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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 Poltavka outlier

The real thing

The enigma of the Kalash

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 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

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...

R1a-Z280 from Early Bronze Age Northern Poland

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