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

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

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...

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, https://dx.doi.org/10.1016/j.meegid.2016.11.011

See also...

R1a-Z280 from Early Bronze Age Northern Poland

Lipka Tatars vs Balto-Slavs

Note the 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).

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.

Citation...

Lazaridis et al., The genetic structure of the world's first farmers, bioRxiv preprint, posted June 16, 2016, doi: https://dx.doi.org/10.1101/059311

Around 65% LN/EBA European ancestry in the Hindu Kush (?)

One of the toughest nuts to crack in population genetics has proved to be the story of the people of the Hindu Kush. However, using TreeMix and ancient genomes from the recent Allentoft et al. and Haak et al. papers, I'm seeing most of the Kalash and Pathan individuals from the HGDP modeled as ~65% Late Neolithic/Early Bronze Age (LN/EBA) European and ~35% Central Asian. This, to me at least, makes a lot of sense. For instance:

The Kalash and Pathan samples that can't be modeled in this way, at least with the reference populations that I'm using, are fitted within a framework that closely resembles the old two-way Ancestral South Indian/Ancestral North Indian model (ASI/ANI). They usually score ~12% admixture from the branch leading to the Dai of southern China, which is obviously the proxy for ASI.

Both of these models are correct; they just show the same thing in different ways. So if we mesh them together the Kalash and Pathans come out ~65% LNE/EBA European (which includes substantial Caucasus or Caucasus-related ancestry), ~12% ASI, and ~23% something as yet undefined.

If I had to guess, I'd say the mystery ~23% was Neolithic admixture from what is now Iran. But ancient DNA has thrown plenty of curve balls at us already, so that's a low confidence prediction, even though it does make good sense.

It's also interesting to see the migration edges running from the Ulchi of east Siberia to the LN/EBA Europeans. This might be a signal of minor Eastern non-African (ENA), in other words East Eurasian, admixture. Then again, it might just be the algorithm trying to compensate for something, like excess Eastern Hunter-Gatherer (EHG) ancestry.

The full output from my analysis can be downloaded here. The reference samples and markers are listed here and here.

See also...

The Poltavka outlier

The real thing

The enigma of the Kalash

Badasses of the Bronze Age: Analysis of Andronovo, Battle-Axe, Corded Ware and Sintashta genomes - part one

From the Eneolithic to the Late Bronze Age vast areas of Eurasia were inhabited by a series of highly mobile and innovative groups that mostly relied on pastoralism for subsistence and, judging by their warlike grave goods, didn't mind a bit of biffo.

In Europe, where they first appeared, their archeological remains are generally classified as part of the Corded Ware Culture (or its Battle-Axe and Single Grave offshoots), and in Asia, where they expanded rapidly from the Trans-Urals to the Pamirs and south Siberia, as part of the Sintashta, Petrovka and Andronovo cultures.

It's likely that these groups had a profound impact on the Bronze Age world, including on Mycenaean Greece and Hittite Anatolia. The Sintashta Culture, for instance, is credited with the development of the spoked-wheel chariot, which became widely used in warfare all the way from Egypt to China.

Unfortunately, a lot of nonsense has been written on this topic in the past. In my view, one of the most sensible and up do date sources currently online is the thesis The Origin and Spread of the War Chariot by Elias Manuel Morgado Pinheiro.

Indeed, the obvious awesomeness of these ancient people has stirred much controversy about their origins and legacy. The academic consensus is that they were closely related, and that at least some of their ancestors were early Indo-Europeans from Eneolithic Eastern Europe. But a few archeologists have argued that the Corded Ware Culture was native to Central Europe, and others that the Sintashta population arrived in the Trans-Urals from Iran or even Syria.

Moreover, linguists generally consider the Sintashta/Andronovo people as the most likely candidates for the Proto-Indo-Iranians, and thus the precursors of the Indo-Aryans. But this is contested by many Indologists, who prefer to see the deepest roots of the Indo-Iranians closer to India and often oppose the idea of an Aryan conquest of South Asia during the Bronze Age.

In the near future, probably within the next couple of years, ancient genomics will leave very little room for debate in these matters and the arguments will cease, at least in mainstream academia.

But we already have a reasonable collection of ancient DNA from the relevant archeological cultures. Does it back the general consensus? Let's take a look, starting with the Y-chromosome data sorted by culture. The bracketed numbers are the sample sources, which are listed at the bottom of the post.

Corded Ware, Germany, Individuals 2,3,4 [1], R1a
Corded Ware, Germany, I0104 [3], R1a
Corded Ware, Germany, RISE434 [4], R1a
Corded Ware, Germany, RISE436 [4], R1a
Corded Ware, Poland, RISE1 [4], R1b?
Corded Ware, Germany, RISE446 [4], R1a
Corded Ware, Poland, RISE431 [4], R1a

Single Grave?, Denmark, RISE61 [4], R1a

Battle-Axe, Sweden, RISE94 [4], R1a
Battle-Axe?, Sweden, RISE98 [4], R1b

Sintashta, Trans-Urals, Russia, RISE386 [4], R1a
Sintashta, Trans-Urals, Russia, RISE392 [4], R1a

Andronovo, South Siberia, Russia, S07 [2], C
Andronovo, South Siberia, Russia, S10 [2], R1a
Andronovo, South Siberia, Russia, S16 [2], R1a
Andronovo, Altai region, Russia, RISE512 [4], R1a

Fascinating stuff. Keep in mind also that at higher resolution, most, if not all, of these R1a lineages are actually R1a1a1, which is estimated to be only around 5,000-6,000 years old based on full Y-Chromosome sequences. In other words, these groups were certainly closely related, and in large part the descendants of a patriarch who lived no earlier than the Middle or even Late Neolithic.

Now, based on that list it might seem as if both R1a and Corded Ware were indeed native to North-Central Europe. But this is not so.

R1a appears to be an Eastern Hunter-Gatherer (EHG) marker that in all likelihood failed to penetrate west of present-day Ukraine until the Late Neolithic, because it's missing in all the relevant samples before this period. So it probably first arrived in Central Europe with the Corded Ware people. We know that the Corded Ware people were foreign to Central Europe because their genome-wide genetic structure is starkly different from that of the Middle Neolithic farmers who lived there before them.

This is easy to demonstrate. The Principal Component Analyses (PCA) below show where two ancient samples cluster alongside a variety of present-day West Eurasians from the Human Origins dataset [3]. Note that Esperstedt_MN, a Middle Neolithic sample from a Baalberge Group burial in east-central Germany [3], looks more at home in Sardinia than Central Europe. On the other hand, the Corded Ware sample [4], also from east-central Germany, is sitting at the other end of the plot, among groups from the Volga-Ural region.

I'll throw in a few more PCA featuring Corded Ware, Battle-Axe, Sintashta and Andronovo genomes that offered enough data to be placed on the plots with a high degree of accuracy [4]. Note that the only clear outlier is RISE512, an Andronovo sample with an inflated level of East Eurasian admixture. If you're having trouble finding the ancient samples, download the PDF files and use the PDF search field.

Corded_Ware_RISE00_Estonia

Corded_Ware_RISE431_Poland

Battle-Axe_RISE94_Sweden

Battle-Axe_RISE98_Sweden

Single_Grave_RISE61_Denmark

Sintashta_RISE386_Russia

Sintashta_RISE392_Russia

Sintashta_RISE394_Russia

Sintashta_RISE395_Russia

Andronovo_RISE500_Russia

Andronovo_RISE503_Russia

Andronovo_RISE505_Russia

Andronovo_RISE512_Russia

However, the meat and potatoes of ancient genomics are formal statistics. So in part 2 of this series I'll explore the genetic ancestry and legacy of the so called badasses of the Bronze Age using the ADMIXTOOLS software package.

Update 28/04/2016: I'm gearing up to finally write the second part of the Badasses of the Bronze Age. But before I do that, I need to update the first part, because I now have two more sets of ancient samples that can be described as truly badass in the context of this series: Potapovka and Srubnaya.

Incredibly, seven out of the eight Potapovka and Srubnaya males belong to R1a. One of the Potapovka individuals turned out P1, but that was only because of a lack of data, otherwise, in all likelihood, he'd also belong to R1a.

Potapovka, Samara, Russia, I0419 [5], R1a

Srubnaya, Samara, Russia, I0232 [5], R1a
Srubnaya, Samara, Russia, I0360 [5], R1a
Srubnaya, Samara, Russia, I0361 [5], R1a
Srubnaya, Samara, Russia, I0423 [5], R1a
Srubnaya, Samara, Russia, I0424 [5], R1a
Srubnaya, Samara, Russia, I0430 [5], R1a

Also, I recently changed the way I run PCA. Indeed, I can now accurately plot samples on a typical genetic map of West Eurasia with as little as 15K SNPs. So instead of a few plots featuring the best Potapovka and Srubnaya sequences separately, here's a plot with all of the badasses together.

Update 22/09/2017: Unfortunately, I won't be able to finish this series anytime soon. Things are moving very quickly, but the full picture won't be known to us for a while yet. Some recent developments are covered at my other blog under these links...

R1a-M417 from Eneolithic Ukraine!!!11

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

Citations...

1. Haak et al., Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age, PNAS, Published online before print November 17, 2008, doi:10.1073/pnas.0807592105

2. Keyser et al., Ancient DNA provides new insights into the history of south Siberian Kurgan people, Human Genetics, Saturday, May 16, 2009, doi: 10.1007/s00439-009-0683-0

3. Haak et al., Massive migration from the steppe is a source for Indo-European languages in Europe, bioRxiv, Posted February 10, 2015, doi: https://dx.doi.org/10.1101/013433

4. Allentoft et al., Bronze Age population dynamics, selection, and the formation of Eurasian genetic structure, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

5. Mathieson et al., Genome-wide patterns of selection in 230 ancient Eurasians, Nature, 528, 499–503 (24 December 2015), doi:10.1038/nature16152

R1a1a from an Early Bronze Age warrior grave in Poland

Ancient DNA tests on a skeleton from an Early Bronze Age "warrior" grave near Hrubieszow, southeastern Poland, have revealed that the remains belong to Y-haplogroup R1a1a [source].

Mitochondrial sequences were also obtained from seven other samples from the same burial site, and assigned to mt-haplogroups H1a, H1b (two), H2a (two), H6 and U5b1.

R1a1a is by far the most frequent Y-haplogroup in Poland today, and its presence in the remains from a high-status burial might be a clue as to how it became so common in East-Central Europe.

Interestingly, the site is classified as part of the Strzyżow Culture, which is considered by Polish archaeologists to be the result of contacts between local communities in southeastern Poland and Kurgan newcomers from the North Pontic steppe.

All of the other ancient R1a1a samples reported to date from Central Europe are also younger than the Middle Neolithic and from presumably steppe-derived Indo-European archeological cultures:

- Late Neolithic, Eulau, Germany, Corded Ware Culture, three related samples

- Late Neolithic, Esperstedt, Gemany, Corded Ware Culture, one sample

- Late Bronze Age, Halberstadt, Germany, Urnfield Culture (?), one sample

- Late Bronze Age, Lichtenstein Cave, Germany, Urnfield Culture, two samples

More info about the Bronze Age Pole, including photos of a facial reconstruction, can be found here and here (in Polish).

See also...

R1a-Z280 from Early Bronze Age Northern Poland

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

Ancient DNA from Iron Age and Medieval Poland

A new paper at PLoS ONE featuring ancient mitochondrial (mtDNA) data from Wielbark, Przeworsk and early Slavic remains argues for matrilineal continuity in present-day Poland since the Iron Age. It's actually based on a thesis that I blogged about more than two years ago (see here). However, it does include some fresh insights, so it's worth a look even if you read the thesis. RoIA stands for Roman Iron Age.

Three modern populations or groups of populations (Lithuanians and Latvians, Poles, and Czechs and Slovaks) were found to contain significantly higher percentages (p,0.05) of shared informative haplotypes with the RoIA samples compared to other present-day populations (Figure 2, Table S4). Notably, modern Poles shared the highest number (nine) of informative mtDNA haplotypes with the RoIA individuals.

...

Of particular interest are three RoIA samples assigned to subhaplogroup H5a1, which were recovered from the Kowalewko (sample K1), the Gaski, and the Rogowo (samples G1 and R3) burial sites (see Figure 1). Recent studies on mtDNA hg H5 have revealed that phylogenetically older subbranches, H5a3, H5a4 and H5e, are observed primarily in modern populations from southern Europe, while the younger ones, including H5a1 that was found among RoIA individuals in our study, date to around 4.000 years ago (kya) and are found predominantly among Slavic populations of Central and East Europe, including contemporary Poles [15]. Notably, we also found one ME sample belonging to subhaplogroup H5a1 (sample OL1 in Table 3). The presence of subclusters of H5a1 in four ancient samples belonging to both the RoIA and the ME periods, and in contemporary Poles, indicates the genetic continuity of this maternal lineage in the territory of modern-day Poland from at least Roman Iron Age i.e., 2 kya.

...

The evolutionary age of H5 sub-branches (,4 kya) [15] also approximates the age of N1a1a2 subclade found in the RoIA population (sample KA2) (Table 2). The coalescence age of N1a1a2 is around 3.4–4 kya, making this haplotype one of the youngest sub-branches within hg N [52]. The N1a1a2 haplotype found in one RoIA individual was classified as unique because no exact match was found among the twelve comparative populations or groups of populations used in the haplotype sharing test. Notably, a similar N1a1a2 haplotype carrying an additional transition at position 16172 was found in a modern-day Polish individual [53].

I suspect the publication of these results at this time, so many months after they were first revealed in the aforementioned thesis, is part of an effort to drum up interest and secure funding for a new project on the genetic history of Greater Poland, which was announced late last year (see here). I say that because one of the people organizing the project, Janusz Piontek, is also listed as a co-author on this paper. So if we're lucky we might soon see full genome sequences from a few of these Iron Age and Medieval samples.

Citation...

Juras A, Dabert M, Kushniarevich A, Malmstro¨m H, Raghavan M, et al. (2014) Ancient DNA Reveals Matrilineal Continuity in Present-Day Poland over the Last Two Millennia. PLoS ONE 9(10): e110839. doi:10.1371/journal.pone.0110839