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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 Northern Europe and Central Asia 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 and chronology. The bracketed numbers are the sample sources, which are listed at the bottom of the post.

Corded Ware, Germany, 4600 BP, Individuals 2,3,4 [1], R1a
Corded Ware, Germany, 4348 BP, I0104 [3], R1a
Corded Ware, Germany, 4161 BP, RISE434 [4], R1a
Corded Ware, Germany, 4124 BP, RISE436 [4], R1a
Corded Ware, Poland, 4117 BP, RISE1 [4], R1b?
Corded Ware, Germany, 4015 BP, RISE446 [4], R1a
Corded Ware, Poland, 3762 BP, RISE431 [4], R1a

Battle-Axe, Sweden, 4025 BP, RISE94 [4], R1a
Battle-Axe?, Sweden, 3736 BP, RISE98 [4], R1b

Sintashta, Trans-Urals, Russia, 3775 BP, RISE386 [4], R1a
Sintashta, Trans-Urals, Russia, 3626 BP, RISE392 [4], R1a

Andronovo, South Siberia, Russia, 3600 BP, S07 [2], C
Andronovo, South Siberia, Russia, 3600 BP, S10 [2], R1a
Andronovo, South Siberia, Russia, 3600 BP, S16 [2], R1a
Andronovo, Altai region, Russia, 3119 BP, 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 and the lone Saami.



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

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...

Genetic substructures among Late Neolithic/Bronze Age Scandinavians

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...

Large-scale recent expansion of European patrilineages

Population genetics of Copper and Bronze Age inhabitants of the Eastern European steppe

Eastern Europe as a bifurcation hotspot for Y-hg R1

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

Thursday, October 23, 2014

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

Monday, October 6, 2014

The power of imputation


The latest version of the Affymetrix Human Origins genotype dataset, published last month along with Lazaridis et al. 2014, is an awesome resource for population genetics (see here). However, it lacks Polish samples, which is a major drawback as far as this blogger is concerned.

Hopefully this oversight is corrected soon. In the meantime, I decided to include 15 Poles from the Eurogenes Project dataset in my copy of the Human Origins. But in order to do that I first had to impute around 460K genotypes for each of these people.

Imputing so many markers might sound pretty crazy, but it's actually very doable, especially for genetically homogeneous groups with relatively low haplotype diversity, like the Polish population. I used BEAGLE 3.3.2 for the job, mostly because I'm familiar with it, but also because it's quick and accurate.

My reference panel included 1090 individuals, most of them shared by Eurogenes and Human Origins, and just over 1 million markers. Only around 130K of the markers were shared by the two datasets, but well over 50% of the 1 million genotypes were observed in each of the Poles. This meant that I was imputing sporadically missing data, which is certainly a more sensible strategy than attempting to fill in long stretches of empty calls.

Everything seems to have worked out just fine, and the proof is in the pudding. Below are two Principal Component Analyses (PCA) featuring the Poles alongside 50 samples from the HGDP. The first PCA is based on observed genotypes, while the second on markers that were imputed into the Polish genomes. PCA are very sensitive to artifacts like genotyping errors, but as you can see, there's very little difference between these results. Also, keep in mind that the SNPs used in the Human Origins were specifically chosen for population genetics, while those in the Eurogenes dataset come from chips mostly designed for commercial ancestry and medical work.


Also, here's a PCA based on more than 300K SNPs, both observed and imputed in the Poles, featuring all of the West Eurasian samples from the filtered version of Human Origins, as well as the 15 Polish individuals. Note that the Poles cluster more or less between the Czechs and groups from the East Baltic region, and overlap most strongly with Belarusians, which makes sense.



Citations...

Brian L. Browning, Sharon R. Browning, A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals, AJHG, Volume 84, Issue 2, p210–223, 13 February 2009, DOI: http://dx.doi.org/10.1016/j.ajhg.2009.01.005

Lazaridis et al., Ancient human genomes suggest three ancestral populations for present-day Europeans, Nature, 513, 409–413 (18 September 2014), doi:10.1038/nature13673