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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,

See also...

R1a-Z280 from Early Bronze Age Northern Poland

Wednesday, July 27, 2016

Lipka Tatars vs Balto-Slavs

Huge difference in this ADMIXTURE bar graph from the recent Pankratov et al. paper between Lipka Tatars from Belarus and nearby Balts and Slavs. The Lipka Tatars are almost identical to Volga Tatars despite residing in their current homeland for about 500 years. I'm guessing the fact that they're Sunni Muslims might have something to do with it.

Pankratov, V. et al. East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars. Sci. Rep. 6, 30197; doi: 10.1038/srep30197 (2016).

Saturday, June 18, 2016

Poles in the new Human Origins dataset

Harvard's Human Origins dataset is being updated with 238 new samples, including 23 from Poland (15 from Poznan in western Poland and 8 from Lublin in eastern Poland). It should be available for download soon at the Reich Lab website here, although many of the new samples will only be accessible to people who sign a waiver. Below is a Principal Component Analysis (PCA) from Lazaridis et al. 2016 featuring the new samples. Interestingly, most of the Poles, probably those from Poznan, cluster with Sorbs from eastern Germany.


Lazaridis et al., The genetic structure of the world's first farmers, bioRxiv preprint, posted June 16, 2016, doi:

Sunday, May 1, 2016

Ancient Polish admixture in Denmark

This ESHG 2016 presentation about Danish population structure is sure to be interesting. I wonder how the authors were able to discern ancient Polish admixture from more recent Polish admixture? Keep in mind that lots of Poles settled in Denmark during the past 150 years or so. For instance, former Danish national team goalkeeper Peter Schmeichel is half Polish. And Caroline Wozniacki is totally Polish.

Abstract: Denmark’s genetic history has never been studied in detail. In this work, we analysed genetic and anthropometrical data from ~800 Danish students as part of an outreach activity promoting genomic literacy in secondary education. DNA analysis revealed remarkable homogeneity of the Danish population after discounting contributions from recent immigration. This homogeneity was reflected in PCA and AMOVA, but also in more sophisticated LD-based methods for estimating admixture. Notwithstanding Denmark’s homogeneity, we observed a clear signal of Polish admixture in the East of the country, coinciding with historical Polish settlements in the region before the Middle Ages. In addition, Denmark has a substantially smaller effective population size compared to Sweden and Norway, possibly reflecting further lack of strong population structure. None of these three Scandinavian countries seems to have suffered a depression due to the Black Death in the Middle Ages. Finally, we used the students’ genetic data to predict their adult height after training a novel prediction algorithm on public summary statistics from large GWAS. We validated our prediction using the students’ self-reported height and found that we could predict height with a remarkable ~64% accuracy.

Athanasiadis et al., Nationwide genomic study in Denmark reveals remarkable population homogeneity, ESHG EMPAG 2016 Presentation Abstract, P18.091C

Update 24/08/2016: The paper is now available at Genetics and open access. See here: On the remarkable genetic homogeneity of Denmark.

Monday, March 21, 2016

Scandinavians in medieval Poland

The genetic evidence presented in this paper is underwhelming; a single, low resolution mtDNA haplogroup I haplotype that appears to be of Scandinavian origin because it was also found in remains from Iron Age Denmark (sample B5 in Melchior et al. 2008). However, the authors' conclusions are also based on archaeological evidence, and they also match recent isotopic results (see here).

Abstract: Contemporary historical anthropology and classical archaeology are concerned not only with such fundamental issues as the origins of ancient human populations and migration routes, but also with the formation and development of inter-population relations and the mixing of gene pools as a result of inter-breeding between individuals representing different cultural units. The contribution of immigrants to the analysed autochthonous population and their effect on the gene pool of that population has proven difficult to evaluate with classical morphological methods. The burial of one individual in the studied Napole cemetery located in central Poland had the form of a chamber grave, which is typical of Scandinavian culture from that period. However, this fact cannot be interpreted as absolute proof that the individual (in the biological sense) was allochtonous. This gives rise to the question as to who was actually buried in that cemetery. The ancient DNA results indicate that one of the individuals had an mtDNA haplotype typical of Iron Age northern Europe, which suggests that he could have arrived from that area at a later period. This seems to indirectly confirm the claims of many anthropologists that the development of the early medieval Polish state was significantly and directly influenced by the Scandinavians.

Płoszaj T. et al., Analysis of medieval mtDNA from Napole cemetery provides new insights into the early history of Polish state, Ann Hum Biol. 2016 Mar 11:1-4., DOI:10.3109/03014460.2016.1151550

Tuesday, February 2, 2016

PCA of RISE595, RISE596 and RISE598

I wasn't confident enough to run these three ancient genomes in Principal Component Analyses (PCA) when they were first published last year. Their SNP counts were too low for comfort. But since then I've discovered a few things about PCA projection, so here goes:

RISE595 and RISE596 are samples from present-day Montenegro dated to the Late Bronze Age and Iron Age, respectively. I haven't been able to dig up a lot of information about their archaeological contexts, but both are from Kurgan-like Tumuli burials.

If their PCA placements are correct, then I'd say they more or less resemble the samples from Bronze Age Hungary (marked on the plot as Hungary_BA). What this suggests is that their DNA, like their burial style, is in large part of steppe origin.

RISE598 is a Late Bronze Age sample from a bog burial near the present-day Lithuanian/Polish border. This individual clusters close to Unetice samples from the Czech Republic, Germany and Poland, as well as present-day Poles, which, at least to me, makes good sense.

See also...

101 ancient Eurasian genomes (Allentoft et al. 2015)

Monday, December 21, 2015

Bronze Age steppe warrior affinity test

Reich Lab et al. are now targeting more than 1.2 million sites in the ancient samples that they genotype, including over one million from the Illumina genotype array. This is great because it means that I can now run analyses with these ancients on the present-day populations in my Illumina array-based dataset using as many as 500K SNPs, which makes things more accurate and interesting.

Below are a few sets of D-statistics of the form D(Outgroup,X)(Population1,Population2), featuring several ancient populations from the recent Allentoft et al., Haak et al. and Mathieson et al. papers. I'm basically testing how much closer X is to either Population1 or Population2.

The results look very solid considering the spatio-temporal and archaeological origins of the samples. However, the outcomes for the smaller Northern European nations perhaps look slightly inflated. This is probably due to their peculiar demographic histories and resulting relative genetic homogeneity. At this stage, I don't know how to test this and limit its effects, if indeed it is a problem.

Poltavka 0.4678
Yamnaya_Kalmykia 0.4667
Yamnaya_Samara 0.4659
Srubnaya 0.4583
Corded_Ware_Germany 0.4554

Full output here

Sintashta 0.4584
Poltavka 0.4571
Srubnaya 0.4566
Yamnaya_Samara 0.4556
Afanasievo 0.455

Full output here

Poltavka 0.4617
Yamnaya_Samara 0.4594
Afanasievo 0.4556
Yamnaya_Kalmykia 0.454
Srubnaya 0.4522

Full output here

Yamnaya_Samara 0.4658
Afanasievo 0.4616
Yamnaya_Kalmykia 0.4602
Corded_Ware_Germany 0.4555
Srubnaya 0.4551

Full output here

Srubnaya 0.4572
Poltavka 0.4568
Sintashta 0.4534
Yamnaya_Samara 0.4518
Corded_Ware_Germany 0.4514

Full output here

Poltavka 0.4555
Srubnaya 0.454
Andronovo 0.4537
Yamnaya_Samara 0.4536
Corded_Ware_Germany 0.4523

Full output here

Andronovo 0.4567
Srubnaya 0.4553
Poltavka 0.4526
Yamnaya_Kalmykia 0.4507
Unetice_EBA 0.4506

Full output here

Poltavka 0.4571
Yamnaya_Samara 0.4565
Afanasievo 0.454
Corded_Ware_Germany 0.4538
Unetice_EBA 0.4528

Full output here

Afanasievo 0.4644
Poltavka 0.464
Yamnaya_Samara 0.463
Srubnaya 0.4523
Andronovo 0.4513

Full output here

Poltavka 0.4669
Yamnaya_Kalmykia 0.4615
Afanasievo 0.4612
Srubnaya 0.4554
Corded_Ware_Germany 0.4542

Full output here

See also...

qpAdm tour of the Eneolithic/Bronze Age steppe

At least three genetically distinct Indo-European migrations into South Asia

Sunday, October 11, 2015

The sun and the moon, Srubnaya people, and R1a-Z93

The recently revised Mathieson et al. preprint has some interesting comments about genetic ties between Bronze Age Eastern Europe and South Asia:

After the Poltavka period, population change occurred in Samara: the Late Bronze Age Srubnaya have ~17% Anatolian Neolithic or EEF ancestry (Extended Data Fig. 2). Previous work documented that such ancestry appeared east of the Urals beginning at least by the time of the Sintashta culture, and suggested that it reflected an eastward migration from the Corded Ware peoples of central Europe5. However, the fact that the Srubnaya also harbored such ancestry indicates that the Anatolian Neolithic or EEF ancestry could have come into the steppe from a more eastern source. Further evidence that migrations originating as far west as central Europe may not have had an important impact on the Late Bronze Age steppe comes from the fact that the Srubnaya possess exclusively (n=6) R1a Y chromosomes (Extended Data Table 1), and four of them (and one Poltavka male) belonged to haplogroup R1a-Z93 which is common in central/south Asians12, very rare in present-day Europeans, and absent in all ancient central Europeans studied to date.


This represents a direct link between the European steppe and central/south Asia, an intriguing observation that may be related to the spread of Indo-European languages in that direction.

Actually, several Corded Ware samples from previous studies carried the M417 and Z645 mutations, which are ancestral to Z93. So who's to say that the main patriarch of the Sintashta and Srubnaya cultures, both of which appear to have been rich in R1a-Z93, didn't live somewhere within the Corded Ware horizon, even as far west as Germany or Poland?

In any case, it's nice to see academia finally mention R1a-Z93 in the context of the Indo-European expansion into South Asia. I've been saying for years that this looks like the marker of the Proto-Indo-Iranians and Proto-Indo-Aryans (see here and here).

I also recently wrote how the early Indo-Europeans, all the way from Scandinavia to South Asia, were obsessed with the sun and the moon, otherwise known as the Divine Twins (see here). After seeing the results in Mathieson et al., I did some Googling about the Srubnaya Culture, and found these news features:

Illuminating! Ancient Slab May Be Sundial-Moondial

Photos: Ancient Sundial-Moondial Discovered

Fascinating stuff. Anyone know if similar Sundial-Moondials dating to the Bronze or Iron Age have been found in South Asia?

See also...

The Srubnaya outlier

The Poltavka outlier

Lactase persistence and ancient DNA

Friday, September 18, 2015

Recent admixture in West Eurasia (including Europe)

A new open access paper at Current Biology looks at the role of recent admixture in the formation of the present-day West Eurasian gene pool. It appears to be an updated version of a paper from last year which I found somewhat disappointing (see here). This effort is a lot better; it's more detailed and sophisticated, and the authors are more cautious with their interpretations of the data.

That's it for now, but I'll have a lot more to say about these results soon at my other blog when more ancient DNA data rolls in from southern Europe and the Near East.

Below is Figure 4A from the paper, which shows the proportions of admixture from outside of Europe and West Asia among a wide variety of West Eurasian groups.


Busby et al., The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape, Current Biology, DOI:

Wednesday, September 2, 2015

Finno-Ugric Poles in Kushniarevich et al. 2015

PLoS One has just put out a major paper on the genetic structure of Balto-Slavs, and unfortunately I have to say it's a major disappointment.

Kushniarevich A, Utevska O, Chuhryaeva M, Agdzhoyan A, Dibirova K, Uktveryte I, et al. (2015) Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data. PLoS ONE 10(9):e0135820. doi:10.1371/journal.pone.0135820

The authors used a very small number of Polish samples for their genome-wide analysis, mostly from the Estonian Biocentre (see here and here). At least 10 of these Poles come from Estonia, and some even resemble northern Russians with their unusual ancestry proportions. Note the dichotomy in the levels of the lemon yellow "Siberian/Volga-region" component within the Polish set in the ADMIXTURE bar graph from the paper.

I raised this issue with Estonian Biocentre Research Director Mait Metspalu a while ago when these samples were first published, and this was his response.

What we have is self identity. As you can see from Supplementary table 1 these samples have been collected in Estonia and the donors are self reported Poles.

Well, I'm sure there are people in South America who identify as Spanish. But would anyone in their right mind use them to make inferences about the genetic structure and history of the people of Spain?

Fine-scale population genetic analyses like this should only be done with lots of samples from the right places. Self-reported Poles from Estonia, and perhaps also Russia, who clearly don't resemble Poles from Poland aren't good enough. Estonian Biocentre scientists do a lot of useful work, but in this particular instance they were rather sloppy in labeling these Estonian Poles as simply Polish.

Kushniarevich et al. were very sloppy in not stating where their Polish samples were really from (their map shows the middle of Poland) and not bothering to remove obvious outliers from their dataset.

See also...

Lipka Tatars vs Balto-Slavs

Recent admixture in West Eurasia (including Europe)