search this blog

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 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

Saturday, May 20, 2017

Shared maternal ancestry between Slavs and Germanics probably dates to the Metal Ages


Over at the Russian Journal of Genetics behind a paywall at this LINK. Emphasis is mine:

Abstract: The structure and diversity of mitochondrial DNA (mtDNA) macrohaplogroup U lineages in Russians from Eastern Europe are studied on the basis of analysis of variation of nucleotide sequences of complete mitochondrial genomes. In total, 132 mitochondrial genomes belonging to haplogroups U1, U2e, U3, U4, U5, U7, U8a, and K are characterized. Results of phylogeographic analysis show that the mitochondrial gene pool of Russians contains mtDNA haplotypes belonging to subhaplogroups that are characteristic only of Russians and other Eastern Slavs (13.7%), Slavs in general (11.4%), Slavs and Germans (17.4%), and Slavs, Germans, and Baltic Finns (9.8%). Results of molecular dating show that ages of mtDNA subhaplogroups to which Russian mtDNA haplotypes belong vary in a wide range, from 600 to 17000 years. However, molecular dating results for Slavic and Slavic-Germanic mtDNA subhaplogroups demonstrate that their formation mainly occurred in the Bronze and Iron Ages (1000–5000 years ago). Only some instances (for subhaplogroups U5b1a1 and U5b1e1a) are characterized by a good agreement between molecular dating results and the chronology of Slavic ethnic history based on historical and archaeological data.

Malyarchuk, B.A., Derenko, M.V. & Litvinov, The macrohaplogroup U structure in Russians, A.N. Russ J Genet (2017) 53: 498. doi:10.1134/S1022795417020053

Tuesday, May 16, 2017

Globular Amphora people 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...

Tuesday, March 28, 2017

Hints of deep genetic substructure in Iron Age Poland


A paper at Infection, Genetics and Evolution looks at the susceptibility to infectious diseases in two late Iron Age groups from Central Poland. I can't wait to see genome-wide and Y-chromosome data from these and other ancient Polish populations. Judging by the outcomes presented in this paper, and also rumors that I've heard from Polish labs, we're in for some major surprises. Emphasis is mine:

Abstract: For thousands of years human beings have resisted life-threatening pathogens. This ongoing battle is considered to be the major force shaping our gene pool as every micro-evolutionary process provokes specific shifts in the genome, both that of the host and the pathogen. Past populations were more susceptible to changes in allele frequencies not only due to selection pressure, but also as a result of genetic drift, migration and inbreeding. In the present study we have investigated the frequency of five polymorphisms within innate immune-response genes (SLC11A1 D543N, MBL2 G161A, P2RX7 A1513C, IL10 A-1082G, TLR2 –196 to –174 ins/del) related to susceptibility to infections in humans. The DNA of individuals from two early Roman-Period populations of Linowo and Rogowo was analysed. The distribution of three mutations varied significantly when compared to the modern Polish population. The TAFT analysis suggests that the decreased frequency of SLC11A1 D543N in modern Poles as compared to 2nd century Linowo samples is the result of non-stochastic mechanisms, such as purifying or balancing selection. The disparity in frequency of other mutations is most likely the result of genetic drift, an evolutionary force which is remarkably amplified in low-size groups. Together with the FST analysis, mtDNA haplotypes' distribution and deviation from the Hardy-Weinberg equilibrium, we suggest that the two populations were not interbreeding (despite the close proximity between them), but rather inbreeding, the results of which are particularly pronounced among Rogowo habitants.

...

Although no sound evidence of population differentiation was found when comparing the samples of Linowo and Rogowo, it is worth noticing that the distribution of mtDNA haplotypes between these two settlements differs remarkably. Apart from the two haplotypes (rCRS and 16126C) that occur in both studied groups, no other pattern of mtDNA SNPs is shared between them. The lack of reflection of these dissimilarities in the FST analysis is probably a result of the low-size group which is more exposed to result bias or low diversity of haplotypes among Rogowo individuals. All of the above allows to draw the theoretical conclusion that although these two settlements date back to the same period and are located within 55 km (or around 160 km along the Vistula River) of one another, they are genetically remote.

Lewandowska et al., The genetic profile of susceptibility to infectious diseases in Roman-Period populations from Central Poland, Infection, Genetics and Evolution, Volume 47, January 2017, Pages 1–8, http://dx.doi.org/10.1016/j.meegid.2016.11.011

See also...

R1a-Z280 from Early Bronze Age Northern Poland