Basques are not simply a fusion of Iberian hunter-gatherers and early farmers

I thought I'd revisit the issue of Basque origins with my new Principal Component Analysis (PCA) of West Eurasian genetic variation. The useful thing about this PCA is that it gets around two problems that routinely affect PCA featuring ancient samples: projection bias, otherwise known as shrinkage, and exaggerated outcomes for individuals with high counts of homozygous genotypes.

A couple of recent papers argued that Basques were the direct descendants of local hunter-gatherers and early Neolithic farmers who arrived in Iberia from the eastern Mediterranean. This is probably correct for the most part, but it doesn't tell the whole story.

On the PCA above, Basques are quite distinct from Early Neolithic, Middle Neolithic and Copper Age Iberians (marked Iberia_EN, Iberia_MN and Iberia_CA, respectively), because they are significantly more eastern. In fact, they cluster with the only Bronze Age Iberian on the plot (Iberia_BA), which is the same individual that I found to harbor steppe-related ancestry (see here).

Thus, the story told by the PCA is that Basques are the progeny of Bronze Age Iberians, who, unlike their Copper Age predecessors, experienced a pulse of steppe-related admixture from the east.

Formal statistics back this up. For instance, here's a quote from the recently revised Mathieson et al. preprint:

However, the statistic f4(Basque, Iberia_Chalcolithic; Yamnaya_Samara,Chimp)=0.00168 is significantly positive (Z=8.1), as is the statistic f4(Spanish, Iberia_Chalcolithic; Yamnaya_Samara, Chimp)= 0.00092 (Z=4.6). This indicates that steppe ancestry occurs in present-day southwestern European populations, and that even the Basques cannot be considered as mixtures of early farmers and hunter-gatherers without it (4).

The key question now is who brought the steppe-related ancestry to Basque country. Were they Indo-Europeans or speakers of Proto-Basque? Also, did they actually come from the steppe, or somewhere nearby, like the Carpathian Basin?

The reason I mention the Carpathian Basin is because, as per the PCA, Basques more or less cluster between Copper Age Iberians and some of the Bronze Age Hungarians (marked Hungary_BA). But this is just one possibility, and I'm not sure at this stage how plausible it looks with, say, formal statistics.

In this analysis I used samples from the Allentoft et al., Gunther 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. If you're confused by some of the acronyms in the PCA key, see here.

New PCA format

From now on, every time a new dataset of ancient West Eurasian samples is made available online, I'll run it in a Principal Component Analysis (PCA) like this:

Please note that the plots above include the majority of recently published ancient samples, and yet they are not affected by projection bias, otherwise known as shrinkage. If you're confused by some of the acronyms in the PCA key, see here.

See also...

Basques are not simply a fusion of Iberian hunter-gatherers and early farmers

Uralian genes

Below is a graph based on a couple of D-statistics. Note that out of the five Uralic-speaking groups, only Hungarians remain under the upward-sloping red line, clustering among Indo-European-speakers. On the other hand, the Indo-European-speaking Russians from Kargopol cluster with Uralic speakers. However, Russia is a complex affair in this context, because much of the north and east of European Russia was Uralic-speaking until very recently. The relevant D-stats are available here.

See also...

Ancient genomes from NE Europe suggest the tandem spread of Siberian admixture and Uralic languages into the region >3,500 ya

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.

In this analysis I used samples 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...

No significant genetic substructures within (eastern) Yamnaya

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 artefact 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.

See also...

The Poltavka outlier

The mystery of the Sintashta people

The real thing

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.

In this analysis I used samples 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.

Update 12/09/2015: Matt posted these graphs in the comments. The first graph shows Yamnaya-related ancestry proportions for a series of points along the Yamnaya-Middle Neolithic continuum, which can be used to estimate Yamnaya-related admixture in samples that cluster near these points.

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 this. One of the main factors, I'd say, is that languages can be learned or imposed very quickly, and this happened often 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.

In this analysis I used samples 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

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.

In this analysis I used samples 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.

See also...

A multidimensional approach

D(Outgroup, PopTest) (Pop1, Pop2)

I ran these tests using 65-112K transversion sites, so the results should be very solid. The spreadsheet is here. My impression is that MA1-related (ANE?) ancestry was present in South Central Asia before R1a-Z93 steppe people moved into the area during the Bronze Age. Any thoughts?

All of the samples are from the recent Allentoft et al. and Haak et al. papers, available on request from the authors and here, respectively.

Kets are rich in Ancient North Eurasian (ANE) ancestry

There's an interesting and very thorough preprint at bioRxiv looking at the genomic structure of Kets, the last nomadic hunter-gatherers of Siberia. From the paper:

Based on all analyses, we can tentatively model Kets as a two-way mixture of East Asians and ANE. Therefore, ANE ancestry in Kets can be estimated using various f4-ratios from 27% to 62% (depending on the dataset and reference populations), vs. 2% in Nganasans, 30 ‒ 39% in Karitiana, and 23 ‒ 28% in Mayans (Suppl. file S7, see details in Suppl. Information Section 8). Integrating data by different methods, we conservatively estimate that Kets have the highest degree of ANE ancestry among all investigated modern Eurasian populations west of Chukotka and Kamchatka. We speculate that ANE ancestry in Kets was acquired in the Altai region, where the Bronze Age Okunevo culture was located, with a surprisingly close genetic proximity to Mal'ta. Later, Yeniseian-speaking people occupied this region until the 16th-18th centuries. We suggest that Mal'ta ancestry was later introduced into Uralic-speaking Selkups, starting to mix with Kets extensively in the 17-18th centuries.

I'd say these findings make a lot of sense. Below is a spatial map put together by Sergey, based on my K8 model, showing the distribution of ANE across much of Eurasia. Note the ANE peak of around 28% among the Kets.

Citation...

Flegontov et al., Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry, bioRxiv, Posted August 13, 2015, doi: https://dx.doi.org/10.1101/024554