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Monday, June 19, 2017

Polish aDNA PCA


Below is a Principal Component Analysis (PCA) that I put together for an upcoming presentation on Polish ancient DNA (aDNA). The five RISE samples are from Allentoft et al. 2015, including RISE569, the early Slavic genome from the Czech Republic, which was initially wrongly labeled as that of a Czech Bell Beaker (see here). PL_N17 is an Early Bronze Age (EBA) sample from Gustorzyn, Northern Poland (see here).


I also organized f3 outgroup statistics of the form f3(European_pop,Test,Yoruba) for each of these samples to compare their genetic affinities to present-day European populations. Although f3 outgroup statistics aren't as sensitive as haplotype tests, I think these results look interesting and useful, with both PL_N17 and RISE569 seemingly showing strong links to modern-day West Slavs. The full output is available in a zip file here.

Poland_EBA PL_N17
Lithuanian 0.175778
Ukrainian_West 0.174866
Sorb 0.174334
Estonian 0.174313
Icelandic 0.17397
Irish 0.173863
Polish_West 0.173743
Polish_East 0.173549
Czech 0.173545
Norwegian 0.173533

Early Slav RISE569
Sorb 0.169171
Lithuanian 0.168945
Estonian 0.168819
Polish_West 0.168267
Polish_East 0.168143
Irish 0.168092
Czech 0.167941
Norwegian 0.167787
Icelandic 0.167696
Finnish 0.167685

See also...

Testing for genetic continuity in Poland from the Bronze Age to the present

Tuesday, May 16, 2017

Globular Amphora people were starkly different from Yamnaya people


The figure below is from the recent Mathieson et al. 2017 preprint; slightly edited to highlight the results of nine Globular Amphora Culture (GAC) samples from two burial sites in what are now Poland and Ukraine.


Despite living in East Central Europe at about the same time as the nearby Yamnaya people of the Pontic-Caspian Steppe, these GAC individuals show practically zero Yamnaya-related or steppe ancestry (note the almost total absence of the orange "Yamnaya" component in the Globular_Amphora results in the ADMIXTURE bar graph). Instead, they're very similar to Chalcolithic and Middle Neolithic Central and Western Europeans, with whom they overlap in the Principal Component Analysis (PCA).

During the tail end of the GAC period, East Central Europe was suddenly dominated by a new archaeological complex called the Corded Ware Culture (CWC). Although most CWC individuals sampled to date show minor GAC-related ancestry, they're overwhelmingly Yamnaya-like, which suggests that by and large the CWC population has its origins on the Pontic-Caspian Steppe. In fact, some of the earliest CWC examples from the Baltic States, such as Latvia_LN in the ADMIXTURE bar graph, are basically identical to Yamnaya people.

It was suggested not long ago that the presence of Yamnaya-related ancestry in modern-day Europeans could be mostly explained by the so called Isolation-by-Distance phenomenon (see here). But as I said at the time, this was a major faux pas, and thanks to these GAC samples I now have direct evidence from ancient DNA to back me up. So forget the idea of anything resembling a gentle cline in Yamnaya-like ancestry east to west across Europe before proto-CWC and Yamnaya exploded from the steppes.

By the way, in that critique I said that it's not possible to recapitulate ancient populations with ADMIXTURE components. I stand by that statement, although as we can see in Mathieson et al. 2017, it is possible to get close at times with enough of the right ancient samples; close enough to make some general observations anyway.

Interestingly, on the PCA plot, the European Bronze Age cluster is more or less half way between GAC and Latvia_LN. This is also where modern-day Poles and Ukrainians cluster on such plots when they're not significantly skewed by projection bias or shrinkage. Thus, I do wonder if the Slavs of East Central Europe are essentially a 50/50 mixture of early CWC and late GAC? I'll try and test this when the Mathieson et al. 2017 dataset goes online.

Reference...

Mathieson et al., The Genomic History Of Southeastern Europe, bioRxiv, Posted May 9, 2017, doi: https://doi.org/10.1101/135616

See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...