Planet Earth

Population replacement in Neolithic Spain?

Gene ExpressionBy Razib KhanJun 28, 2012 5:16 PM

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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 not related to current populations from either the Iberian Peninsula or Southern Europe.

Here's another PCA showing one individual on a more fine-grained representation of European populations:

Perhaps the most interesting aspect here is something Dienekes pointed out from the supplements: these two individuals are not only outside of the range of extant European populations in their positioning on a global PCA plot, but they are shifted toward East Asians.

The fact that these two individuals, who really come close to being one data point because they are likely rather closely related, are outside of the modern European population distribution isn't too surprising. 7,000 years is a long time, and we can't assume that ancient populations can be recomposed as combinations of the variation of modern populations. But, the shift toward East Asians is surprising to me, because they are Iberian individuals. In PCA and model-based (e.g., ADMIXTURE) clustering frameworks modern Iberians, and populations from Southwest Europe in general, are the most distant from East Eurasians of all West Eurasians. Dienekes opines:

It now appears clear that the Mesolithic substratum in Europe was: 1. Well outside the modern range, contributing a little to extant populations 2. Its contribution in northern populations was higher than in southern ones 3. It may be responsible for the pattern of Asian-shift observed for non-Mediterranean European populations ...It seems that this was the composition of the pre-Neolithic population of Europe that was later supplanted first by the "Mediterranean"/"Southern" components during the early Neolithic, and later by the "West_Asian"/"Caucasus"/"Gedrosia" components, perhaps during the Copper Age. We'll see whether my prediction pans out soon enough.

On the broadest level I think Dienekes model is entirely possible. I'd give it the highest probability of the range of options, though I have a high uncertainty.

The question is the weight of the contributions.

Let's rename the various groups A, B, and C, for the three waves in chronology (hunter-gatherers, first wave farmers, and second wave farmers). Then any European population is: xA + yB + zC, where x + y + z = 1 About 10 years ago B + C would be one class, so B, and you had a pan-European estimate of: 0.75A + 0.25B Now some scholars are trying to revise that, and reduce the weight for A. I think we need to be very careful, because we've already been burned by overly elegant and simplistic models of the settlement of Europe. For example, here are my made-up estimates quantitatively from everything I'd read so far: Finns = 0.90A + 0.05B + 0.05C Lithuanians = 0.85 A + 0.05B + 0.10C Irish = 0.60 A + 0.30B + 0.10C Germans = 0.60 A + 0.20B + 0.20C Basques = 0.40 A + 0.60B North Italians = 0.40 A + 0.30B + 0.30C

The exercise above was not to give you accurate numbers that I'm sure of, but to give you numbers instead of verbal labels which are imprecise. I'm quite willing to "update" my estimate in the future, and expect to. In the paper the authors highlight that the mtDNA lineages that the two individuals carry is modal in the Sami of northern Finland. Genetically the Sami seem more Finnish that the Finns. But, they also clearly have an "eastern" affinity (diminished, but still present in Finns as well). This dovetails with linguistic connections to North-Central Eurasia, and the margins of Western Siberia. What's going on here? One hypothesis has been that the Finnic languages (and the Sami) are culturally intrusive, and the Siberian genetic affinity is a signal of this ancient core admixed with the local substrate, which resembles that of Scandinavians. These results make me update my assessment, and increase my own probability that the Finnic people have deep cultural roots in Northeast Europe. This was already my hunch based on model-based clustering which seemed to show that there were "southern" modal elements present in Scandinavians lacking in Finns or Sami. If Finns or Sami were relatively late arrivals, I would have expected to be more diverse in the complement of ancestral elements, not less. Now the set of results form Mesolithic European genomes indicate to me that what we may be seeing in the Siberian affinity of the Sami (and to a lesser extent the Finns) are the echos of a post-Ice Age expansion of Palearctic peoples from the center of Eurasia which ranged west toward the Atlantic and east toward the Sea of Japan. I suspect that this Palearctic population did not move into a totally empty landscape, so the Mesolithic peoples which the West Asian and East Asia farmers displaced or assimilated were not entirely similar. Rather, they were themselves syntheses between hunter-gatherer groups. Obviously this is an interesting time to moot these questions. The major issue we need to keep in mind is not to move from one enthusiasm to another. A model of preponderant biological continuity between European hunter-gatherers and early agriculturalists is now in serious doubt, especially for southern Europe. But that does not mean that we should move to a model where the hunter-gatherers were replaced in totality by agriculturalists. This does not seem to have happened in northeast Europe, and the model of replacement itself is probably more complex than a single-step transition. Citation: Current Biology, 28 June 2012 doi: 10.1016/j.cub.2012.06.00

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