The Khvalynsk men

This is where the three Samara Eneolithic or Khvalynsk samples from the recent Mathieson et al. paper plot on my Principal Component Analysis (PCA) of ancient West Eurasia. They're labeled as Steppe_CA (steppe Copper Age). I've also marked them with their Y-chromosome haplogroups.

Individual 10433, belonging to Y-chromosome haplogroup R1a, is almost a pure Eastern European Hunter-Gatherer, which is perhaps surprising, considering he was buried with copper artifacts. On the other hand, sample 10434, the one belonging to haplogroup Q1a, and positioned further east than the other two, appears to have been whacked over the head a few times and simply thrown into a ditch.

The PCA also has most of the other samples featured in Mathieson et al., including Neolithic Anatolians (labeled Anatolia_N), as well as extra samples from Allentoft et al. and Jones et al.

See also...

The Khvalynsk men #2

CHG and the Indo-European question

The recent Jones et al. palaeogenomics paper focusing on Caucasus hunter-gatherers (CHG) has this to say about the Indo-European and Indo-Aryan expansions:

CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

...

It has been proposed that modern Indians are a mixture of two ancestral components, an Ancestral North Indian component related to modern West Eurasians and an Ancestral South Indian component related more distantly to the Onge [25]; here Kotias proves the majority best surrogate for the former [28,29] (Supplementary Table 10). It is estimated that this admixture in the ancestors of Indian populations occurred relatively recently, 1,900–4,200 years BP, and is possibly linked with migrations introducing Indo-European languages and Vedic religion to the region (28).

...

Finally, we found that CHG ancestry was also carried east to become a major contributor to the Ancestral North Indian component found in the Indian subcontinent. Exactly when the eastwards movement occurred is unknown, but it likely included migration around the same time as their contribution to the western European gene pool and may be linked with the spread of Indo-European languages. However, earlier movements associated with other developments such as that of cereal farming and herding are also plausible.

To their credit, in that last quote the authors leave open the possibility that CHG arrived in South Asia in multiple waves and with a variety of groups, including Neolithic farmers. Nevertheless, I'd say their comments are still confusing and perhaps also incredibly naive, because essentially they appear to be hoping that in CHG they've identified the Proto-Indo-European and Proto-Indo-Aryan genetic component.

Indeed, a lot of people actually believe that the overwhelming part of the West Eurasian admixture in South Asia should be attributed to the Indo-Aryans. But that's just stupid.

After all, many Dravidian groups that in all likelihood never spoke Indo-Aryan languages carry significant ratios of West Eurasian ancestry. Some of this influence can be explained by admixture with Indo-Aryans, but uniparental markers suggest that much of it was brought from West Asia by the Proto-Dravidians (see here).

Below is the aforementioned Supplementary Table 10. Note that two of the Indian populations that are best modeled with D-stats as mixtures of Kotias (one of the two CHG genomes) and Onge are Dravidian speakers (Mala and Vishwabrahmin or Viskwakarma, a Malayali community). Another three are Indo-Aryans (GujaratiC, GujaratiD and Lodhi), but with high levels of Ancestral South Indian (ASI) admixture, which suggests their ancestors might have been language shifters.

On the other hand, the three populations that are best modeled as Afanasievo (a pastoralist group from the Early Bronze Age steppe) and Onge are all Indo-Aryans (GujaratiA, GujaratiB and Tiwari).

But like I say, South Asia is a complex melting pot of Indo-Aryans, Dravidians, and several other linguistic groups, so a more comprehensive analysis than a comparison of a few D-stats is needed to unravel the origins of its people in a meaningful way.

By the way, Jones et al. also argue that CHG is basically an offshoot of the so called Basal Eurasian clade, which was first described in Lazaridis et al. 2014. I'm highly skeptical of this claim, and I might check it out after I get my hands on the CHG genomes.

Citation...

Jones, E. R. et al. Upper palaeolithic genomes reveal deep roots of modern eurasians. Nat. Commun. 6:8912 doi: 10.1038/ncomms9912 (2015).

See also...

The "fourth strand" of European ancestry came from the Caucasus

The "fourth strand" of European ancestry came from the Caucasus

From a news feature about a forthcoming palaeogenomics paper:

"The question of where the Yamnaya come from has been something of a mystery up to now," said one of the lead senior authors Dr Andrea Manica, from Cambridge's Department of Zoology.

"We can now answer that as we've found that their genetic make-up is a mix of Eastern European hunter-gatherers and a population from this pocket of Caucasus hunter-gatherers who weathered much of the last Ice Age in apparent isolation. This Caucasus pocket is the fourth major strand of ancient European ancestry, one that we were unaware of until now," he said

Read more at: 'Fourth strand' of European ancestry originated with hunter-gatherers isolated by Ice Age

Update: the paper is now out and open access at Nature Communications.

The two ancient Georgian genomes belong to Y-chromosome haplogroup J. So it looks like I was right when I said that this type of ancestry mostly entered the European steppe from the Caucasus via female mediated gene flow during the Bronze Age (see here and here).

However, one of the Eastern European Hunter-Gatherers (EHG) from Mathieson et al. 2015 also belonged to haplogroup J. This suggests that there was intermittent gene flow, including some paternal gene flow, between the Caucasus and the steppe well before the Bronze Age.

Nevertheless, it's now even more difficult to accept that Y-haplogroup R1 and the Proto-Indo-Europeans might have originated south of the steppe. Clearly, R1 appears to be a steppe marker from way back, and I seriously doubt that Indo-European languages were introduced into highly patriarchal steppe societies by female migrants from the Caucasus.

Image credit: Nature Communications, dx.doi.org/10.1038/ncomms9912

Mitochondrial DNA from Maykop + Wolfgang Haak on Near Eastern-related ancestry in Yamnaya

From page 166 of a report posted recently at Academia.edu:

Majkop verfügen sowohl über eine «paläolithische» Haplogruppe (U8) als auch über «neolithische» Haplogruppen: V (Недолужко u. a. 2014), T2, N1. Bei einem Objekt aus einem Grab bei der Staniza Novosvobodnaja fanden wir auch die Haplogruppe М52. Die gewonnenen Daten sprechen für eine (auf dem Niveau der mitochondrialen DNA) mögliche genetische Gemeinschaft der archäologischen Kulturen von Majkop und Novosvobodnaja.

The presence of Indian-specific mtDNA haplogroup M52 is surprising. Maykop territory was located just south of the steppe, but M52 isn't found in any of the Bronze and Iron Age samples from the steppe tested to date.

Here's the comment from Haak, from an abstract titled The role of the Caucasus in the formation of the Eurasia's genetic makeup: Insights and questions from ancient DNA research.

Recent genetic research on autosomal and uniparentally-inherited markers has shown a remarkable genetic uniformity of Caucasian populations despite the region’s notable linguistic and cultural diversity. When compared to neighbouring regions, the smooth genetic transition from the Near/Middle East to the Caucasus is in stark contrast to the marked differences to populations from the East European steppes. Flanked by the Black and the Caspian Seas, it remains unclear to what extent the Caucasus served as a corridor and whether and if so when ancient migrations had affected and shaped the region’s genetic profile. Ancient DNA research on Mesolithic, Neolithic and Bronze Age individuals from Western Eurasia have recently thrown fresh light on the Caucasus as region, which appears to have played a critical role in the formation of the genetic ancestry of the Yamnaya people, Bronze Age pastoralist of the east European steppes. The Yamnaya carry strong signals of eastern hunter-gatherer (EHG) ancestry and ancient Near Eastern ancestry that is different from the one that giving rise to early European farmers. While modern-day Armenians are the best proxy for the putative source population of the EHG dilution in the steppes, it is highly likely that prehistoric cultural groups from the Caucasus will provide a much better temporal and contextual fit.

Actually, I'd say western Georgians are the best proxy for the putative source population of the EHG dilution in the steppes. See here...

Yamnaya's exotic ancestry: The Kartvelian connection

See also...

Steppe Maykop: a buffer zone?

Genetic borders are usually linguistic borders too

On the genetic prehistory of the Greater Caucasus (Wang et al. 2018 preprint)

Plague germs may have facilitated Bronze Age expansions from the steppe

Update 07/12/2018: Europe's ancient proto-cities may have been ravaged by the plague

...

Open access at Cell:

Summary: The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

Rasmussen et al., Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago, Cell, Volume 163, Issue 3, p571–582, 22 October 2015, DOI: https://dx.doi.org/10.1016/j.cell.2015.10.009

Also, some juicy quotes at ScienceDaily:

Study co-author Dr Marta Mirazón-Lahr, from Cambridge's Leverhulme Centre for Human Evolutionary Studies (LCHES), points out that a study earlier this year from Willerslev's Copenhagen group showed the Bronze Age to be a highly active migratory period, which could have led to the spread of pneumonic plague.

"The Bronze Age was a period of major metal weapon production, and it is thought increased warfare, which is compatible with emerging evidence of large population movements at the time. If pneumonic plague was carried as part of these migrations, it would have had devastating effects on small groups they encountered," she said.

"Well-documented cases have shown the pneumonic plague's chain of infection can go from a single hunter or herder to ravaging an entire community in two to three days."

University of Cambridge. "Plague in humans 'twice as old' but didn't begin as flea-borne, ancient DNA reveals." ScienceDaily, 22 October 2015. www.sciencedaily.com/releases/2015/10/151022124532.htm.

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

Eight thousand years of natural selection in Europe - take 2

Open access at bioRxiv [LINK]. Lots of new samples in this updated version. The Principal Component Analysis (PCA) below from the paper appears to be affected by projection bias or shrinkage, but it's more or less correct. Can't wait to get my hands on the genotype data.

Abstract: The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

Mathieson et al., Eight thousand years of natural selection in Europe, bioRxiv revised preprint, posted October 10, 2015, doi: https://dx.doi.org/10.1101/016477

See also...

Lactase persistence and ancient DNA

Yamnaya's exotic ancestry: The Kartvelian connection

I've made a discovery. The Near Eastern-related ancestors of the Yamnaya steppe pastoralists were also the ancestors of present-day Georgian Mingrelians, or their very close relatives, and in all likelihood speakers of Kartvelian, which has a long history in the Caucasus. Here's a nice map from Wikipedia and a pic of some Mingrelians. Check out the impressive headware.

TreeMix is very specific and precise about this. In my analyses, based on a couple of different methods, the Mingrelians are the only population chosen as a source for the Near Eastern-related ancestry in the Yamnaya.

Keep in mind, this is an unsupervised test and the algorithm has an infinite number of choices, because migration edges can run from any part of the tree, and yet it chooses the Mingrelians. By the way, if anyone's wondering, I did also try the Bronze Age Armenians, to no avail.

This outcome is also more or less reproducible with more complex topologies that include samples from Central Asia. In the graph below the Georgian Mingrelians form a clade with the Near Eastern-related ancestry of the Yamnaya. It'd be interesting to see if other Georgian groups, like the Svans, do even better, if that's actually possible, but they're not available at the moment.

I actually came up with basically the same result earlier this year using qpAdm (see here). But at the time I was skeptical of its usefulness because qpAdm only offers a supervised test, so picking Georgians as a reference population and getting a good statistical fit doesn't mean as much as a reproducible unsupervised migration edge.

Now, judging by their ADMIXTURE results, these Georgian Mingrelians do carry some Early European farmer-related ancestry, which is missing in the Yamnaya (see here). Therefore, it's likely that ancient samples from the west or northwest Caucasus will prove to be even better proxies for the Near Eastern-related ancestry in the Yamnaya.

The samples used to produce the above TreeMix graphs are listed here. They're sourced from the Allentoft et al., Haak et al., and Lazaridis et al. datasets. I limited the markers to ~65K transversion (high confidence) SNPs that overlap between these datasets.

Updates...

Caucasus hunter-gatherers (CHG) and the Indo-European question

'Fourth strand' of European ancestry originated with (Caucasus) hunter-gatherers isolated by Ice Age

Mixed marriages on the early Eneolithic steppe

Linguistics, Archeology and Genetics (L-A-G) Conference abstracts

The Max Planck Institute is holding a conference in a few days dedicated to the latest developments in the search for the Indo-European homeland.

Linguistics, Archeology and Genetics: Integrating new evidence for the origin and spread of Indo-European languages

A draft book of presentation abstracts is available here. This one from Danish linguist Guus Kroonen looks very promising.

Pre-Indo-European speech carrying a Neolithic signature emanating from the Aegean

Guus Kroonen, Institute for Nordic Studies and Linguistics, Copenhagen University, Copenhagen

When different Indo-European speaking groups settled Europe, they did not arrive in terra nullius. Both from the perspective of the Anatolian hypothesis and the Steppe hypothesis the carriers of Indo-European speech likely encountered existing populations that spoke dissimilar, unrelated languages. Relatively little is known about the Pre-Indo-European linguistic landscape of Europe, as the Indo-Europeanization of the continent caused a largely unrecorded, massive linguistic extinction event. However, when the different Indo-European groups entered Europe, they incorporated lexical material from Europe’s original languages into their own vocabularies. By integrating these “natural samples” of Pre-Indo-European speech, the original European linguistic and cultural landscape can partly be reconstructed and matched against the Anatolia and the Steppe hypotheses. My results reveal that Pre-Indo-European speech contains a clear Neolithic signature emanating from the Aegean, and thus patterns with the prehistoric migration of Europe’s first farming populations. These results also imply that Indo-European speech came to Europe following a later migration wave, and therefore favor the Steppe Hypothesis as a likely scenario for the spread of the Proto-Indo-Europeans.

Also, we've known for a while now that the good people at Broad MIT/Harvard have analyzed remains from Neolithic Anatolia, but it's nice to see this framed in the context of the Indo-European homeland debate.

Close genetic relationship of Neolithic Anatolians to early European farmers

Iosif Lazaridis et al.

We study 1.2 million genome-wide single nucleotide polymorphisms on a sample of 26 Neolithic individuals (~6,300 years BCE) from northwestern Anatolia. Our analysis reveals a homogeneous population that was genetically similar to early farmers from Europe (FST=0.004±0.0003 and frequency of 60% of Y-chromosome haplogroup G2a). We model Early Neolithic farmers from central Europe and Iberia as a genetic mixture of ~90% Anatolians and ~10% European hunter-gatherers, suggesting little influence by Mesolithic Europeans prior to the dispersal of European farmers into the interior of the continent. Neolithic Anatolians differ from all present-day populations of western Asia, suggesting genetic changes have occurred in parts of this region since the Neolithic period. We suggest that the language spoken by the homogeneous Anatolian-European Neolithic farmers is unlikely to have been the same as that spoken by the Yamnaya steppe pastoralists whose ancestry was derived from eastern Europe and a different population from the Caucasus/Near East [Haak et al. 2015], and discuss implications for alternative models of Indo-European dispersals.

Indeed, my view is that the implications of this data for the Anatolian hypothesis are fatal (see here). It might also have dire implications for the Armenian Plateau hypothesis, although for the time being this hypothesis limps on.

Feel free to post and discuss your favorite abstracts in the comments below. If anyone reading is going to this thing, I'd love to hear more about the Y-haplogroups of the Anatolian farmers.