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

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:

Background
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.

Results
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.

Conclusions
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.

spain1

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.

spain2

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).

spain3

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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