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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 from the Estonian Biocentre for their genome-wide analysis (see here). Most 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.

Friday, August 14, 2015

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


The recent Allentoft et al. paper on the ancient genomics of Eurasia featured an Early Bronze Age Corded Ware/proto-Unetice individual belonging to Y-haplogroup R1a. His remains came from a kurgan burial in present-day Greater Poland, or Wielkopolska, known as one of the four Pyramids of Wielkopolska.

Of course, R1a is by far the most common Y-haplogroup in Poland today, and Greater Poland is generally accepted to be the cradle of the Polish nation.

It's tempting to think that all of this isn't just a happy coincidence, and that this kurgan man and/or his close relatives are the ancestors of modern-day Poles. Considering that we have some of his genome, can we actually test this hypothesis?

Unfortunately, the sequence by itself is too limited to allow such a high resolution analysis. However, the Allentoft et al. dataset includes six other Bronze Age samples from Poland; one other Corded Ware individual from Greater Poland, and five Unetice individuals from Silesia. Thus, it's possible to combine these samples and at least run a preliminary analysis comparing them to present-day Europeans, including Poles, to test their affinities.

The only reliable way to do this is to use formal statistics, and specifically D-statistics. That's because, unlike model-based analyses, D-stats ignore recent genetic drift and, unlike f3-stats, they're able to discriminate correctly at a very fine scale between samples with somewhat different numbers of markers. Below are two sets of results of the form D(Outgroup, PopulationTest) (Population1, Population2).

D(Ju_hoan_North, Poland_Bronze_Age) (BedouinB, European)

D(Ju_hoan_North, Poland_Bronze_Age) (Polish, European)

Basically, what the results show is that western Poland was inhabited by a very northern people during the Bronze Age. They were similar to present-day Balts, Scandinavians, Irish, and...Poles.

Indeed, in these sorts of tests small Northern European countries tend to get the best scores with most prehistoric Europeans. I believe that this isn't just because of shared ancestry, but also relative isolation and homogeneity. So the fact that Poland is the only really big country at the top of the list above might be very important.

That's pretty much it for now. As far as I can see, there's nothing to suggest that present-day Poles can't be the direct descendants of these ancients. But as I say, this was a preliminary analysis and a work in progress. I'll revisit this issue when more samples come in. By the way, I also ran a bunch of other D-stats that might be of interest.

D(Ju_hoan_North, Bell_Beaker) (BedouinB, European)

D(Ju_hoan_North, Corded_Ware) (BedouinB, European)

D(Ju_hoan_North, EHG) (BedouinB, European)

D(Ju_hoan_North, Hungary_BA) (BedouinB, European)

D(Ju_hoan_North, Loschbour) (BedouinB, European)

D(Ju_hoan_North, Motala_HG) (BedouinB, European)

D(Ju_hoan_North, Stuttgart) (BedouinB, European)

D(Ju_hoan_North, Unetice_EBA) (BedouinB, European)

D(Ju_hoan_North, Yamnaya) (BedouinB, European)


It's useful to plot D-stats against each other when looking for patterns in the data. For instance, in the graphs below Basques and southern French often look like obvious outliers. What this means is that there's something peculiar about their genetic history. What might that be I wonder? Any suggestions?












The present-day Polish samples, eleven in all, came from here. Most of the other samples are from the Allentoft et al. (Rise Project), Haak et al. and Lazaridis et al. datasets, all of which are publicly available.

See also...

R1a1a from an Early Bronze Age warrior grave in Poland

Monday, July 27, 2015

Corded Ware in the Central and Southern Balkans


I never knew that corded ware penetrated deep into the Balkans. According to this recent paper, it certainly did, even as far as present-day Greece.

Abstract: The analysis of corded ware and accompanying artifacts reveals the nature of its appearance across the Central and Southern Balkan Eneolithic during three cultural-chronological horizons. The first horizon corresponds to the Early Eneolithic, namely the Bubanj-Salcuta-Krivodol cultural complex (BSK), while the second corresponds to the Cotofeni culture. The third horizon, showing chronological continuity with the second, and set within the Late Eneolithic/Early Bronze Age, has a site distribution that encompasses the territory of nearly the entire Balkan Peninsula, where corded ware is found together with other steppe elements which are present in large numbers, such are burials under mounds and the appearance of the domestic horse.


Aleksandar Bulatovic, Corded Ware in the Central and Southern Balkans: A Consequence of Cultural Interaction or an Indication of Ethnic Change?, The Journal of Indo-European Studies, Volume 42, Number 1 & 2, Spring/Summer 2014

See also...

Population genomics of Early Bronze Age Europe in three simple graphs

Saturday, July 18, 2015

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 real thing

The enigma of the Kalash

Population genomics of Early Bronze Age Europe in three simple graphs

Tuesday, June 23, 2015

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


From the Eneolithic to the Middle 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.

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: http://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

See also...

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

Sunday, May 3, 2015

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...

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

Monday, December 22, 2014

Ancient East European and West Asian admixture deep in Siberia


The full mito sequences from this new Derenko at al. study should come in very handy when many more ancient genomes from across North Eurasia are published. The paper is open access, but here are a few excerpts anyway:

Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected previously in mitochondrial gene pools of modern Siberians.

We report here 166 new complete mitochondrial DNA (mtDNA) sequences that allow us to expand and re-analyze the available data sets of western Eurasian lineages found in northern Asian populations, define the phylogenetic status of Siberian-specific subclades and search for links between mtDNA haplotypes/subclades and events of human migrations. From a survey of 158 western Eurasian mtDNA genomes found in Siberia we estimate that nearly 40% of them most likely have western Asian and another 29% European ancestry. It is striking that 65 of northern Asian mitogenomes, i.e. ~41%, fall into 19 branches and subclades which can be considered as Siberian-specific being found so far only in Siberian populations. From the coalescence analysis it is evident that the sequence divergence of Siberian-specific subclades was relatively small, corresponding to only 0.6-9.5 kya (using the complete mtDNA rate) and 1–6 kya (coding region rate).

...

Overall, the phylogeographic analysis strongly implies that the western Eurasian founders, giving rise to Siberian specific subclades, trace their ancestry only to the early and mid-Holocene, though some of genetic lineages may trace their ancestry back to the end of LGM. Importantly, we have not found the modern northern Asians to have western Eurasian genetic components of sufficient antiquity to indicate traces of pre-LGM expansions, that originated from the Upper Paleolithic industries present both in the southern Siberia and Siberian Arctic, and that date back to ~30 kya, well before the LGM [43]–[45]. Apparently, the Upper Paleolithic population of northern Asia, whose western Eurasian ancestry was approved recently by complete genome sequencing of 24 kya-old individual from Mal’ta and 17 kya-old individual from Afontova Gora in south-central Siberia, did not leave a genetic mark on the female lineages of modern Siberians. It is probable that the initial population expansion in the southern Siberia region involved maternal lineages other than present now, or that there was a substantial gene flow into the region after the LGM, most probably from eastern Asian sources as have been suggested by Raghavan et al. [7].

Citation...

Derenko et al.: Western Eurasian ancestry in modern Siberians based on mitogenomic data. BMC Evolutionary Biology 2014 14:217. doi:10.1186/s12862-014-0217-9