support. Consider that the expansion of farming across much of southern European Russia and Ukraine could only occur after the state had pacified, expelled, or assimilated, the mobile Turkic populations which were wont to extract unsustainable rents out of isolated and vulnerable peasant populations.

Finally, what’s up with the strong north-south differentiation across the Mediterranean basin, peaking in the west? It’s as if there were two waves of demographic and cultural advance which laid the ground work, and later perturbations haven’t disrupted that bedrock. It suggests to me the critical importance of lateral coastal transport in connecting cultural colonies, as opposed to more long distance jumps across the open sea. The latter were probably important for the transport of luxury goods and the exchange of memes, but not so much for the exchange of genes.

(Republished from Discover/GNXP by permission of author or representative)
 
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ResearchBlogging.org In light of my last post I had to take note when Dienekes today pointed to this new paper in the American Journal of Physical Anthropology, Population history of the Red Sea—genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup. The authors looked at the relationship of mitochondrial genomes, with a particular emphasis upon Yemen and the Horn of Africa. This sort of genetic data is useful because these mtDNA lineages are passed from mother to daughter to daughter to daughter, and so forth, and are not subject to the confounding effects of recombination. They present the opportunity to generate nice clear trees based on distinct mutational “steps” which define ancestral to descendant relationships. Additionally, using neutral assumptions mtDNA allows one to utilize molecular clock methods to infer the time until the last common ancestor of any two given lineages relatively easily. This is useful when you want to know when a mtDNA haplgroup underwent an expansion at some point in the past (and therefore presumably can serve as a maker for the people who carried those lineages and their past demographic dynamics).

What did they find? Here’s the abstract:

Archaeological studies have revealed cultural connections between the two sides of the Red Sea dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus our attention here on the mitochondrial haplogroup HV1 that is present in both the Arabian Peninsula and East Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the first time) affiliated into this haplogroup testify to its emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via population expansions when climatic conditions improved. Detailed phylogeography of HV1 sequences shows that more recent demographic upheavals likely contributed to their spread from West Arabia to East Africa, a finding concordant with archaeological records suggesting intensive maritime trade in the Red Sea from the sixth millennium BC onwards. Closer genetic exchanges are apparent between the Horn of Africa and Yemen, while Egyptian HV1 haplotypes seem to be more similar to the Near Eastern ones.

Much of this is totally concordant with the results we’ve generated from the autosomal genome. Though the autosomal genome is much more difficult when it comes to implementing many of the tricks & techniques of phylogeography outlined above, it does offer up a much more robust and thorough picture of genetic relationships between contemporary populations. Instead of a a distinct and unique line of paternal or maternal ancestry, thousands of autosomal SNPs can allow one t o get a better picture of the nature of the total genome, and the full distribution of ancestors.

The map to the left shows the spatial gradients of the broader haplogroup under consideration, HV1. But what about the branches? Below is an illustration of the phylogenetic network of branches of HV1, with pie-charts denoting the regional weights of a given lineage:

Since the shading is so difficult, let me jump to the text:

…Curiously, the HV1 root haplotype with substitution at position 16,067 was not observed in the Arabian Peninsula except in four Yemeni Jews, but was observed in 11 Caucasus, four Egyptian, one European, two Maghreb, and six Near Eastern samples, thus supporting a possible origin in the Near East. Haplotype 16,067–16,362, possibly defining a pre-HV1 haplogroup, has so far been observed in Dubai (one), Ethiopia (four), Maghreb (one), and Yemen (three)….

I think you have be very, very, careful to not read too much into mtDNA lineage distributions and what they may tell you about the past, at least in and of themselves. With the rise of ancient DNA and deeper analyses of mtDNA sequences as well as better geographical coverage many of the inferences of the last 10 years are being radically revised. But, combined with the autosomal results the origin of these mtDNA haplogroups in the Middle East within the last ~10 thousand years seems eminently possible.

Finally, here are their time until the most recent common ancestor estimates:

…The TMRCA estimate for HV1 was 22,350 (14,737–30,227) years when taking into consideration the sequences without the polymorphism at 15,218—a figure which closely matches the estimate of 18,695 (13,094–24,449) years when not considering those two sequences. The control region age estimate of HV1 also presents a similar age, dating to 19,430 (6,840–32,023) years. Age estimates of HV1 daughter sub-haplogroups are only slightly lower—15,178 (8,893–21,671) years for HV1a and 17,682 (10,320–25,316) years for HV1b. The common Arabian Peninsula and East African sub-haplogroups HV1a3 and HV1b1 share a close age of 6,549 (2,456–10,746) years and 10,268 (4,792–15,918) years, respectively. Sub-haplogroups HV1a1 and HV1a2, which despite being rare seem to have a wider geographical distribution, have TMRCA of 10,268 (3,602–17,194) years and 9,518 (3,963–15,255) years, respectively. The ratio of the dates based on the ρ statistic for the synonymous clock relative to the complete sequence was 1.24, closely overlapping in most branches except for HV1a1 which has a very broad age estimate based only on synonymous diversity [23,616 (4,917–42,315) years]….

The confidence intervals on these estimates are really large. All you can say with a high degree of certainty is that the expansion of the family of HV1 haplogroups does not predate the Last Glacial Maximum, 15 to 20 thousand years ago. Many of the daughter branches seem to have emerged in the Holocene, possibly after the rise of agriculture. But with the huge possible set of ranges these temporal estimates come close to offering up pretty much zero additional clarity on the chronology of population dynamics in this region .

Readers might also be interested this from last January, Internal Diversification of Mitochondrial Haplogroup R0a Reveals Post-Last Glacial Maximum Demographic Expansions in South Arabia (with some of the same authors). One aspect of these sorts of papers working with mtDNA is that they remain generally oriented toward the proposition that Pleistocene population structure is extremely important in predicting contemporary patterns of genetic variation. I’m not sure this is such a robust model. The autosomal and uniparental data from Ethiopia and Somalia strongly leans us toward the proposition of admixture of two very distinct populations, one in East Africa (“Ancestral East Africans”), and Eurasian group which are likely to have been intrusive. The genetic distance between the Eurasian inferred ancestral component, which is nearly identical to that of southern Arabia, and other Eurasian components is not so large that it seems plausible that there could have a separation during the Pleistocene. In other words, there was a lot of Holocene migration. If I had to guess I would say it had something to do with the agricultural and pastoral lifestyles brought by Arabians to the Horn of African within the last 10,000 years. Simple ecology imposed a limit upon the expansion of these peoples into more classical lush tropical Africa. Eventually a population did emerge to exploit these territories, Bantus from west-central Africa. Just like the Arabian-AEA hybrid population they encountered ecological, and also demographic, limits on the margins of the Semitic and Cushitic dominated territories in the Horn of Africa. And then of course there are the Nilotes….

Citation: Musilová, Eliška, Fernandes, Verónica, Silva, Nuno M., Soares, Pedro, Alshamali, Farida, Harich, Nourdin, Cherni, Lotfi, Gaaied, Amel Ben Ammar El, Al-Meeri, Ali, Pereira, Luísa, & Černý, Viktor (2011). Population history of the Red Sea—genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup American Journal of Physical Anthropology : 10.1002/ajpa.21522

(Republished from Discover/GNXP by permission of author or representative)
 
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A new paper in Proceedings of the Royal Society dovetails with some posts I’ve put up on the peopling of Japan of late. The paper is Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages:

Languages, like genes, evolve by a process of descent with modification. This striking similarity between biological and linguistic evolution allows us to apply phylogenetic methods to explore how languages, as well as the people who speak them, are related to one another through evolutionary history. Language phylogenies constructed with lexical data have so far revealed population expansions of Austronesian, Indo-European and Bantu speakers. However, how robustly a phylogenetic approach can chart the history of language evolution and what language phylogenies reveal about human prehistory must be investigated more thoroughly on a global scale. Here we report a phylogeny of 59 Japonic languages and dialects. We used this phylogeny to estimate time depth of its root and compared it with the time suggested by an agricultural expansion scenario for Japanese origin. In agreement with the scenario, our results indicate that Japonic languages descended from a common ancestor approximately 2182 years ago. Together with archaeological and biological evidence, our results suggest that the first farmers of Japan had a profound impact on the origins of both people and languages. On a broader level, our results are consistent with a theory that agricultural expansion is the principal factor for shaping global linguistic diversity.

I don’t know the technical details of linguistics to comment, but the alignment between the linguistic model and archeology is pretty impressive to me. There’s a 95% confidence interval which can push the time back to 4,000 years, so there’s some fudge factor too. The basic technique is borrowed from phylogenetics. This is pretty clear when you notice that one of the algorithms seems to be the same one used in the rice genomics paper. Nick Wade covers the paper in The New York Times, so no need for me to give a blow-by-blow in a domain where I don’t have much insight anyway.


Dienekes Pontikos really likes these results and the method which they use. He, rightly in my opinion, believes that they lend more credence to the thesis promoted in the early 2000s using the same technique that the last common ancestor of Indo-European languages is very far back in time. I’m skeptical of this model, at least in its simple general form, but these results do push me into thinking that that model is more plausible. But to really understand this stuff I probably need to teach myself some rudimentary linguistics, so I guess we’ll see.

More broadly this gets to the question: did farming spread through demographic expansion or cultural diffusion? Obviously it’s not an either/or. There’s a small residual of Amerindian ancestry in American whites, so there was some diffusion through genetic assimilation. The Xhosa tribe of South Africa seem to have ~20% Khoisan ancestry. They’re the group on the Bantu farming frontier, the last before the Bantu toolkit ceased to be effective and the Khoisan managed to maintain their hold before the whites arrived. Some of the admixture is from pastoralist Khoi, but some of it may also be from hunter-gatherer Bushmen. But here’s my issue at this point: what are the examples where we know that hunter-gatherers picked up agriculture? The instances of Japan and the Bantu expansion are two where we’re now rather sure that it was demographic expansion and replacement. Was it so different in the past? I think it may have been insofar as farming was less advanced a cultural toolkit in terms of its ability to overpower hunter-gatherers. And yet still I am becoming more convinced of the thesis of that farming spread through procreation, not propagation. My hesitation is mostly due to the reality that our understanding of the past is so clouded as a fundamental matter.

(Republished from Discover/GNXP by permission of author or representative)
 
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ResearchBlogging.orgThe Pith: Over the past 10,000 years a small coterie of farming populations expanded rapidly and replaced hunter-gatherer groups which were once dominant across the landscape. So, the vast majority of the ancestry of modern Europeans can be traced back to farming cultures of the eastern Mediterranean which swept over the west of Eurasia between 10 and 5 thousand years before the before.

Dienekes Pontikos points me to a new paper in PNAS which uses a coalescent model of 400+ mitochondrial DNA lineages to infer the pattern of expansions of populations over the past ~40,000 years. Remember that mtDNA is passed just through the maternal lineage. That means it is not subject to the confounding dynamic of recombination, allowing for easier modeling as a phylogenetic tree. Unlike the autosomal genome there’s no reticulation. Additionally, mtDNA tends to be highly mutable, and many regions have been presumed to be selectively neutral. So they are the perfect molecular clock. There straightforward drawback is that the history of one’s foremothers may not be a good representative of the history of one’s total lineage. Additionally the haploid nature of mtDNA means that genetic drift is far more powerful in buffeting gene frequencies and introduced stochastic fluctuations, which eventually obscure past mutational signals through myriad mutations. Finally, there are serious concerns as to the neutrality of mtDNA…though the authors claim to address that in the methods. I should also add that it also happens to be the case that there is less controversy and more surety as to the calibration of mutational rates of mtDNA than the Y chromosomal lineages of males. Their good for determining temporal patterns of demographic change, and not just tree structures.

Here’s the abstract, Rapid, global demographic expansions after the origins of agriculture:

The invention of agriculture is widely assumed to have driven recent human population growth. However, direct genetic evidence for population growth after independent agricultural origins has been elusive. We estimated population sizes through time from a set of globally distributed whole mitochondrial genomes, after separating lineages associated with agricultural populations from those associated with hunter-gatherers. The coalescent-based analysis revealed strong evidence for distinct demographic expansions in Europe, southeastern Asia, and sub-Saharan Africa within the past 10,000 y. Estimates of the timing of population growth based on genetic data correspond neatly to dates for the initial origins of agriculture derived from archaeological evidence. Comparisons of rates of population growth through time reveal that the invention of agriculture facilitated a fivefold increase in population growth relative to more ancient expansions of hunter-gatherers.

As Dienekes notes until recently the orthodoxy was that the genetic variation of modern populations was well explained by the genetic variation of Paleolithic groups after the Last Glacial Maximum ~20,000 years B.P. In this line of thought agriculture spread often by cultural diffusion, and the first local adopters in a region would then enter into a phase of demographic expansion. Bryan Sykes’ Seven Daughters of Eve and Stephen Oppenheimer’s The Real Eve are expositions of this point of view, which really was the historical genetic mainstream. This also dovetailed with the anthropological bias of “pots-not-people,” whereby cultural forms moved through transmission and not migration. There were some dissenters, such as Peter Bellwood, but by and large the genetic evidence at least was robust enough that they could be dismissed.

So what happened? Several things. First, the sample sets of mtDNA and Y chromosomes kept getting larger. There was deeper sequencing of informative regions. Thick SNP-chip autosomal studies came to the fore, with different conclusions. Finally, ancient DNA extraction allowed scientists to compare the real lineages of hunter-gatherers in ancient Europe vs. what they had presumed were hunter-gatherer descendant lines in modern Europeans. The strong disjunction often found was indicative of a major failing in the prior assumptions of the theorists of the early 2000s: that they could infer confidently past events from the palimpsest of modern genetic variation. They couldn’t. We know that because they seem to have been wrong.

Let’s give India as an example of “what went wrong.” Here’s a paper from 2005, Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans:

Since the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.

The Upper Paleolithic is pre-Holocene. I generally accepted this, until the the studies came out from the SNP-chips which had hundreds of thousands of autosomal markers. To be short about it Indians just seemed too close to West Eurasians if the mtDNA results were correct, and, representative. In fact, if Reconstructing Indian History is correct, about half the South Asian genome in aggregate is very close to that of West Eurasians, to the point where it seems likely to have a common ancestry in the Holocene. The mistaken inference from mtDNA may be due in part to sex-biased gene flow. That is, the South Asian exogenous genome was strongly biased toward male migration, while the deep time mtDNA substrate has tended to persist underneath all these successive layers.

Moving to the paper in question, they use a “Bayesian skyline” method to reconstruct past demographic history. Specifically, the history of the direct maternal lineage. We wouldn’t really pay attention if they didn’t have interesting results. And they do indeed.

The table is rather straightforward. They partitioned the samples they had into putative hunter-gatherer and Neolithic lineages. Notice the difference. For some of these cases we have very robust non-genetic evidence of expansion. This is true especially for the African and Southeast Asian Holocene cases. Their methods here predict exactly what we already know. So the key value add is that the methods are predicting something which is more in dispute: the demographic history of contemporary European mtDNA lineages. The concordance of the archaeological evidence of the Neolithic transition in Europe and the inferred demographic expansion of European Neolithic mtDNA lineages is striking.

The plot to the left is the curve of demographic expansion predicted from their method for Neolithic and Paleolithic lineages in Europe. The y-axis is log-scaled, so it naturally understates the explosive growth of Neolithic lineages. It comports well with what we know of how agricultural societies tend to expand and stabilize over time. During a phase of “land surplus” they enter into rapid demographic expansion, forcing the frontier of settlement out. Once the land is “filled up” we enter into the classic Malthusian “stationary state,” where the grinding misery of the peasantry becomes the lot of most. In contrast hunter-gatherer lineages didn’t experience such an explosive shift. Though pre-modern hunter-gatherer landscapes were more diversified than what we experience today, because they had access to the rich “bottom lands” and seashores now monopolized by agriculturalists, the carrying capacity of the land was generally lower for their lifestyle, and waxed and waned more gradually with shifts in ecology.

The authors also did some neat geo-visualization, if I do say so (and I’m jealous!). The two panels illustrate the spread of agriculture as inferred from archaeology, and the rate of population growth calculated from the joint information of the time of onset of a farming lifestyle in a region and the point on the “growth curve” for the Middle Eastern lineages at that time. So above you see the spread of agriculture from the eastern Mediterranean from 8000 BC to 2500 BC. Then, you see a geographical illustration of the S-shaped growth curve of the farmers. Their initial colonies experienced modest growth, but there was a transition zone in the middle of rapid expansion. Why? Perhaps there was a necessary critical mass, before the superiority of numbers began to wear down the hunter-gatherers. But this itself was a transient, as the farmer societies ran up against the limits of ecology along the northern European plain (or, perhaps just as likely, they encountered dense hunter-gatherer societies which were able to temporarily withstand their aggressive expansion on the European maritime fringe). I suspect that the models are more complex than a one-two punch, in either time or space. There were likely several pulses and distinct streams coming out of the Middle East which populated Europe.

They conclude that “Mesolithic ancestry makes up only a fraction of contemporary European genomes. U5a, U5b1, V, and 3H combined account for ≈15% of western Europeans mtDNA haplogroups.” Note that U5a and U5b are modal among the Finnic peoples of Europe. V seems widely distributed, and modal in northern Scandinavia and the western Mediterranean. I can’t seem to find easy information on 3H.

From the supplements here are the European haplgroups they selected:

We chose haplogroups associated with an origin in Near Eastern populations during the Holocene: T1, T2, J1a, K2a, and H4a. These haplogroups (T1, T2, J1a, and K) all appear to have Near Eastern founders that migrated to Europe after the Younger Dryas (2). After inspecting the haplogroup K network in Behar et al. (4), we chose the subgroup K2a, which appears to be present in the Near East (including non-Ashkenazi Jews) and European populations (but not North Africa). Haplogroup H4a is thought to have expanded throughout Europe during the Neolithic (5). However, the location of its origin is still not certain (6). Removing H4a from the Skyline analysis did not substantively change the timing of Holocene period expansion (results not shown). European haplogroups U5, V, and 3H are associated with an indigenous origin in Europe (2). Haplogroups U5a, U5b1, V, and 3H have all been attributed a TMRCA during the Last Glacial Period (2, 7–9)

Readers more well versed in the literature on mtDNA haplogroups can pick these details apart.

Where does this leave us? If this and other recent papers are correct. then the expansion of farming to Europe from the Middle East resembles the settlement of the New World far more than we may have thought! In some regions there was likely near total replacement of the substrate, perhaps like the United States. In others there was modest uptake of the indigenous substrate, as is the case in Argentina. Finally, there were regions where the indigenous hunter-gatherer substrate may have persisted to a far greater extent. I think this may be the case mostly in Baltic Europe, which combined both the possibility of relatively high hunter-gatherer carrying capacities because of marine resources and a climatic regime rather unsuitable to the initial Middle Eastern crops.

Citation: Gignoux CR, Henn BM, & Mountain JL (2011). Rapid, global demographic expansions after the origins of agriculture. Proceedings of the National Academy of Sciences of the United States of America, 108 (15), 6044-9 PMID: 21444824

(Republished from Discover/GNXP by permission of author or representative)
 
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After linking to Marnie Dunsmore’s blog on the Neolithic expansion, and reading Peter Bellwood’s First Farmers, I’ve been thinking a bit on how we might integrate some models of the rise and spread of agriculture with the new genomic findings. Bellwood’s thesis basically seems to be that the contemporary world pattern of expansive macro-language families (e.g., Indo-European, Sino-Tibetan, Afro-Asiatic, etc.) are shadows of the rapid demographic expansions in prehistory of farmers. In particular, hoe-farmers rapidly pushing into virgin lands. First Farmers was published in 2005, and so it had access mostly to mtDNA and Y chromosomal studies. Today we have a richer data set, from hundreds of thousands of markers per person, to mtDNA and Y chromosomal results from ancient DNA. I would argue that the new findings tend to reinforce the plausibility of Bellwood’s thesis somewhat.

The primary datum I want to enter into the record in this post, which was news to me, is this: the island of Cyprus seems to have been first settled (at least in anything but trivial numbers) by Neolithic populations from mainland Southwest Asia.* In fact, the first farmers in Cyprus perfectly replicated the physical culture of the nearby mainland in toto. This implies that the genetic heritage of modern Cypriots is probably attributable in the whole to expansions of farmers from Southwest Asia. With this in mind let’s look at Dienekes’ Dodecad results at K = 10 for Eurasian populations (I’ve reedited a bit):


neolith

Modern Cypriots exhibit genetic signatures which shake out into three putative ancestral groups. West Asian, which is modal in the Caucasus region. South European, modal in Sardinia. And Southwest Asian, which is modal in the Arabian peninsula. Cypriots basically look like Syrians, but with less Southwest Asian, more balance between West Asian and South European, and far less of the minor components of ancestry.

Just because an island was settled by one group of farmers, it does not mean that subsequent invasions or migrations could not have an impact. The indigenous tribes of Taiwan seem to be the original agriculturalists of that island, and after their settlement there were thousands of years of gradual and continuous cultural change in situ. But within the last 300 years settlers from Fujian on the Chinese mainland have demographically overwhelmed the native Taiwanese peoples.

During the Bronze Age it seems Cyprus was part of the Near East political and cultural system. The notional kings of Cyprus had close diplomatic relations with the pharaohs of Egypt. But between the end of the Bronze Age and the Classical Age Cyprus became part of the Greek cultural zone. Despite centuries of Latin and Ottoman rule, it has remained so, albeit with a prominent Turkish minority.

One thing notable about Cyprus, and which distinguishes it from mainland Greece, is the near total absence of a Northern European ancestral component. Therefore we can make the banal inference that Northern Europeans were not initially associated with the demographic expansions of farmers from the Middle East. Rather, I want to focus on the West Asian and Southern European ancestral components. One model for the re-population of Europe after the last Ice Age is that hunter-gatherers expanded from the peninsular “refugia” of Iberia and Italy, later being overlain by expansions of farmers from the Middle East, and perhaps Indo-Europeans from the Pontic steppe. I have a sneaking suspicion though that what we’re seeing among Mediterranean populations are several waves of expansion out of the Near East. I now would offer the tentative hypothesis that the South European ancestral element at K = 10 is a signature of the first wave of farmers which issued out of the Near East. The West Asians were a subsequent wave. I assume that the two groups must correlate to some sort of cultural or technological shift, though I have no hypothesis as to that.

From the above assertions, it is clear that I believe modern Sardinians are descendants of that first wave of farmers, unaffected by later demographic perturbations. I believe that Basques then are a people who emerge from an amalgamation of the same wave of seafaring agriculturalists with the indigenous populations preceding them (the indigenes were likely the descendants of a broad group of northern Eurasians who expanded after the end of the last Ice Age from the aforementioned refugia). They leap-frogged across fertile regions of the Mediterranean and pushed up valleys of southern France, and out of the Straits of Gibraltar. Interestingly, the Basque lack the West Asian minority element evident in Dienekes’ Spaniards, Portuguese, as well as the HGDP French (even up to K = 15 they don’t shake out as anything but a two way admixture, while the Sardinians show a minor West Asian component). Also, the West Asian and Southern European elements are several times more well represented proportionally among Scandinavians than Finns. The Southern European element is not found among the Uyghur, though the Northern European and West Asian one is. I infer from all these patterns that the Southern European element derived from pre-Indo-European farmers who pushed west from the Near East. It is the second largest component across much of the Northwestern Europe, the largest across much of Southern European, including Greece.

A second issue which First Farmers clarified are differences between the spread of agriculture from the Near East to Europe and South Asia. It seems that the spread of agriculture across South Asia was more gradual, or least had a longer pause, than in Europe. A clear West Asian transplanted culture arrived in what is today Pakistan ~9,000 years ago. But it does not seem that the Neolithic arrived to the far south of India until ~4,000 years ago. I think that a period of “incubation” in the northwest part of the subcontinent explains the putative hybridization between “Ancient North Indians” and “Ancient South Indians” described in Reconstructing Indian population history. The high proportion of “Ancestral North Indian,” on the order of ~40%, as well as Y chromosomal markers such as R1a1a, among South Indian tribal populations, is a function of the fact that these groups are themselves secondary amalgamations between shifting cultivators expanding from the Northwest along with local resident hunter-gatherer groups which were related to the ASI which the original West Asian agriculturalists encountered and assimilated in ancient Pakistan (Pathans are ~25% ASI). I believe that the Dravidian languages arrived from the Northwest to the south of India only within the last 4-5,000 with the farmers (some of whom may have reverted to facultative hunter-gathering, as is common among tribals). This relatively late arrival of Dravidian speaking groups explains why Sri Lanka has an Indo-European presence to my mind; the island was probably only lightly settled by farming Dravidian speakers, if at all, allowing Indo-European speakers from Gujarat and Sindh to leap-frog and quickly replace the native Veddas, who were hunter-gatherers.

Note: Here is K = 15.

* Wikipedia says there were hunter-gatherers, but even here the numbers were likely very small.

(Republished from Discover/GNXP by permission of author or representative)
 
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A new paper in The New Journal of Physics shows that a relatively simple mathematical model can explain the rate of expansion of agriculture across Europe, Anisotropic dispersion, space competition and the slowdown of the Neolithic transition:

The front speed of the Neolithic (farmer) spread in Europe decreased as it reached Northern latitudes, where the Mesolithic (hunter-gatherer) population density was higher. Here, we describe a reaction–diffusion model with (i) an anisotropic dispersion kernel depending on the Mesolithic population density gradient and (ii) a modified population growth equation. Both effects are related to the space available for the Neolithic population. The model is able to explain the slowdown of the Neolithic front as observed from archaeological data

The paper is open access, so if you want more of this:
fareq

Just click through above. Rather, I am curious more about their nice visualization of the archaeological data:


euroneolithic

Note how much variance there is in terms of the rate of change of the clines. As I’ve observed before there was a “break out” of the LBK farmers into Central Europe nearly 7,000 years ago, but it took much longer to close the gap between the farms on the frontier and the sea. This is well known from the archaeology, as there seems to have been a pause of ~1,000 years across much of the north European plain. On the scale of 10,000 years that’s not much time, but that’s about 40 generations. In Frisia it looks like the spreading of farming stopped for nearly ~2000 years!

Why the abatement of the spread of farming? I think the authors of the above paper are correct in their acceptance of the conventional wisdom of greater Mesolithic densities in Northern Europe. But I think perhaps a better description might be maritime Northern Europe. We often imagine early farmers displacing hunters and gatherers of game and herb, but what if in much of the world the main clash numerically was between dense populations oriented toward the sea, and those who were depended on the land? About seven years ago a study came out which argued for a rapid transition from seafood to meat in the diets of early Britons, Why Did Ancient Britons Stop Eating Fish?:

When cattle, sheep, pigs, and wheat arrived on the shores of Great Britain about 5,000 years ago, fish quickly fell off the Neolithic menu, according to an analysis of human bones scattered throughout the island.

“Farming really took off in Britain during the Neolithic. The main questions concerning the speed of change relates to how quickly Mesolithic peoples adapted—or otherwise—to the new farming methods and/or the spread of farming into Britain by new farming communities,” he said.

The research by Richards and colleagues Rick Schulting at Queen’s University Belfast and Robert Hedges at the University of Oxford tracks the shift in diet by examining the dietary signature stored in the bones.

They find that the shift was rapid and complete at the onset of the Neolithic. “Marine foods, for whatever reason, seem to have been comprehensively abandoned,” the researchers conclude in the September 25 issue of the journal Nature.

“We determined that after the introduction of domesticates, as well as the other artifacts associated with the Neolithic, the isotope values showed that marine foods were not used anymore,” he said. “We then infer that this is a switch from wild foods such as fish and shellfish to the new domesticates that arrive at this time.”

Richards said there are three plausible reasons why the British abandoned seafood from the beginning of the Neolithic: the domesticated plants and animals presented a steady source of food; the shift was forced by a climate change; or cultural pressure.

In the early 2000s the idea of wholesale rapid demographic replacement was not in the air. I think we need to put that back on the table. Here is the chart on isotope ratios from the 2003 paper:
culwar

Notice the sharp discontinuity. Richards et al. in 2003 interpreted this as a rapid cultural acquisition of the Neolithic lifestyle ~2500-3000 BC. They note in the media reports that later Britons, for example at the time of the Roman conquest, seem to have utilized fish a bit more in their diet than these early Neolithics. This stands to reason, much of Britain is not too far from the sea. To me the very sharp drop in marine consumption is indicative more of a food taboo, than a practical shift. Obviously farmers would primarily be subsistent on grain, but there’s no necessary reason to avoid meat or fish, but as it happens in many parts of the world societies preserve and perpetuate exactly such norms. These norms may have spread through cultural diffusion, for example through an adoption of a new religion. Or, the norms may have been brought by a new group which arrived in large numbers and replaced the indigenous population.

Here is an equivalent chart from Denmark from an earlier paper by the same group:

denmark

800px-Saami_Family_1900pacnortWhen we think of peoples who aren’t farmers, we often think of marginalized nomadic or semi-nomadic groups. Many of the remaining hunter-gatherers such as Bushmen, as well societies which supplement their conventional lifestyle with a lot of hunting & gathering, such as the indigenous peoples of Siberia or the Sami of northern Scandinavia, occupy territory which is simply not viable for conventional agriculture. But this was not so in the past. Before the farmers arrived the rich bottom-lands were occupied by hunters & gatherers, of fish, game, grain, and nuts. In certain ecologies, such as around productive estuaries one could imagine enormous aggregations of these peoples. Additionally, it seems likely that a sedentary lifestyle predates farming. A good contemporary analog for what ancient Northern Europe may have been like was the Pacific Northwest before the European settlement. These native tribes were relatively affluent because of the abundance of salmon runs, and engaged in lavish signalling, such as with their famous potlatches. Seeing as how there are Atlantic salmon runs in places like Norway and Scotland one can make even closer correspondences perhaps!

Stonehenge-GreenAs I have stated before just because we have no written records of this period, we can not assume that these were necessarily the fragmented and scattered “small-scale societies” which we’re familiar with today. There may have been ideologically motivated political coalitions and alliances which broke down along ethnic and cultural lines. In the paper above the authors argue that there is evidence that a climatic constraint, crops which do not have a good yield in cooler or warmer temperatures, is a weak hypothesis. If so I wonder if it is a bit too pat to simply model the dynamics as a diffusive “bottom up” process. Seems plausible enough for much of Europe where Mesolithic populations were thin on the ground because of local carrying capacity, but I suspect that the encounter between dense agglomerations of farmers and fishermen resulted in an inevitable ramp up of political integration and consolidation, as villages and tribes had to coordinate together because of a positive feedback loop of conflict.

Image Credit: Lordkinbote, Mactographer

(Republished from Discover/GNXP by permission of author or representative)
 
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