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Thread: Spanish Eastern Pyrenees Population Structure

  1. #1
    Advisor Angela's Avatar
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    Spanish Eastern Pyrenees Population Structure

    They cluster both with Iberians and French Basque, as is to be expected, but there's an amazing amount of structure even within the villages, resulting in high runs of homozygosity. Lots of drift because of isolation, is also to be expected, and the date for population formation is about 2500 years ago, or about 500 BC, before the Roman Era or Islamic Invasions.

    See:

    https://www.nature.com/articles/s41431-021-00875-0


    "The area of the Spanish Pyrenees is particularly interesting for studying the demographic dynamics of European rural areas given its orography, the main traditional rural condition of its population and the reported higher patterns of consanguinity of the region. Previous genetic studies suggest a gradient of genetic continuity of the area in the West to East axis. However, it has been shown that micro-population substructure can be detected when considering high-quality NGS data and using spatial explicit methods. In this work, we have analyzed the genome of 30 individuals sequenced at 40× from five different valleys in the Spanish Eastern Pyrenees (SEP) separated by less than 140 km along a west to east axis. Using haplotype-based methods and spatial analyses, we have been able to detect micro-population substructure within SEP not seen in previous studies. Linkage disequilibrium and autozygosity analyses suggest that the SEP populations show diverse demographic histories. In agreement with these results, demographic modeling by means of ABC-DL identify heterogeneity in their effective population sizes despite of their close geographic proximity, and suggests that the population substructure within SEP could have appeared around 2500 years ago. Overall, these results suggest that each rural population of the Pyrenees could represent a unique entity."

    The largest amount of haplotype sharing, however, seems to be with the Basques, followed by Sardinians, and then the Spanish.






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    Forgive my impertinence, but what in tarnation is Yosemite Jew? Four of them seem to cluster identically with one another, while Urgell is the oddball, with less Sardinian, more Basque, and less Orcadian, the latter I suspect is some signature of Steppe ancestry, as Orcadians are an amalgam of high-steppe Norwegian and Scots highlander populations.

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    Advisor Angela's Avatar
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    Quote Originally Posted by Joey37 View Post
    Forgive my impertinence, but what in tarnation is Yosemite Jew? Four of them seem to cluster identically with one another, while Urgell is the oddball, with less Sardinian, more Basque, and less Orcadian, the latter I suspect is some signature of Steppe ancestry, as Orcadians are an amalgam of high-steppe Norwegian and Scots highlander populations.
    I don't see any impertinence in your question. Perhaps there is something I don't know about Jewish populations, but I assumed the writing program they were using wrote Yosemite instead of Yemenite Jew.

    The paper goes into great detail about the differences between the villages.

    "geographic isolation within SEP is likely the cause of the identified substructure. This isolation should have appeared after major migrations into the region, or these had a very limited impact in the genetic makeup of SEP. In particular, it has been claimed that fine genetic variation has been shaped in Spain by linguistic and geopolitical boundaries at the time of Muslim rule in Spain [34]. However, the Roman and Visigoth people only represented a 2.2–4.4% of the SEP population, while the Islamic conquest of this region lasted only 80 years [35]. In this line, ABC-DL suggests that the population structure observed in SEP originated around 2500 years ago. Furthermore, the low effective population sizes inferred from genomic data support genetic isolation as the main factor for explaining the geographic structure. However, it is interesting to notice the large heterogeneity in the estimates of the effective population size given the geographic proximity of the SEP populations. These estimations are in agreement with the estimated levels of autozygosity and LD. Therefore, despite the short distances between populations, the particular demographic histories of the different villages played a role in shaping the genomic landscape of the regions. In fact, these counties traditionally shared a rural lifestyle but considered different methods of subsistence depending on their geographic location and period [35]."

    "
    Alt Urgell region showed the smallest effective population size (mean of the posterior distribution = 332.79; 95% CI ranging from 207.48 to 539.60 chromosomes);"

    That led to it having the most inbreeding, which would lead to more drift.

    There is absolutely no evidence for differential migrations to this area of the Pyrennees. These villagers date genetically from 500 B.C. That is the date for the split from other populations around them, who would after that time have experienced effects from different migrations. The subtle differences between the villages also result from drift. That's how isolated and inbred they are.

    Keep in mind that the authors found the differences between these villagers to be subtle indeed. In certain less specialized tests, they are largely the same.

    The same thing happened in my father's villages in the northern Italian Apennines, as explored for decades by Cavalli Sforza. Not only were these mountain dwellers different from those of the plains, but they were different from each other. In that case, the differences could be tracked by altitude differences.

    In the case of the people studied here, it's not as simple as geographical barriers between the villages explaining what went on. I would think they would need to investigate ancient documents or the oral history of the area. Who knows? It could have been feuds or any number of events.

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    Basques are very interesting. I see no mystery as to their autosomal origin, but the issue of negative HR is an interesting one.

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