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Wednesday, September 2, 2015

A multidimensional approach

This is arguably the most interesting Principal Component Analysis (PCA) I've run to date. Note that overall the ancient steppe genomes appear to be the crucial link in the Indo-European chain, basically bridging the gap between European and South Asian Indo-European-speakers. A plot with all of the samples labeled individually can be downloaded here. If you have any questions about the methodology, just ask in the comments.

The samples are from the Allentoft et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.

Sunday, August 30, 2015

The focus turns to the Globular Amphora people

Just a teaser, but a very interesting one. It looks like they're using the same enrichment capture methods as Haak et al. 2015. Can't wait to get my hands on the data.

Archaeological evidence shows a marked discontinuity in Late Neolithic farming societies in Europe: large settlements were abandoned, anthropomorphic figurines and painted pottery disappeared. Some scholars, as Gimbutas, interpreted these changes hypothesizing a migration of pastoral groups from the steppes of southern Ukraine, also associated with the spread of proto-Indo-European languages (Kurgan hypothesis). The Globular Amphora culture assumes a crucial role in this theory. It was distributed across central and eastern Europe, from the Elbe to the middle Dnieper, around 3400-2800 BC and was characterized by an apparently mobile economy, presence of domestic horse, distinctive pottery and burial rituals. Furthermore, the physical type of the Globular Amphora population was regarded as similar to those of the steppe region. Alternative explanations have been put forward for the spread of Indo-European languages, including Renfrew’s theory based on the Neolithic demic diffusion, and the Armenian hypothesis by Gamkrelidze and Ivanov. We selected 17 individuals from the Megalithic barrow of Kierzkowo (Poland, Kujawy-Pomorze), an excellent example of rituals of the Globular Amphora culture. We are applying advanced molecular procedures based on Next Generation Sequencing and target enrichment in order to analyze genetic variation in this community. Our aim is to contribute to the Indo-European debate, by comparing our data with the available genetic data about ancient and modern Europeans, quantifying population relationships, and testing for the possible demographic implications of the Kurgan hypothesis upon the Globular Amphora culture.

Vai et al., Genetic variability in a late Neolithic Megalithic Burial from Poland: The Globular Amphora Culture and the Indo-European debate, presentation abstract, 21° CONGRESSO dell’Associazione Antropologica Italiana, Bologna/Ravenna September 3-5, 2015.

Saturday, August 29, 2015

Children of the Divine Twins

The Trundholm sun chariot was found in a peat bog on the island of Zealand, Denmark, in 1902. It's thought to be an Indo-European religious artifact dating back to the Nordic Bronze Age; a representation of a horse pulling the sun and perhaps also the moon in a spoked wheel chariot. So one way or another it appears to be a reference to the Divine Twins mythos.

The Divine Twins are a key part of Indo-European religion, and they appear in the Rigveda, the most archaic of the Indo-Aryan Vedic texts.

However, because the concept includes the spoked wheel chariot, it probably can't be much older than 2,000 BC. That's because the invention of the spoked wheel chariot is more often than not credited to the Sintashta Culture of the Trans-Urals, which is dated to 2100-1800 BC.

Considering these cultural and technological ties between Bronze Age Scandinavia and South Asia, it's an interesting question whether there were also strong genetic links between these two outposts of the early Indo-European world.

Unfortunately, we don't yet have any ancient genomes from South Asia to compare to the Late Neolithic/Bronze Age (LN/BA) Nordic genomes published recently with Allentoft et al. 2015. However, we do have the Kalash.

The Kalash people of the Hindu Kush are Indo-Aryans, but they're also an extreme cultural and genetic isolate. It's likely that they haven't mixed very much with any of their neighbors since the Bronze Age. About half of them also practice a unique Vedic religion that celebrates the sun and moon (see section 1.5.4. "Creation myths" in Witzel 2002).

In the TreeMix analysis below I used three random Kalash individuals from the Human Origins dataset (HGDP00311, HGDP00313 and HGDP00315). I didn't run the whole set of 18 because they seem to create a genetic monolith that is impossible to break down and analyze correctly with TreeMix.

Note that after their Central Asian admixture is accounted for with a migration edge of 33%, the Kalash sit on what seems to be an early Indo-European branch that also includes the LN/BA Scandinavians. The full output from this analysis is available for download here.

I also employed the qpAdm software to model all of the Kalash from the Human Origins as a mixture of LN/BA Scandinavians, various ancient and present-day West Asians and Dai from south China. The ancestry proportions are listed at the bottom of the sheets. To check the success of the models consult the chisq, tail prob and standard (std.) errors.

Nordic LN-BA/Armenia BA/Dai

Nordic LN-BA/Iranian/Dai

Nordic LN-BA/Iranian Jew/Dai

Nordic LN-BA/Georgian/Dai

Now, qpAdm is easy to run but very difficult to use correctly. However, even when fumbling around like a drunk with this software, it's easy to pick up some useful hints. Clearly, even if the ancestry proportions are way off, the Kalash show stronger affinity to the ancient Scandinavians than to West Asians. Also, the models more or less reflect the TreeMix analysis above.

Thus, the answer to my question is a resounding yes; there were indeed strong genetic ties between Scandinavia and South Asia during the Bronze Age. Moreover, these ties were in all likelihood not mediated via West Asia, but via the Sintashta Culture of the Eurasian steppe and its close relatives.

See also...

The real thing

Monday, August 24, 2015

Pre- and Post-Kurgan Europe

The Principal Component Analysis (PCA) below is based on four sets of D-statistics. The second image shows what they are and how they affect the components. The datasheet is available here. If you don't know what EHG, SHG and WHG stand for, see here.

Note that the post-Kurgan Europeans are shifted east, towards the Bronze Age steppe groups (most of which are in fact classified as Kurgan cultures), relative to the pre-Kurgan Europeans. Coincidence? Certainly not. Interestingly, the West Asians show a similar shift to the east, although it's not yet clear who caused it and when.

The samples are from the Allentoft et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.

See also...

Smarter than the average bear

Smarter than the average bear

Using a few ancient hunter-gatherer sequences, formal statistics, and enough present-day samples, I can predict with basically 100% accuracy whether an ethnic group is of European or extra-European origin. Actually, there's probably an infinite number of ways of doing the same thing nowadays, but I thought this was an effective way of visualizing it. The datasheet can be downloaded here.

I also tried to analyze the Indo-European expansion in a similar way. The results are a lot less obvious, and there are a number of reasons for that. One of the main factors, I'd say, is that languages can be learned or imposed very quickly, and this happened a lot during historic times, well after the Proto-Indo-European dispersals.

For instance, Sardinians spoke Paleo-Sardinian or Nuragic languages until they adopted Indo-European speech, in the form of Latin, from the Romans (see page 118 here). Indeed, it's highly unlikely that any Proto-Indo-Europeans ever stepped foot on Sardinia. The relevant datasheet is here.

The samples are from the Allentoft et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.

See also...

Pre and Post-Kurgan Europe

Sunday, August 23, 2015

Archeogenetics of Roopkund skeletons (teaser)

I posted a link to an earlier version of this abstract back in June (see here). This version includes an interesting detail at the end which suggests that the authors may have stumbled upon the remains of an unadmixed Indo-Aryan group with unexpectedly strong affinities to Europeans (or rather Andronovo steppe nomads?) and Near Easterners (BMAC agriculturists?).

Note that they managed to sequence 80 full mitogenomes and capture a lot of genome-wide markers for 25 of the samples, so they have plenty enough data to draw the right conclusions. But how is it possible for unadmixed Indo-Aryans to still be around anywhere in South Asia during the 8th century AD? I can't wait to see the paper and get my hands on the data.

The high-altitude (5029 meters) Roopkund lake is situated in the Himalayan mountains within the Northern Indian state of Uttaranchal. Here, 70 years ago, several hundred human skeletons were found, in the lake itself and in its vicinity. This discovery was puzzling as the reasons for which so many people would have travelled and found their end there remained elusive. This is the first study to address the origin of these individuals through genetic and biological analysis of the skeletal remains. Using amelogenin marker; it was found that the majority of the individuals were males. In the same time, AMS dating of the bones revealed that the individuals had lived in the 8th century AD. To address the ancestry of this population, DNA was extracted from the bones of 80 individuals and the complete mitochondrial genome of each of them was sequenced; furthermore, for 25 of them, 200,000 autosomal markers were also genotyped. The comparative genetic analysis, which includes modern day data from both 700 individuals living in the vicinity of the Roopkund site and 22,000 individuals from across India, suggests that the 8th century Roopkund population comprised two groups of genetically distinct individuals. The majority showed genetic affinity with present day European and Middle Eastern populations, while the others displayed common haplogroups with the Austro-Asiatic population of the North Indian Himalayas. Finally, genetic continuity was observed in the area, with the present day inhabitants of the Indian Himalayas showing genetic closeness to the ancient Roopkund population. To conclude, this is the first ancient DNA study of a North Indian population; we find evidence of admixture between a putative Indo-Aryan migrating population and an older Austro-Asiatic population in India
Source: Rai et al., Archeogenetics of Roopkund deads, Young Investigators' Meeting 2015 poster presentation

Wednesday, August 19, 2015

No significant genetic substructures within (eastern) Yamnaya

It's interesting and perhaps important that there's practically no difference between the two sets of Yamnaya samples published to date, despite the fact that they're from regions separated by ~1,000 kilometers. Yamnaya_Rise is from between the Black and Caspian seas, while Yamnaya_Haak from just north of the Caspian.

Note the lack of significant Z scores (around 3 or more) in these D-stats. Although the almost significant Z score with Loschbour, a Mesolithic Western Hunter-Gatherer (WHG) from Luxembourg, does look somewhat curious.

It's difficult to know what all of this means exactly without seeing any ancient samples from archaeological cultures that preceded Yamnaya on the Pontic-Caspian Steppe. However, it could mean that the Yamnaya nomads arrived north of the Caspian from the south, which is also what preliminary Y-chromosome data is hinting at (see here).

Yamnaya was succeeded northeast of the Caspian by its offshoot, the Poltavka Culture, which in turn was replaced by the Sintashta Culture. The most widely accepted theory, based on archaeological data, is that Sintashta formed from a chain of cultures derived from the late Corded Ware horizon of East-Central Europe. This is backed up by the D-stats below, which suggest some western admixture in Sintashta that is missing in Yamnaya.

The samples used in this analysis are from the Allentoft et al. (Rise Project), Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.