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

June 28, 2012

Population replacement in Neolithic Spain?

Filed under: Agriculture,Anthroplogy,Neolithic,Paleolithic Europeans — Razib Khan @ 12:16 pm

There’s a new ancient DNA paper out which examines the maternal lineage and the autosomal background of two individuals extracted from a Spanish site dated to 7,000 years before the present. That is, during the European Mesolithic. In other words, these are the last wave of Iberian hunter-gatherers before agriculture. I have placed the PCA, with some informative labels, to illustrate the peculiarity of these samples. Here’s the abstract:

The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic…is poorly understood, both due to the scarcity of human remains from that period…The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are ...

January 8, 2012

Europe, 10,000 B.C.

Filed under: Anthroplogy,Europe,Paleolithic Europeans — Razib Khan @ 12:31 am

The image above come from John Hawks’ weblog. I was thinking today about the resettlement of Europe since the Last Glacial Maximum. It is clear that much of northern Europe was not habitable until the Holocene, after the Ice Age. And those regions which were habitable were often marginal. But, there were zones of southern Europe which remained relatively clement. One model of how Europe was settled after the warming is that hunter-gatherers expanded north out of these southern refuges. This can explain the lower heterozygosity of northern populations (see map to left). They may have lost their genetic diversity to some extent through population bottlenecks or simply drift on the wave of demographic advance. And yet something jumped out at me on this map: the southwest portion of Portugal is reputedly the zone with the highest African admixture in continental Europe (for historical reasons). The heterozygosity may simply be a function then of the fact that southern Europe has been in greater contact with other regions of the world because of geographic proximity.

There is also a second pattern which has always elicited curiosity in me: why is it that the largest component of genetic variation in Europe separates north vs. south, as opposed to east vs. west? This does not seem to comport well with a model of expansion from southern refuges. Should not the west-east genetic variation of Ice Age Europeans who faced the tundra and ice be represented among modern populations as they expanded their range northward simultaneously? Something is wrong with the model.

First, it seems clear that a lot has changed since the Last Glacial Maximum. As recently as the late aughts authors were claiming that by ~20,000 years before the present the general shape of genetic variation we see around us had been set. I’d be willing to bet $5,000 dollars that that’s wrong. In the specific case of Europe there may be many explanations for the set of patterns we’re seeing. It may be that the original populations of the refuges were later replaced. Northern Europeans may be legitimate descendants of those groups, but the original patterns of genetic variation in southern Europe were washed away due to being overwhelmed by Neolithic populations from Anatolia. Or, it may be that modern people in the north of Europe descend from a group which moved laterally, and replaced and assimilated the original inhabitants of the continent.

There are many plausible models, and combinations of models. From what I have read people in the Reich lab are now attempting to construct a scenario for the ethnogenesis of Europeans analogous to that of South Asians. In other words, modern Europeans are a compound of the descendants of the Paleolithic hunter-gatherers with an intrusive population. The same lab seems to be positive that Indo-Europeans did have a substantial effect on genetics of South Asians. If so, then I see no reason why the same would not be so in Europe.

In any case, interesting times. We’ll know a lot more in exceedingly great detail soon enough (I’d be willing to bet money on that too!).

October 29, 2011

Unfrying the egg

Dienekes has a long post, the pith of which is expressed in the following:

If I had to guess, I would propose that most extant Europeans will be discovered to be a 2-way West Asian/Ancestral European mix, just as most South Asians are a simple West Asian/Ancestral South Indian mix. In both cases, the indigenous component is no longer in existence and the South Asian/Atlantic_Baltic components that emerge in ADMIXTURE analyses represent a composite of the aboriginal component with the introduced West Asian one. And, like in India, some populations will be discovered to be “off-cline” by admixture with different elements: in Europe these will be Paleo-Mediterraneans like the Iceman, an element maximally preserved in modern Sardinians, as well as the East Eurasian-influenced populations at the North-Eastern side of the continent.

This does not seem to be totally implausible on the face of it. But it seems likely that any “West Asian” component is going to be much closer genetically to an “Ancestral European” mix than they were to “Ancestral South Indians,” because the two former elements are probably part of a broader West Eurasian diversification which post-dates the separation of those groups from Southern and Eastern Eurasians. In other words, pulling out the distinct elements in Europeans is likely a more difficult task because the constituents of the mixture resemble each other quite a bit when compared to “Ancestral North Indians” vs. “Ancestral South Indians.”

The bigger issue which this highlights though is that the reality that many of these clustering methods are temporally sensitive. Given enough time a “hybrid” population is no longer a hybrid, but rather a new distinctive population which itself can be a “parent.” Recombination breaks apart the long range genetic physical associations which are the hallmarks of distinctive admixed ancestry on the genomic scale. That is why clustering methods easily generate a pure “South Asian” component. After at least ~3-4,000 years of continuous admixture the synthesis is now far less coarse, and the elements much more de facto miscible. And yet via other clustering techniques, such as principle components analysis, you get different results. The peculiar position of the “South Asian” individuals between Europeans and East Asians in direct proportion to their caste and regional origins becomes highly indicative of some sort of admixture event in different proportions as a function of geography and social context. The technique in Reconstructing Indian population history allowed for a resolution of this paradox by sifting through the variation and extracting out the ancestral components. The recent papers which came out on Australian Aboriginal genetics do something similar, in terms of making sense of somewhat puzzling results which are found when generating inferences from aggregate genomic variation.

Imagine how much more difficult the task would have been if the ancestral components were much closer! I suspect that’s what’s going on in Europe. I’m not privy to any big secrets, but I have heard of whispers of research groups using Sardinians as a “pure” outgroup to model the changing demographics of Europe since the arrival of agriculture. What David Reich stated at the conference was not particularly surprising to me in light of that possibility. Sardinia regularly pops out as a weird outlier in many analyses. One simple possibility here is that that’s simply a function of the fact that it’s an island, and therefore has diverged from mainland populations due to isolation from conventional village-to-village mate exchange. Another possibility, mooted by Dienekes, is that it may be a repository of European genetic variation from earlier periods, relatively unaffected by later perturbations due to demographic changes. The main reason that I can give some credit to Dienekes’ thesis has less to do with Sardinians than Basques. The French Basques in the HGDP are less atypical than the Sardinians, but in some runs they do lack a component which is most obviously classed as “West Asian,” and which other French have. In Dienekes’ own runs with a diverse array of Iberian populations this same distinction emerges.

All of this reminds us that clustering methods give us great insights into how populations are related to each other, but they don’t tell us about the details of how that relatedness came to be. It makes a great difference if an element is the outcome of relatively recent (<10,000 years) hybridization events, as opposed to having deeper roots. For example, admixture between Polynesians and Melanesians brings together two components, whatever their own prior origins, diverged on the order of 50,000 years before the present. And yet if the two groups mentioned earlier are correct than the Melanesian component itself must be decomposed into two fractions, one of which is much closer to the Polynesians than the other, our understanding of the past changes.

As I implied earlier today I think the era of wild hypothesis generation in the area of the settling of Europe over the last 10,000 years is coming to the end. The combination of more powerful analytic techniques and the emergence of ancient DNA samples with which to calibrate, peg, and check, inferences from those techniques, will probably clarify our understanding of the past to a great extent.

Image credit: yomi955

June 27, 2011

First Farmers Facing the Ocean

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 ...

December 8, 2010

The men of the north: the Sami

Ole Magga, Norwegian politician

ResearchBlogging.orgOn this blog I regularly get questions about the Sami (Lapp*). That’s because I often talk about Finnish genetics, have readers such as Clark who are of part-Sami origin, and, the provenance and character of the Sami speak to broader questions about the emergence of the modern European gene pool. More precisely questions about the Sami are relevant to the broader nature of the Finnic presence in Europe, and their relationship to other Baltic and northern populations. Are these people “indigenous” to Europe, or relatively newcomers (prehistoric Magyar or Turks).? These questions are prompted by the peculiarity of their languages (as well as the physical appearance of some of the Sami). With Basque they are the only living non-Indo-European European languages whose origins are prehistoric (Magyar and Turkish were arrivals within the last 1,000 years).**

Because of affinities to other Uralic languages which are found in Central Siberia it has often been conjectured that the Finns, Sami, and Estonians are relative newcomers to Norden from that region. This has some equivocal support from Y chromosomal lineages. On the other hand, there are those who argue that the Finnic peoples were present in the north of Europe before the arrival of Indo-European speakers (often these are Finnish nationalists). This has some support from maternal lineages. Naturally, some have been tempted to synthesize these two genetic lines of evidence, and the linguistic affinities, to argue that Finns are a hybrid population of Asiatic men and Paleolithic European women! But we need to go further than uniparental markers, the direct male and female ancestral lines. We need to look across the broader swath of the genome. It just happens that a new paper was published in The European Journal of Human Genetics on autosomal Sami affinities to other populations, A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies:

The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise FST statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, FST was smallest for the comparison with the Russians (FST=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations.

They had 352 Sami samples, and looked at ~38,000 SNPs. For the questions they’re focusing on 38 K SNPs seems fine. That’s enough to smoke out inter-population variation. In their paper they compared the Sami to the HGDP populations using standard techniques. Assuming 7 ancestral populations in the data set, this what ADMIXTURE popped out:


There is a definite “eastern” affinity among the Sami. Interestingly, it is broken down into a major and minor component. The major one is what is found among the Han, while the minor one resembles Native Americans. The natural interpretation for this is that what one is seeing is the shadow of the circumpolar northern Eurasian populations which spanned eastern Europe to Siberia. In comparison with other European populations the Sami affinity with Russians is clear, though interestingly they lack the “blue” component which peaks in northwest South Asian populations, which the Russians have, and Sardinians and French Basque lack.

samieigenTo the left you see a PCA which breaks out the top two components of genetic variation for the data set. The two axes seem to be roughly west-east, north-south. Whatever ancient affinities the Sami may have with Southern Europeans via mtDNA haplogroup U5, it is not evident in the total genome content. The position of the Sami between Russians and Orcadians (from north of Scotland) is probably attributable to the fact that the Sami share much genetically with other Scandinavians, who are closer to British populations than the Russians are.

I’m not sure these analyses really shed any light on the on the questions I mentioned earlier. The authors themselves note that the “eastern” component of the ancestry in the Sami is probably very old, so they may be an ancient stabilized hybrid population, mostly indigenous with a non-trivial exogenous element. That does not tell us whether Finnic languages are indigenous to Europe, or whether they are indigenous to Central Siberia (indigenous here is in reference to the Indo-European languages). Additionally, there is the matter that for such fine-grained questions the HGDP sample is suboptimal as reference populations. Dienekes Pontikos points this out:

It is unfortunate that they included Native American HGDP populations, but did not include the most relevant published data on Siberians that I first used to study population structure across north Eurasia here and here and here.

Hence, they discover a “Native American”-like component in Saami, which in all likelihood can be further resolved into Siberian-specific components utilizing the Rasmussen et al. dataset.

The “closest approximation” to the East Eurasian component in Saami in the HGDP panel are the Yakuts, but finer-scale analysis (see my previous posts) reveals that the Yakuts are made up almost entirely of an Altaic-specific component tying them to Turkic, Mongol, and Tungusic populations, while the eastern component in European Finns, Vologda Russians and Chuvashs has relationships with Central Siberians such as Kets, Selkups, and Nganasans, all of which are missing in this paper.

Below is a re-edited ADMIXTURE plot from Dienekes:


Note: There are many ways to spell Sami. They used two a’s, but I find that confusing, so I just used one in my text.

Citation: Maki-Torkko, Elina, Aikio, Pekka, Sorri, Martti, Huentelman, Matthew J, & Camp, Guy Van (2010). A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies European Journal of Human Genetics : 10.1038/ejhg.2010.179

* Apparently “Lapp” is considered derogatory among Norwegians, though Finnish Sami refer to themselves as lappalainen. I will use Sami to avoid irritating Norwegian terminology police.

** I am implicitly excluding much of European Russia west of the Urals, but so be it.

October 17, 2010

Völkerwanderung back with a vengeance


The German magazine Der Spiegel has a rather thick new article out reviewing the latest research which is starting to reintroduce the concept of mass folk wanderings into archaeology. The title is How Middle Eastern Milk Drinkers Conquered Europe. In the story you get a good sense of the recent revision of the null model once dominant within archeology that the motive forces of history manifested through the flow of pots and not people. This viewpoint came to ascendancy after World War II, and succeeded an older method of interpretation which presumed a tight correlation between race and culture. It repudiated the idea that the flow and change of pottery styles and extant patterns of linguistic dialects may have been markers for the waxing and waning of peoples.

Obviously a pots-not-people model had some major exceptions even during its heyday. The demographic explosion of European peoples after 1492, and especially the Anglo peoples after 1700, occurred within the light of history. Even if it hadn’t it would be ludicrous on the face of it to assert that the modern American population were derived from the indigenous populations, and that they had simply adopted the language, religion and folkways of the British conquerors of North America. But outside the presumed aberration of the European imperialist and colonial venture of the modern era the details on the ground were obscure enough that a model could be imposed from without.

No longer. In non-European societies such as China with extensive records it is clear that demographic increase and colonization were driving forces of the expansion of a given cultural domain. A neglect of this reality could only occur via ignorance of the primary documents. Plausible if one did not know Chinese. As in the case of Spanish conquest of the New World the demographic wave was not total; biological and cultural amalgamation with the native substrate south of the Yangtze did occur to produce a new synthesis. But the revision does not occur just through space, but time as well. The methods of genetics, whereby samples from ancient burials may be retrieved and compared to modern populations, have allowed us to reject the post-World War II assumption that the Etruscans were an indigenous Italian culture. Due to the lack of copious records a theoretical presupposition was able to interject itself into the data. When the story about Etruscan genetic relationships to Near Eastern groups broke in early 2007 I actually proceeded to skim the latest archaeological monographs on the archaeology of this group, and most of them had erudite expositions on exactly how the myriad distinctive aspects of Etruscan culture which suggested an exogenous origin were in fact derived from the antecedent Bronze Age societies of Tuscany.

Ancient DNA extraction is now allowing scholars to map the change in frequencies of genetic markers of archaeologically known groups as a function of both space and time more broadly. I think one can safely see that there are more perturbations, fluctuations, and turnovers, than any pots-not-people model could predict. On the specific issue of lactase persistence it is almost certainly a genetic novelty in Eurasia which arose over the last 10,000 years in a co-evolutionary fashion with animal husbandry. The genomes of modern Europeans suggest this, but we have confirmation from ancient DNA extraction as well. A rise in frequency of a particular allele does not entail a replacement of one population with another; lactase persistence today can exhibit a great deal of variance as a function of geography and ecology because its frequency no doubt responds to local selective pressures. But, in concert with other DNA data (mostly maternal lineages) as well as a fresh look at evidence of cultural discontinuity and rapid pulses of colonization in late Paleolithic and early Neolithic Europe, one must be open to the possibility that the spread of animal husbandry, copious raw milk consumption, and an aggressive and fecund population, were all concurrent processes which were tightly interlocked in some causal sense.

An aspect of this story which I am fuzzy and weak on is the archaeology. You likely know nearly as much about the Linear Pottery Culture as I do. It seems though that this cultural-complex brought agriculture deep into the heart of Central Europe ~7,000 years ago, and there are clear signs that its origin was to the southeast, from the Eastern Mediterranean region. L. L. Cavalli-Sforza’s ‘demic diffusion’ model which argued for the expansion of Neolithic farmers from the Middle East into Paleolithic Europe seemed to suggest that it occurred through a ‘wave of advance‘ impelled by endogenous population growth and gradual migration. The model as reported by Der Spiegel seems at some variance with this. Instead of a gradual advance it seems that there may have been periodic pulses and explosions of demographic advance. Using the historical examples we have this should not be particularly surprising. Overlain atop the reality of an inexorable push across the ‘frontier’ in both North America and China by the colonizing peoples I alluded to earlier it is important to remember that there were periodic punctuations of gradualism by bursts of mass colonization, displacement, and relocation. The migration out of overpopulated New England to the Great Lakes and Upper Midwest in the early 19th century, the retreat to the south by the Han Chinese after the collapse of their first dynasty and the conquest of the north by barbarians. Both of these are examples of the explosive process in demographics and migration which can revolutionize the cultural landscape within a generation or two. From the data that the archaeologists have collected this seems to have occurred with the expansion of agricultural society in Central Europe as well, as the Linear Pottery Culture and its descendants proceeded in fits & starts.

Unfortunately as this is the domain of prehistory we won’t ever know in concrete terms exactly what occurred. In the Der Spiegel piece they report that the agriculturalists had a 500 year pause. Why? If demic diffusion was the primary dynamic through which they expanded there should be no pause. But we can think of a host of scenarios. Perhaps the Middle Eastern cultural toolkit had reached its natural outer boundary, and it was here that the tide turned to the indigenous Paleolithic societies of Europe, which maintained an advantage in the north because of the lack of the adaptability of southerners to new conditions. Humans can be stubbornly conservative in their ways. It is famously asserted that the Norse of Greenland did not adapt to a more inclement regime, and so went extinct (or, possibly evacuated to Iceland). The adoption of potatoes and other productive and useful crops among European peasants was retarded by their instinctive conservatism. We need not imagine a scenario where Paleolithic hunters and gathers would naturally wish to take up the hoe. Nor is it plausible that the agriculturalists would wish to refashion their tried & tested traditions so as to push the outer boundary of their limes.

But all things must change. Something happened, and the agriculturalists shifted the modus vivendi, and the hunter-gatherers gave way. There are detailed historical processes which can give us insight as to how such long-held boundaries could rapidly collapse. Europeans had circumnavigated Africa by 1500, and had had factories and trading posts around the continent’s fringe for over 400 years by the late 19th century. But deep into the 1800s the European presence in Africa was marginal. By 1914 the continent was divided into European zones of control. What happened in the space of a few decades? Quinine and machine guns. The biological barrier to Europeans fell away, and the military superiority was amplified by orders of magnitude. What could have occurred in an analogous fashion in Central Europe? The combination of a mutation for lactase persistence and animal husbandry may have resulted in rapid population growth, leading to densities which precipitated the outbreak of an epidemic. A reduction in population may have had much greater impact on the less numerous and resistant hunter-gatherers. Additionally the economic changes wrought by animal husbandry may have allowed for a scaling up of the organization of war. The Mongol Empire exploded onto the scene in mere decades to sweep across most of Eurasia. Why couldn’t something similar plausibly have occurred in Central Europe on a much smaller scale 7,000 years ago?

Ultimately we’ll never know the details. But in constructing our plausible scenarios for prehistory I suspect that we moderns have a bias toward viewing pre-literate societies as usually small-scale, at best simple chiefdoms. I believe this is a false model, and that there was a non-trivial level of scalability possible among pre-literate societies. Going back to the Mongol example, I see no reason why the initial existence of their polity necessitated literacy, though it may have been essential for its administration and perpetuation. Cultural forms likely marched with confederacies and were driven forward by warlords. This would easily explain the punctuated pattern of the spread of agriculture, as the rise and fall of states has a somewhat spasmodic and periodic character.

Finally, I want to emphasize that the Der Spiegel piece verges on a maximalist position which I am not comfortable with. There is much we don’t know, and I am in no hurry to replace one tired and dogmatic orthodoxy with another. Because the article was translated from German into English I can understand that that is responsible for the artlessness of some of the assertions. But phrases such as “There was no interbreeding between the intruders and the original population” from a German magazine really makes me think they’re suggesting that there were Stone Age Nuremberg Laws. Ethnic separation and differentiation was a reality among many ancient peoples, but so was intermarriage and assimilation. I am aware of the starkness of some of the DNA analyses, which suggest disjoint frequencies across the two populations, but the results are far too spotty at this point to make definitive assertions.

Note: The accompanying map is worth perusing.

(referral credit, Steve Sailer)

Image Credit: Wikimedia Commons

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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