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Thread: Title: The population genomics of archaeological transition in west Iberia

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    Title: The population genomics of archaeological transition in west Iberia

    Title: The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods.

    We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740- 1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.

    http://biorxiv.org/content/biorxiv/e...34254.full.pdf
    Gerard Corcoran
    R1b-DF21-S5456-S6166, H1C1

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    Table 1 - Summary of the samples sequenced in the present study.

    IMG_1573.jpg
    Gerard Corcoran
    R1b-DF21-S5456-S6166, H1C1

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    "Our analyses yield both signals of continuity and change between Portuguese Neolithic and Bronze Age samples. ADMIXTURE analysis showing similar ancestral components, and higher order branching in fineSTRUCTURE clustering suggest a level of continuity within the region. Also, both show a degree of local European HG admixture (relative to central European HG influence) that is not observed within other samples in the data set. However, final fineSTRUCTURE clustering and the PCA plot places the Portuguese BA as a separate group which is intermediate between Atlantic Neolithic samples and the Central European Bronze Age individuals. D-statistics support some influx of ancestral elements derived from the east, as is seen in the northern Bronze Age, and a distinct change in Y-chromosome haplotypes is clear - all three Iberian BA males are R1b, the haplogroup that has been strongly associated with Steppe-related migrations. Patterns of haplotype affinity with modern populations illustrate the Portuguese population underwent a shift from southern toward northern affinity to a distinctly reduced degree to that seen with other regional Neolithic-BA transitions."

    Taken together this is suggestive of small-scale migration into the Iberian Peninsula which stands in contrast to what has been observed in Northern, Central [4,5] and Northwestern Europe [11] where mass migration of steppe pastoralists during the Copper Age has been implied. The Y-chromosome haplotype turnover, albeit within a small sample, concords with this having been male-mediated introgression, as suggested elsewhere for the BA transition [32].
    Several candidate windows for the entry of Steppe ancestry into Portugal exist. The first is the possible emergence of Bell Beaker culture in Southwest Iberia and subsequent establishment of extensive networks with Central and NW European settlements, opening up the possibility of back-migration into Iberia. Indeed, Central European Bell Beaker samples have been observed to possess both steppe-related ancestry and R1b-P312 Y-chromosomes [4,5]. Furthermore, through the analysis of modern samples, it has been proposed that the spread of Western R1b-lineages fits with the temporal range of the Corded Ware and Bell Beaker complexes [33].

    Two alternate theories for the origin and spread of the Indo-European language family have dominated discourse for over two decades: first that migrating early farmers disseminated a tongue of Neolithic Anatolian origin and second, that the third Millennium migrations from the Steppe imposed a new language throughout Europe [37,38] [4]. Iberia is unusual in harbouring a surviving pre-Indo-European language, Euskera, and inscription evidence at the dawn of history suggests that pre-Indo- European speech prevailed over a majority of its eastern territory with Celtic-related language emerging in the west [39]. Our results showing that predominantly Anatolian- derived ancestry in the Neolithic extended to the Atlantic edge strengthen the suggestion that Euskara is unlikely to be a Mesolithic remnant [17,18]. Also our observed definite, but limited, Bronze Age influx resonates with the incomplete Indo- European linguistic conversion on the peninsula, although there are subsequent genetic changes in Iberia and defining a horizon for language shift is not yet possible. This contrasts with northern Europe which both lacks evidence for earlier language strata and experienced a more profound Bronze Age migration.
    22
    Gerard Corcoran
    R1b-DF21-S5456-S6166, H1C1

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    I'm looking forward to a good analysis of the files they uploaded.

    Raw data and aligned reads have been submitted to http://www.ebi.ac.uk/ena/data/view/PRJEB14737, secondary accession ERP016408.

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    I can't wait to see them on Gedmatch!

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    This thread needs to be merged with http://www.anthrogenica.com/showthre...In-West-Iberia

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    Seems like the Portuguese Bronze Age individuals lacked the CHG/Teal component.

    Quote Originally Posted by Martiniano.et.al.2017
    A recurring feature of ADMIXTURE analyses of ancient northern Europeans is the
    appearance and subsequent dissemination within the Bronze Age of a component (teal)
    that is earliest identified in our dataset in HGs from the Caucasus (CHG). Unlike
    contemporaries elsewhere (but similarly to earlier Hungarian BA), Portuguese BA
    individuals show no signal of this component, although a slight but discernible increase
    in European HG ancestry (red component) is apparent. D-Statistic tests would suggest
    this increase is associated not with Western HG ancestry, but instead reveal significant
    introgression from several steppe populations into the Portuguese BA relative to the
    preceding LNCA (S4 Text, S6 Table). Interestingly, the CHG component in
    ADMIXTURE is present in modern-day Spaniards and to a lesser extent in the Basque
    population.

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    Fig 1. CHROMOPAINTER/fineSTRUCTURE Analysis.

    (A) PCA estimated from the CHROMOPAINTER coancestry matrix of 67 ancient samples ranging from the Paleolithic to the Anglo-Saxon period. The samples belonging to each one of the 19 populations identified with fineSTRUCTURE are connected by a dashed line. Samples are placed geographically in 3 panels (with random jitter for visual purposes): ( Hunter-gatherers; (C) Neolithic Farmers (including Ötzi) and (D) Copper Age to Anglo-Saxon samples. The Portuguese Bronze Age samples (D, labelled in red) formed a distinct population (Portuguese_BronzeAge), while the Middle and Late Neolithic samples from Portugal clustered with Spanish, Irish and Scandinavian Neolithic farmers, which are termed “Atlantic_Neolithic” (C, in green).

    IMG_1574.jpg

    Fig 3. Total Variation Distance between vectors of median haplotype donation from Bronze Age (purple) and Neolithic (green) samples from different regions in Europe to modern populations.
    Circle size varies according to the absolute difference between Neolithic and Bronze Age samples in terms of the number of haplotypes donated to present day populations. Regardless of the geographical locations of the ancient samples, Neolithic samples tend to donate comparatively more haplotypes to Southern populations, while Bronze Age show the opposite pattern, with an excess of haplotype contribution to Northern Europeans. This pattern is present, but distinctly weaker in the Portuguese Neolithic- Bronze Age comparison.

    IMG_1579.jpg

    A recurring feature of ADMIXTURE analyses of ancient northern Europeans is the appearance and subsequent dissemination within the Bronze Age of a component (teal) that is earliest identified in our dataset in HGs from the Caucasus (CHG). Unlike contemporaries elsewhere (but similarly to earlier Hungarian BA), Portuguese BA individuals show no signal of this component, although a slight but discernible increase in European HG ancestry (red component) is apparent. D-Statistic tests would suggest this increase is associated not with Western HG ancestry, but instead reveal significant introgression from several steppe populations into the Portuguese BA relative to the preceding LNCA (S4 Text, S6 Table). Interestingly, the CHG component in ADMIXTURE is present in modern-day Spaniards and to a lesser extent in the Basque population.

    IMG_1577.jpg

    Fig 5. Average genomic height for each of the Western Eurasian samples in the imputed dataset, plotted against its approximate date, highlighting temporal trends in genetic height.
    We excluded from this analysis Russian Bronze and Iron Age individuals containing variable amounts of Siberian admixture, but polygenic scores for all imputed samples can be seen in S7 Text.

    IMG_1578.jpg
    Gerard Corcoran
    R1b-DF21-S5456-S6166, H1C1

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    Quote Originally Posted by ArmandoR1b View Post
    I'm looking forward to a good analysis of the files they uploaded.Raw data and aligned reads have been submitted to http://www.ebi.ac.uk/ena/data/view/PRJEB14737, secondary accession ERP016408
    What steps should we take now to download it to Gedmatch?

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    Quote Originally Posted by Piquerobi View Post
    What steps should we take now to download it to Gedmatch?
    I don't know. I've never had the patience to install Linux, and try to learn how to convert the files. The files aren't yet available even though the accession number was included in the paper. Rocca knows how.

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