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March 20, 2019

The population turnover in westernmost Europe over the last 8,000 years

Filed under: Historical Population Genetics,Spain — Razib Khan @ 7:53 pm

The figure above is from The genomic history of the Iberian Peninsula over the past 8000 years. If you had seen something like this five years ago, you’d be gobsmacked. But today this is not atypical, especially in light of the fact that Spain seems to harbor many good sites in relation to the preservation of ancient DNA. In the figure above you see an excellent representation of the different streams of ancestry and settlement within Spain over the last 8,000 years. You can conclude from it, for example, that only a small proportion of the ancestry of modern Spaniards derives from people who were residents of the peninsula during the Pleistocene. Similarly, you can also conclude that a minority, though non-trivial, proportion of the ancestry of modern-day Spaniards derives from people who arrived during Classical Antiquity and the Moorish period.

And, confirming earlier work, the Basques seem to be relatively untouched by these later gene flow events. To some extent, we all knew that, as the Basques were famously exempt from limpieza de sangre, the blood purity laws of medieval Spain. But importantly, the Basques have a substantial amount of ancestry from peoples whose heritage goes back to Central Europe, and to a great extent, the forest-steppe of far eastern Europe. This is a huge change from what was understood fifteen years ago. As the Basques speak a clearly non-Indo-European language, many scholars hypothesized that they were remnants of hunter-gatherer peoples, who had been resident in the Iberian peninsula since the Pleistocene.

But the reality is that the origin of the Basques is likely in the arrival of Near Eastern farmers. The Basques share a strong genetic affinity with the peoples of Sardinia, who are the closest proxies in modern European populations for this group. Importantly, the Basque difference from Sardinians is their much greater proportion of Central European/steppe-like ancestry. How did they get this ancestry?

One of the major results of this paper is that a particular branch of R1b came to dominate Spain around 4,000 years ago. Before this period the dominant Y chromosomal lineages in the Iberian peninsula were those associated with the farmer populations. The frequency of R1b is above 80% in Basque males. This is one reason that earlier scholarship assumed that R1b was associated with European hunter-gatherers (the Basque being the descendants of those people). Today, we know that both branches of R1 seem to have expanded ~4,000 years ago and that the most common lineages in western and southern Eurasia seem to go back to the steppe peoples.

It may be that the Basque language actually derives from the steppe as non-Indo-European peoples expanded along with the Indo-Europeans, adopting similar cultural habits and characteristics. This is not a crazy position. The Magyars, for example, are not Turkic or Indo-European, but they adopted a lifestyle associated earlier and simultaneously with Turkic and Indo-European pastoralists. But let’s set this possibility aside. Another option is that the Basque descend from one of the post-Cardial cultures of southwest Europe. That is, their language has roots in the dialects of the early Anatolian farmers. Unlike other peoples, they absorbed the influx of Indo-Europeans, and culturally assimilated them.

This too is not crazy. But how might they have absorbed the Indo-Europeans? In the paper above they tentatively argue, from some of their results, that the Indo-European influx was more male than female. There are suggestions that Basque society may have had matrilineal aspects. This does not entail that they were “matriarchal,” but rather, that inheritance passed through the maternal line. Matrilineal societies are not necessary pacific. The Iroquois are a case in point. And, they have a natural way of assimilating warbands of alien males: these men could become integrated into the preexistent kinship networks.

How might the rise of R1b lineages have occurred so fast? One could posit those young men with Indo-European fathers may have had connections to hostile Indo-European tribes that their cousins with non-Indo-European fathers lacked. If the Indo-Europeans were patrilineal, as seems likely, and the proto-Basques were matrilineal, then these men would have been well placed to better protect the cultural integrity and political independence of their maternal heritage through connections of their paternal lineage.

I have an explicit model here: the intermarriage of European trappers in the American West with native women. In many cases, the children of these men would be raised within a native context, and so served as a bridge of sorts. And, there is another analogy: the frequency of R1a is quite high in some non-Indo-European groups in South Asia. It will turn out, I believe, that Southern Europe and India share many similarities, as the Indo-Europeans encountered people in these regions with rich and complex societies.

Several years ago, A recent bottleneck of Y chromosome diversity coincides with a global change in culture, was published. The authors note there was an explosive growth several Y chromosomal lineages, including R1b and R1a, on the order of 4,000 years ago. Recently the evolutionary anthropologist Joe Henrich stated that “Religion is a technology for scaling up human societies.” With this in mind, I will state here that patriarchy is a technology for swallowing up human societies. The distribution of Y chromosomal lineages associated with early Indo-European extends outside of the boundaries of Indo-European languages. In fact, the expansion of I1, concordant with R1b, suggests that non-Indo-European lineages were assimilated into expanding Indo-European groups.

There is, of course, a debate whether this expansion was violent or not. I suggest above a way in which Indo-European lineages, at least by origin, could become pervasive in a non-Indo-European society. But, it does seem to more plausible that more direct forms of marginalization were likely. In a pre-modern environment not far from the Malthusian limit it wouldn’t take much for certain male lineages to replace themselves, while others to die out. The descent from antiquity project in Europe is difficult because there does seem to have been an elite paternal lineage rupture with the fall of Rome. Many modern noble families are traceable to the centuries after the fall of Rome, but none of them clearly are linked to before the fall of Rome. This does not mean that there was a massacre of those lineages, but that elite lineages which lost their rents would quickly lose their status.

I do think what we call war was part of the expansion. But war was likely simply one of the many manifestations of the power of rise of these bands of brothers.

September 29, 2018

The sons of Japeth divide the world between them

Filed under: Ancient DNA,Spain — Razib Khan @ 5:22 pm

Most “old hands” in the discipline of historical population genetics remember when grand narratives were constructed out of Y chromosomal haplogroup distributions. One of the most distinctive ones is that of haplogroup R1b, which exhibits very high frequencies in the west of Europe, as high as more than 80% among the Basques. Because the Basques are the only non-Indo-European population which exists today in Western Europe, it was presumed that they are more ancient than other groups. And, their high frequency of R1b (along with other peculiarities such as a high frequency of Rh-), was taken to indicate that they reflected the genetics of Europe’s aboriginal hunter-gatherers when farming arrived.

This turned out to be wrong in a lot of details. Genetically the Basques are quite like the European farmers from Anatolia who replaced the original hunter-gatherers. Less so than the Sardinians, but more so than their neighbors in Iberia. Instead of being the language of European hunter-gatherers, it seems plausible that the Basque language descends from that of the Cardial culture.

Distribution of R1a

So what about R1b? Well, it turns out that the particular branch of R1b that is very common in Europe is not found in the Neolithic farmer populations. Rather, its arrival in places like Britain and Iberia is associated with cultures with original origins in the Eurasian steppe. In the eastern half of Europe and in Central Asia and South Asia, R1a expanded in the period after 2000 BC.

New Scientist is now quoting David Reich has having asserted that this population turnover in Iberia occurred ~4,500 years ago. Reich, in particular, is emphasizing the disruption in the Y chromosomes. I don’t know if Reich’s group is coming out with new data, but we do have some evidence on this in Iberia from earlier publications.

This figure from Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia basically says it all. Around the transition between the Iberian Neolithic and the Bronze Age a new element came into the Iberian peninsula with affinities with populations to the north and east. The samples are not dense enough in terms of time to give a precise date, but this paper seems to suggest somewhere between 4,000 and 4,500 years as the most likely interval. The Reich group probably has more samples and so can date it more precisely. Interestingly, ~4,500 years ago is exactly when R1b bearing males arrived, and there was massive genetic turnover, in the British Isles. Perhaps the correlation between these two regions being overrun at the same time is not coincidental?

Please remember that the post-steppe Corded Ware people had settled in Central Europe by 2900 BC. Time elapsed between this period, and the later expansion west and south. And, I wouldn’t be surprised if the arrival on the eastern steppe of people with ancestry from Europeans (that is, they had some ancestry from Neolithic Europeans) was also due to changes in Central Europe around 2500 BC.

With the demographic superstructure getting really into place for Europe, it’s really time that archaeologists, cultural evolutionists, and anthropologists, start to think about how these processes occurred.

May 27, 2010

The genes in Spain fall rather evenly

Filed under: Genetics,Genomics,Spain — Razib Khan @ 3:23 am

A new paper is out which drills down a bit on the genetic substructure in Spain. Genetic Structure of the Spanish Population:

Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias.

In this study we have sampled over 800 unrelated individuals from the population of Spain, and have genotyped them with a genome-wide coverage. We have carried out linkage disequilibrium, haplotype, population structure and copy-number variation (CNV) analyses, and have compared these estimates of the Spanish population with existing data from similar efforts.

In general, the Spanish population is similar to the Western and Northern Europeans, but has a more diverse haplotypic structure. Moreover, the Spanish population is also largely homogeneous within itself, although patterns of micro-structure may be able to predict locations of origin from distant regions. Finally, we also present the first characterization of a CNV map of the Spanish population. These results and original data are made available to the scientific community.

They used a 160 K SNP-chip for this, though for the PC charts below they were constrained to ~100,000 SNPs. Nothing too revolutionary in the paper. The fact that Spaniards have more haplotype diversity vis-a-vis the “CEU” sample in the HapMap, which consists of Utah Mormons, isn’t too surprising, since those individuals are Northern European and Northern Europeans tend to be a touch less diverse than Southern Europeans (more heterozygosity in Southern Europe than in the North). A common explanation for this is that Northern European populations emerged as subsets of Southern populations which expanded out of Ice Age “refugia” within the last ~10,000 years or so, and this migratory process would have induced some bottlenecks and so reduced their diversity. The findings in this paper are broadly consistent with the idea that Spain was a refugium, and so one of the sources of the population of Northern Europe. But, note that there are lots of controversies about recent European demographic history right now, so I wouldn’t take the aforementioned model as a given. Also, one major issue which sticks out is the lack of Basque populations in the sample, since that’s a group which has long been of interest, and some aspects of many demographic scenarios hinge on their nature. No surprise that Visigoths, Berbers and Arabs didn’t perturb these results too much. I believe that these groups did arrive in Iberia in large numbers, but on a relative scale their proportions were small and they probably didn’t alter Spain’s basically genetic character.

Below are some charts of note.

First, dimensions of genetic variation in the Spanish population using 100,000 SNPs by locality where the sample was collected.


If some of the localities were as obscure to you as me, here is the PC chart with a subset of them rotated and superimposed upon a map of Spain.


Finally, here are the Spanish samples plotted in relation to two HapMap populations, the CEU (American whites of Northern European ancestry) and TSI (Tuscans from Italy).


There are a few outliers here in relation to their putative population cluster, but in general the three groups are nicely separated as expected. Spain is bounded by water and a rather imposing mountain range. These serve as natural barriers to gene flow. But within the peninsula it’s dominated by a high plateau. I really don’t have an intuitive understanding of whether the spatial distribution of Spain’s people (which for ecological reasons probably can be extrapolated back to antiquity) should homogenize it through a circular pattern of gene flow, but perhaps that’s what these data are showing. I am a bit wary of saying that Spain is internally homogeneous without referencing other European populations of the same scale in detail. Perhaps what this group found is what you’d find on this scale with this chip; not much.

Cite: BMC Genomics 2010, 11:326doi:10.1186/1471-2164-11-326

H/T Dienekes

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