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Tuesday, December 11, 2018

How did Y-haplogroup N1c get to Bolshoy Oleni Ostrov?


Y-haplogroup N1c probably entered Europe from Siberia during the Bronze Age or a little earlier. It first appears in the European ancient DNA record in two samples from a burial site at Bolshoy Oleni Ostrov, in the Kola Peninsula, dated to 1523±87 calBCE (see here). These individuals also harbor significant genome-wide Siberian ancestry, but it's possible that this is in large part a coincidence, and that N1c spread into the Kola Peninsula from the south in a population of overwhelmingly European ancestry.

Crazy, huh? Not really. Consider the qpAdm mixture models below for BOO002 and BOO004, the two males from the Bolshoy Oleni Ostrov site belonging to N1c, and BOO006, a female and the most Siberian-admixed individual from the same site. Although BOO002 and BOO004 show a lot of Nganasan-related and thus Siberian ancestry, they also require significant input from a source closely related to Baltic_BA, a fully European Bronze Age population from the East Baltic region. On the other hand, BOO006 doesn't need Baltic_BA for a successful model.

BOO002_&_BOO004
Baltic_BA 0.124±0.029
EHG 0.406±0.032
Nganasan 0.469±0.017
chisq 10.847
tail prob 0.286316
Full output

BOO006
Baltic_BA 0.065±0.043
EHG 0.265±0.084
Nganasan 0.517±0.033
West_Siberia_N 0.152±0.074
chisq 8.847
tail prob 0.355397
Full output

BOO006
EHG 0.367±0.049
Nganasan 0.544±0.031
West_Siberia_N 0.089±0.063
chisq 9.878
tail prob 0.360451
Full output

Keep in mind that N1c is very common in the East Baltic today in populations with minimal Siberian genome-wide ancestry. Indeed, Latvians and Lithuanians can often be modeled with no Siberian input. Thus, it's likely that by the time N1c arrived in the East Baltic, probably during the late Bronze Age or early Iron Age, it did so with populations with heavily diluted Siberian genome-wide ancestry. Such groups may also have taken N1c north of the Baltic and into the Kola Peninsula.

See also...

On the trail of the Proto-Uralic speakers (work in progress)

Thursday, December 6, 2018

Europe's ancient proto-cities may have been ravaged by the plague


The Cucuteni-Trypillia culture of the Eneolithic Balkans and Eastern Europe is best known for its mega-settlements or proto-cities, each one featuring hundreds of homes, temples and other structures, and likely to have been inhabited by as many as 20,000 people. But from around 3,400 BC these mega-settlements were no longer being built, and a few hundred years later the Cucuteni-Trypillia culture vanished.

Two main explanations have been given for its rather swift demise: violent invasions by steppe pastoralists from the east and/or a massive out-migration by its people as a result of environmental impacts from rapid climate change (see here). However, these theories have failed to gain wide acceptance due to a lack of hard evidence in their support.

Now, another potential explanation is being offered, and it is supported by hard evidence. According to Rascovan et al., the plague may have been a key factor in the decline of not only the Cucuteni-Trypillia culture, but much of Neolithic Europe (see here). From the paper, emphasis is mine...

Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

...

In this work, we report the discovery of plague infecting Neolithic farmers in Scandinavia, which not only pre-dates all known cases of plague, but is also basal to all known modern and ancient strains of Y. pestis. We identified a remarkable overlap between the estimated radiation times of early lineages of Y. pestis, toward Europe and the Eurasian Steppe, and the collapse of Trypillia mega-settlements in the Balkans/Eastern Europe.


Citation...

Rascovan et al., Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline, Cell (2019), https://doi.org/10.1016/j.cell.2018.11.005

See also...

Migration of the Bell Beakers—but not from Iberia (Olalde et al. 2018)

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

"The Homeland: In the footprints of the early Indo-Europeans" time map

Monday, December 3, 2018

On the trail of the Proto-Uralic speakers (work in progress)


Historical linguists have long posited that Fennoscandia was a busy contact zone between early Germanic and Uralic languages. The first ancient DNA samples from what is now Finland have corroborated their inferences, by showing that during the Iron Age the western part of the country was inhabited by a genetically heterogeneous population closely related to both the Uralic-speaking Saami and Germanic-speaking southern Scandinavians.

The samples were sequenced and analyzed by two different teams of researches, and their findings published recently in Lamnidis et al. and Sikora et al. (see here and here, respectively).

This is how most of these ancients, whose remains were excavated from the Levanluhta burial site dated to 300–800 CE, behave in a Principal Component Analysis (PCA) based on my Global25 data. Levanluhta_IA are the Saami-related samples, while Levanluhta_IA_o is an Scandinavian-like outlier. Baltic_IA is an Iron Age individual from what is now Lithuania from the recent Damgaard et al. paper (see here). Note the accuracy of the Global25 data in pinpointing their genetic affinities and also the trajectory of the Levanluhta_IA cluster, which seems to be "pulling" towards Levanluhta_IA_o.



The Saami and Levanluhta_IA are clear outliers from the main Northern European cluster. There are two reasons for this: excess East Asian/Siberian-related ancestry and Saami-specific genetic drift. However, this eastern admixture and genetic drift are shared in varying degrees by other North European populations, especially those that also speak Uralic languages, and this is why they appear to be "pulling" towards the Saami/Levanluhta_IA clusters in my PCA. Thus, what this suggests is that the expansion of Uralic languages across Northeastern Europe was intimately linked with the spread of Siberian-related ancestry into the region.

This idea has been around for a long time and is now becoming even more widely accepted (see here). However, Lamnidis et al. also featured samples from a likely pre-Uralic (1523±87 calBCE) burial site at Bolshoy Oleni Ostrov in the Kola Peninsula, present-day northern Russia, and, perhaps surprisingly, found that they showed even more Siberian-related ancestry than Levanluhta_IA. So what's going on?

I'm confident that this discrepancy can be explained by multiple waves of migrations from the east into Northeastern Europe, possibly before, during and after the time of the people buried at Bolshoy Oleni Ostrov, by pre-Uralic, para-Uralic and/or Proto-Uralic-speaking populations.

Consider the following qpAdm output, in which Levanluhta_IA is just barely modeled successfully as a two-way mixture between Levanluhta_IA_o and Bolshoy_Oleni_Ostrov. The statistical fit improves significantly with the addition of Glazkovo_EBA as a third mixture source. This is an ancient population from near Lake Baikal dated to 4597-3726 BC from the aforementioned Damgaard et al. paper.

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.468±0.036
Levanluhta_IA_o 0.532±0.036
chisq 19.129
tail prob 0.0854706
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.241±0.092
Glazkovo_EBA 0.162±0.059
Levanluhta_IA_o 0.597±0.046
chisq 7.756
tail prob 0.734966
Full output

For the sake of being complete, I also tested whether Levanluhta_IA_o could be substituted by other similar ancient samples from the neighborhood, including those associated with the Battle-Axe and Corded Ware cultures. There's not much to report; qpAdm returned poor statistical fits and/or implausible ancestry proportions (for the full output from my runs, see here). Baltic_IA did produce a statistically sound model, but with excess Glazkovo_EBA-related ancestry. I also had to drop Bolshoy_Oleni_Ostrov from the analysis to make things work, which suggests to me that the result shouldn't be taken too literally.

Levanluhta_IA
Baltic_IA 0.677±0.034
Glazkovo_EBA 0.323±0.034
chisq 8.547
tail prob 0.741095
Full output

So as far as I can see, the western ancestry in Levanluhta_IA is likely to be mostly of Germanic origin, and thus Indo-European, meaning that it's logical to look east, perhaps far to the east, for the source of its Uralic ancestry. This might seem like a complicated and uncertain task, considering that Levanluhta_IA could well be at least a thousand years younger than the first entry of Uralic speakers into Fennoscandia. However, take a look what happens when I substitute Glazkovo_EBA with a variety of Uralic-speaking populations from around the Ural Mountains, which is where the Proto-Uralic homeland is generally considered to have been located.

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.210±0.091
Khanty 0.283±0.090
Levanluhta_IA_o 0.507±0.035
chisq 7.007
tail prob 0.798532
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.193±0.098
Levanluhta_IA_o 0.495±0.035
Mansi 0.312±0.100
chisq 7.884
tail prob 0.7237
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.300±0.065
Levanluhta_IA_o 0.337±0.072
Mari 0.363±0.121
chisq 8.393
tail prob 0.677705
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.238±0.084
Levanluhta_IA_o 0.553±0.036
Nenets 0.209±0.067
chisq 7.210
tail prob 0.78181
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.302±0.069
Levanluhta_IA_o 0.324±0.081
Udmurt 0.373±0.135
chisq 9.195
tail prob 0.60393
Full output

All of these models look great, and easily rival the best model with Glazkovo_EBA. Moreover, they make good sense in terms of linguistics. The only problem is that they're anachronistic, because the Uralic-speaking reference populations are younger than Levanluhta_IA. So I can't be certain that they reflect reality without corroboration from ancient DNA. It might turn out, for instance, that an Glazkovo_EBA-like population was already present somewhere deep in Europe before or during the time of Bolshoy_Oleni_Ostrov, while no such population existed around the Ural Mountains until the time of Levanluhta_IA.

By the way, it might be important to note that the present-day Finnish samples in my dataset can't be modeled as a mixture between Levanluhta_IA and Levanluhta_IA_o. But they can be modeled as a mixture between Baltic_IA and Levanluhta_IA. I don't know which part of Finland they're from exactly; probably all over the place, so it'd be useful to test regional Finnish populations to see how they behave in such models. Of course, Finns aren't Saamic speakers, they're Finnic speakers, and they're probably the result of a more recent Uralic expansion into Fennoscandia than the one that gave rise to the Saami.

Finnish
Baltic_IA 0.671±0.076
Levanluhta_IA 0.329±0.076
chisq 14.114
tail prob 0.293508
Full output

Damgaard et al. didn't report the Y-haplogroup for Baltic_IA, but the word round the campfire is that this individual belonged to N1c, which is today the most common Y-haplogroup among Uralic speakers. Obviously, we need a lot more ancient DNA to sort all of this out, but things are already looking pretty much as expected. Stay tuned for new posts in this series following the publication of more ancient DNA relevant to this fascinating topic.

See also...

The Uralic cline in the Global25

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Genetic and linguistic structure across space and time in Northern Europe

Saturday, December 1, 2018

How should we interpret the movements of people throughout Bronze Age Europe?


Below are a couple of interesting talk abstracts from the upcoming Genes, Isotopes and Artefacts conference in Vienna (see here). The first one looks like the abstract from a rewritten version of the Wang et al. preprint on the genetic prehistory of the Greater Caucasus. But I could be wrong. In any case, check out the links at the bottom of the post to see what I've said about this manuscript. Admittedly I've said a lot, maybe too much. Feel free to speculate to your heart's content in the comments about what these abstracts "really" mean, but try to keep it real. Emphasis is mine:

At the interface of culture and biology – First results from a paleogenetic transect through Bronze Age populations of the Caucasus

Svend Hansen, Sabine Reinhold, Wolfgang Haak, Chuan-Chao Wang

The Caucasus is one of the most important geographical joints in Western Eurasia. Linking Europe, Western Asia and the Eurasian steppe zone, this region today is one of the genetically and linguistically most diverse spots of Eurasia. It is easy to imagine that repeated population influx and drain, but similarly compartmentalisation in the remote mountain valley is behind this modern situation. Eneolithic and Bronze Age populations play an important role in this scenario, as they represent the first epochs of formations, which can be regarded either as associated ‘cultures’ and/or coherent biological populations. A first study on the paleogenetic background of 50 individuals from the 5th to the 2nd millennium BC, which represent all cultural formations of Bronze Age Caucasia, give a first insight into highly complex scenarios of interaction. The paleogenetic perspective could proof the presence of populations with different genetic-make ups and different biological vectors of formation among these individuals. Affiliation by material cultural and other archaeological attributes, however, revealed epochs of interaction, where cultural and biological borders were crossed, and those, where no population exchange seemed to have happened among the neighbouring inhabitants of one area. This region thus allows to study in detail the mixing and interdigitation of people, their materiality and cultural systems and challenge many of the too simple models developed for another interface of the Eurasian steppe zone those directed towards Europe.

...

Steppe and Iranian ancestry among Bronze Age Central and Western Mediterranean populations

Ron Pinhasi, Daniel Fernandes, David Reich

Steppe-related ancestry is known to have reached central Europe ca. 3000 BCE, while Iran-related ancestry reached Greece by 1500 BCE. However, the time course and extent of their spread into the central/western Mediterranean remains a mystery. We analysed 48 Neolithic and Bronze Age individuals from Sicily, Sardinia and the Balearic Islands aiming to investigate when and how continental European and Aegean influences affected these insular populations. Results show that the first Balearic settlers had substantial Steppe-related ancestry which was subsequently diluted by increasing proportions of farmer-related ancestry. In Sardinia, we identified the appearance of Iran-related ancestry from the Aegean as early as the Middle Bronze Age, with no genetic influences seen from populations carrying Steppe-related ancestry despite cultural or commercial exchanges with Bell Beaker populations. In Sicily, during the Early Bronze Age, and possibly earlier, we found evidence for admixture with groups carrying both these ancestries. These results suggest that Steppe-related migrants had a crucial role in the settlement of the Balearic Islands and their ancestry reached as far south as Sicily, and that the population movements that brought Iran-related ancestry to the Aegean also impacted the Western Mediterranean around the same time the first civilizations started to develop.

See also...

Yamnaya: home-grown

Big deal of 2018: Yamnaya not related to Maykop

Steppe Maykop: a buffer zone?

Ahead of the pack

Genetic borders are usually linguistic borders too

Yamnaya isn't from Iran just like R1a isn't from India

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

Thursday, November 29, 2018

The Uralic cline in the Global25


The Uralic cline is a concept that was discussed in some detail in the recent Lamnidis et al. palaeogenomics paper on the origin and spread of Siberian ancestry in Europe (see here). It pertains to the most northerly genetic cline that links the populations of West and East Eurasia, and is largely made up of Uralic-speaking peoples rich in Y-haplogroup N1c.

This is what the Uralic cline looks like when inferred from my Global25 Principal Component Analysis (PCA) data. Note that the plot features most of the Lamnidis et al. ancient samples, and they're all more or less sitting along my version of the said cline. The relevant datasheet is available here.

Admittedly though, as pointed out by Lamnidis et al., the Bolshoy samples probably aren't those of Uralic speakers because they're dated to 1523±87 calBCE, which predates most linguistic estimates of the spread of known Uralic languages into the Kola Peninsula. So the important question is why do they cluster along the Uralic cline and 2/2 of the male samples belong to N1c?

The most logical explanation, I'd say, is that the Uralic cline actually represents an older, pre-Uralic contact zone between the east and west. Nevertheless, I think it's likely that the Proto-Uralic language formed somewhere in this ancient contact zone, and the early Uralic-speaking peoples used it to their advantage to spread rapidly both east and west, especially during the Late Bronze/Early Iron Age, when they, and their N1c, finally reached the East Baltic region (see here).

See also...

Corded Ware people =/= Proto-Uralics (Tambets et al. 2018)

The mystery of the Sintashta people

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Monday, November 26, 2018

Steppe ancestry in Chalcolithic Transcaucasia (aka Armenia_ChL explained)


In 2016 Lazaridis et al. published a paper featuring five ancient samples from the famous Areni-1 cave complex, in what is now Armenia, dated to the Chalcolithic (see here). This is how they described the ancestry of these ancients, which they labeled Armenia_ChL, in the supplementary PDF to their paper (page 94):

We do not have a pre-Chalcolithic sample from Armenia. We first model it [Armenia_ChL] as a 2-way mixture of any of WHG, EHG, CHG, Iran_N, Levant_N, Anatolia_N (Table S7.18), but we find no pair of these populations that could be ancestral to Armenia_ChL. We next model it as a 3-way mixture (Table S7.19), and determine that Armenia_ChL can be modeled as 18.3±1.5 EHG, 29.2±2.4% Iran_N, and 52.5±2.2% Anatolia_N. In the absence of a pre-Chalcolithic sample, we cannot be certain whether the Neolithic population of Armenia (which borders Anatolia from the east) was similar to that of Northwestern Anatolia and experienced gene flow from the east and north, or the reverse.

Since then, a lot of opinions have been posted in the comments at this blog and elsewhere about the possible origin and significance of Armenia_ChL. It seems to me that many people see Armenia_ChL as more or less an example of the indigenous Neolithic and Chalcolithic peoples of the South Caucasus. But some have argued that Armenia_ChL was in large part of Central Asian origin and concocted various mixture models to try and back up this rather strange claim.

To me, it was always obvious that Armenia_ChL harbored very recent admixture from the Pontic-Caspian steppe, because I couldn't reconcile its relatively high level of Eastern European Hunter-Gatherer (EHG) ancestry with a deep origin south of the Greater Caucasus range.

Moreover, in any decent Principal Component Analysis (PCA), like the one below, Armenia_ChL appears to form two subtle sub-clusters, with three of its individuals "pulling" more strongly towards Eastern Europe. This suggests that the EHG admixture in Armenia_ChL was present at variable levels and thus likely to be recent, because it didn't yet have time to diffuse evenly throughout the population.

Also, two out of the three Armenia_ChL individuals who are "pulling" north belong to steppe-specific mitochondrial (mtDNA) haplogroups. Armenia_ChL I1634 belongs to mtDNA haplogroup H2a1, which is seen in ancient samples from the Pontic-Caspian steppe associated with the Khvalynsk, Sredny Stog and Catacomb cultures, while Armenia_ChL I1409 belongs to mtDNA haplogroup U4a, which is found in numerous ancient samples, especially foragers, from the Pontic-Caspian steppe and other parts of Eastern Europe (see here). Coincidence? Surely not.


The idea that Armenia_ChL represents a long-standing indigenous Transcaucasian population also took a major hit recently with the release of the Wang et al. manuscript on the genetic prehistory of the Greater Caucasus. The preprint included samples from the Eneolithic Caucasus dated to earlier than Armenia_ChL (4594-4404 calBCE vs 4330-3985 calBCE) which looked typically Caucasian and lacked any discernible signals of ancestry from the steppe. Below is a PCA from Wang et al. featuring both the Eneolithic Caucasus and Armenia_ChL samples.


Unfortunately, modeling the recent ancestry of Armenia_ChL is still difficult, because the genotype data from Wang et al. haven't yet been released, so currently there is still no pre-Armenia_ChL sample available from the Caucasus for me to work with.

The earliest post-Armenia_ChL sample is Armenia_EBA I1658, dated to around a thousand years too late (3347-3092 calBCE). However, this individual is associated with the Kura-Araxes culture, which is generally seen as a direct successor to the native Neolithic cultures of Transcaucasia, and appears to be practically indistinguishable from the Eneolithic Caucasus trio in the Wang et al. PCA. Thus, pending the release of a pre-Armenia_ChL sample I might be able to use Armenia_EBA I1658 as an effective proxy for such a population.

Below are a couple of successful two-way qpAdm mixture models for Armenia_ChL and Armenia_ChL I1634, featuring Armenia_EBA I1658 and Sredny_Stog I6561 (the output for Armenia_ChL I1409 looked wobbly, probably due to a lack of markers). The reason I decided on Sredny_Stog from the North Pontic steppe as the surrogate for the steppe ancestry is because of the position of Armenia_ChL in the Wang et al. PCA relative to Eneolithc Caucasus, which suggests gene flow into the former from a more westerly steppe source than, say, Khvalynsk from the Samara region. Using these reference samples, the inferred ratio of steppe admixture in Armenia_ChL is around 15%, which I think makes sense, more or less, considering its position in both of the PCA above.

Armenia_ChL
Armenia_EBA_I1658 0.862±0.050
Sredny_Stog_I6561 0.138±0.050
chisq 17.038
tail prob 0.148174
Full output

Armenia_ChL_I1634
Armenia_EBA_I1658 0.836±0.065
Sredny_Stog_I6561 0.164±0.065
chisq 13.813
tail prob 0.312808
Full output

The presence of a significant, unambiguous signal of steppe ancestry in a group from a rich archeological site in Chalcolithic Transcaucasia might be very important in the context of the Proto-Indo-European (PIE) homeland debate. That's because it suggests that there was a movement of peoples potentially speaking dialects of PIE from the Eneolithic Pontic-Caspian steppe, the main candidate for the PIE homeland based on historical linguistics data, into cultural hubs south of the Caucasus, which may have acted as early dispersal points for Indo-European languages into other parts of the Near East, such as Anatolia. Admittedly, though, I'm still a fan of the Balkan route for the introduction of Hittite and other Anatolian languages into Anatolia, despite recent claims in scientific literature that this scenario wasn't corroborated by ancient DNA (see here).

Citation...

Lazaridis et al., Genomic insights into the origin of farming in the ancient Near East, Nature volume 536, pages 419–424 (25 August 2016), DOI: https://doi.org/10.1038/nature19310

See also...

Yamnaya: home-grown

Tuesday, November 20, 2018

Yamnaya: home-grown


I have some interesting news. It looks like Khvalynsk_Eneolithic I0434 can be used as essentially a perfect proxy for the Eneolithic steppe trio from Wang et al. 2018 when modeling the ancestry of the Yamnaya people of what is now the Samara region of Russia. Consider the qpAdm mixture models below, sorted by taildiff.

One of the best fitting models that also fairly closely matches archeological data, which suggest that Yamnaya was an amalgamation of the Khvalynsk, Repin and Sredny Stog cultures, is in bold. The worst fitting, and basically failed, models are listed below the dotted line. Note that almost all of these models feature reference populations from West and Central Asia.

Khvalynsk_I0434 + Iberia_ChL 0.681534184 > full output

Khvalynsk_I0434 + Globular_Amphora 0.525961242 > full output

Khvalynsk_I0434 + Iberia_Central_CA 0.515960444 > full output

Khvalynsk_I0434 + Sredny_Stog_I6561 0.485311962 > full output

Khvalynsk_I0434 + Varna 0.430411416 > full output

Khvalynsk_I0434 + Blatterhole_MN 0.328782809 > full output

Khvalynsk_I0434 + Baden_LCA 0.234307235 > full output

Khvalynsk_I0434 + Protoboleraz_LCA 0.231310724 > full output

Khvalynsk_I0434 + ALPc_MN 0.200002422 > full output

Khvalynsk_I0434 + Trypillia 0.193900977 > full output

Khvalynsk_I0434 + Balaton_Lasinja_CA 0.187031564 > full output

Khvalynsk_I0434 + Tiszapolgar_ECA 0.153940224 > full output

Khvalynsk_I0434 + Tisza_LN 0.145465993 > full output

Khvalynsk_I0434 + Balkans_ChL 0.111720163 > full output

...

Khvalynsk_I0434 + Armenia_EBA 0.0108890099 > full output

Khvalynsk_I0434 + Armenia_ChL 0.00882375703 > full output

Khvalynsk_I0434 + Levant_BA_North 0.0078751978 > full output

Khvalynsk_I0434 + Minoan_Lasithi 0.0675240088 > full output

Khvalynsk_I0434 + Peloponnese_N 0.046998906 > full output

Khvalynsk_I0434 + Hajji_Firuz_ChL 0.00269860335 > full output

Khvalynsk_I0434 + Shahr_I_Sokhta_BA1 0.00261908387 > full output

Khvalynsk_I0434 + Sarazm_Eneolithic 0.00120345503 > full output

Khvalynsk_I0434 + Seh_Gabi_ChL 0.00111898703 > full output

Khvalynsk_I0434 + Geoksiur_Eneolithic 0.000178295163 > full output

Khvalynsk_I0434 + Tepe_Hissar_ChL 0.000163698274 > full output

Khvalynsk_I0434 + Bustan_BA 0.000151088148 > full output

Why is this potentially important? Because unless Khvalynsk_Eneolithic I0434 was a recent migrant from the North Caucasus piedmont steppe, which is where the remains of the Eneolithic steppe trio were excavated, then Yamnaya's ethnogenesis might not have anything at all to do with Asia or even the Caucasus region. At least not within any reasonable time frame anyway. Here's a map showing the geographic locations of all of the populations relevant to the highlighted mixture model above.


I won't be fussed if it turns out that the majority of the ancestry of the Yamnaya, Corded Ware and other closely related ancient peoples was sourced from the Eneolithic populations of the North Caucasus piedmont steppe. But I think it's useful to make the point that there are still very few ancient samples available from the steppes between the Black and Caspian seas, so we don't yet have much of a clue how the groups living throughout this region during the Eneolithic and earlier fit into the grand scheme of things.

Update 24/12/2018: I decided to repeat the analysis, but this time with Caucasus Hunter-Gatherers (CHG) as one of the outgroups (or right pops). The reason I initially didn't include CHG in the outgroups was because I didn't want to discriminate, perhaps unfairly, against West and Central Asians with high levels of CHG-related ancestry, and in favor of Europeans with no or minimal CHG-related input. But in my opinion, the new results clearly make more sense, with Sredny Stog and Varna at the top of the list.

Khvalynsk_I0434 + Sredny_Stog_I6561 0.410719649 > full output

Khvalynsk_I0434 + Varna 0.394089365 > full output

Khvalynsk_I0434 + Iberia_ChL 0.16554258 > full output

Khvalynsk_I0434 + Globular_Amphora 0.128348823 > full output

Khvalynsk_I0434 + Iberia_Central_CA 0.126100242 > full output

Khvalynsk_I0434 + Trypillia 0.135306664 > full output

Khvalynsk_I0434 + Baden_LCA 0.0853031796 > full output

Khvalynsk_I0434 + Protoboleraz_LCA 0.0766892008 > full output

Khvalynsk_I0434 + Tisza_LN 0.0661622403 > full output

Khvalynsk_I0434 + Tiszapolgar_ECA 0.0626469042 > full output

Khvalynsk_I0434 + Balaton_Lasinja_CA 0.0536293042 > full output

Khvalynsk_I0434 + ALPc_MN 0.0505788809 > full output

...

Khvalynsk_I0434 + Minoan_Lasithi 0.0439451605 > full output

Khvalynsk_I0434 + Balkans_ChL 0.0436885241 > full output

Khvalynsk_I0434 + Blatterhole_MN 0.0329758292 > full output

Khvalynsk_I0434 + Peloponnese_N 0.0181930605 > full output

Khvalynsk_I0434 + Armenia_EBA 0.014715999 > full output

Khvalynsk_I0434 + Armenia_ChL 0.0060437014 > full output

Khvalynsk_I0434 + Levant_BA_North 0.00514574731 > full output

Khvalynsk_I0434 + Shahr_I_Sokhta_BA1 0.00350059625 > full output

Khvalynsk_I0434 + Hajji_Firuz_ChL 0.00228771991 > full output

Khvalynsk_I0434 + Seh_Gabi_ChL 0.00117061206 > full output

Khvalynsk_I0434 + Sarazm_Eneolithic 0.001118931 > full output

Khvalynsk_I0434 + Bustan_BA 0.00021203609 > full output

Khvalynsk_I0434 + Tepe_Hissar_ChL 0.000200643323 > full output

Khvalynsk_I0434 + Geoksiur_Eneolithic 0.000175941977 > full output

See also...

Big deal of 2018: Yamnaya not related to Maykop

"The Homeland: In the footprints of the early Indo-Europeans" time map

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Saturday, November 17, 2018

What happened to Maykop?


The Maykop culture was probably the result of migrations of settlers from Transcaucasia and beyond into the Northwest Caucasus during the Eneolithic and Early Bronze Age. Its peak lasted for roughly 700 years, from about 3700 BC to 3000 BC, after which it seems to have vanished suddenly. Why? Are there any decent papers on the topic?

The currently rather popular idea that Maykop gave rise to the Yamnaya culture is likely false. It was probably somehow involved in the rise of the contemporaneous Steppe Maykop culture in the steppes abutting the North Caucasus. But, thanks to ancient DNA, we now know that the people associated with this culture were distinct from those associated with Yamnaya.

In fact, when Steppe Maykop disappeared, Yamnaya spread into much of its former territory, and this turnover registers clearly in the time transect of ancient genomic data from the North Caucasus steppes (see here).

My view is that Maykop was generally an alien entity to the indigenous peoples of the steppes. These natives may have emulated it in some ways, but there's no need, I'd say, to go as far as to assume that Maykop was the vector for the spread of Indo-European languages into the Pontic-Caspian steppe.

Indeed, it seems to me that when the technological and economic advantages of Maykop over the steppe peoples eventually eroded, it couldn't hold its ground on the edge of a vastly different and perhaps largely hostile world, and quickly disappeared.

Here's a quote from a recent paper by Trifonov et al. on Maykop jewellery that I found very enlightening in regards to these issues (emphasis is mine):

These deep-rooted Near East traditions of ritualization of the production and use of jewellery pieces made of gold, silver and gemstones in the Maykop culture, on the one hand, maintained familiar canons of ritual behaviour and, on the other, made perception of sophisticated symbolism of gemstones more difficult for neighbouring cultures with different living standards, levels of social development and value systems to understand. The jewellery traditions of the Maykop culture had no successors in the Caucasus or the adjacent steppes. In the third millennium BC , the goldsmiths of Europe and Asia had to reinvent the technique of making thin-walled jointless gold beads from scratch (Born et al. 2009).

I do wonder, in fact, if the language spoken by the Maykop people was even part of a still existing language group, let alone if it belonged to the Indo-European language family.

See also...

Big deal of 2018: Yamnaya not related to Maykop

Sunday, November 11, 2018

The story of the earliest wine


Here's an interesting YouTube video about the origin and spread of wine making. Many of you might also appreciate the discussion about the Kura-Araxes Culture (about 26 minutes into the presentation)...


See also...

A potentially violent end to the Kura-Araxes Culture (Alizadeh et al. 2018)

How relevant is Arslantepe to the PIE homeland debate?

Likely Yamnaya incursion(s) into Northwestern Iran

Monday, November 5, 2018

On the spread of dairy pastoralism to East Asia (Jeong & Wilkin et al. 2018)


Over at PNAS at this LINK. Below is the abstract and a table with the uniparental haplogroups for the 20 ancient samples from the paper. Emphasis is mine.

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.


Jeong & Wilkin et al., Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe, PNAS published ahead of print November 5, 2018 https://doi.org/10.1073/pnas.1813608115

See also...

The mystery of the Sintashta people

Thursday, November 1, 2018

Big deal of 2018: Yamnaya not related to Maykop


I was going to write this post after the genotype data from the Wang et al. preprint on the genetic prehistory of the Greater Caucasus became available, because I wanted to demonstrate a few key points with analyses of my own. But I've got a hunch that the formal publication of the manuscript, and thus also the release of the data, has been indefinitely delayed for one reason or another. So here goes anyway, the big deal of 2018...

This year, ancient DNA has revealed that the populations associated with the Maykop and Yamnaya archeological cultures were genetically distinct from each other, and, in all likelihood, didn't mix to any significant degree. Case in point: an ADMIXTURE analysis from Wang et al. 2018.


No doubt, this is quite a shock for many people, especially those of you who consider Maykop to have been a Proto-Indo-European-speaking culture that either gave rise to Yamnaya or at least Indo-Europeanized it. So now, if you still want to see Maykop as the Indo-Europeanizing agent in the Pontic-Caspian steppe, you'll have to rely solely on archeological and linguistics data, and also keep in mind that ancient DNA has slapped you in the face.

In just a few years, ancient DNA has provided us with plenty of shocks, but this is arguably among the biggest.

However, I honestly can't say that it was a huge surprise for me, because I tentatively predicted this outcome more than two years ago based on a handful of mitochondrial (mtDNA) haplotypes (see here). Certainly, analyzing genome-wide genetic data is what I thrive on, but if that's off limits, then eyeballing even a few mtDNA markers can also be very useful.

Wang et al. easily demonstrate the lack of any meaningful genetic relationship between Maykop (including Steppe Maykop, which shows an unusual eastern influence) and Yamnaya using a range of methods. But, judging by their conclusion, in which they still seem to want to see Maykop as the said Indo-Europeanizing agent in the Pontic-Caspian steppe, they're not exactly enthused by their own results. And they also make the following claim (emphasis is mine):

Based on PCA and ADMIXTURE plots we observe two distinct genetic clusters: one cluster falls with previously published ancient individuals from the West Eurasian steppe (hence termed ‘Steppe’), and the second clusters with present-day southern Caucasian populations and ancient Bronze Age individuals from today’s Armenia (henceforth called ‘Caucasus’), while a few individuals take on intermediate positions between the two. The stark distinction seen in our temporal transect is also visible in the Y-chromosome haplogroup distribution, with R1/R1b1 and Q1a2 types in the Steppe and L, J, and G2 types in the Caucasus cluster (Fig. 3A, Supplementary Data 1). In contrast, the mitochondrial haplogroup distribution is more diverse and almost identical in both groups (Fig. 3B, Supplementary Data 1).

I'd say that what they're almost suggesting there is that the Caucasus and Steppe clusters, hence also the Maykop and Yamnaya populations, shared significant maternal ancestry. If this were true, then perhaps it might mean that the Pontic-Caspian steppe was Indo-Europeanized via female-biased migrations from Maykop? Yes, perhaps, if this were true. However, it's not.

To be sure, Yamnaya does show a close genome-wide genetic relationship with an earlier group from the North Caucasus region: the so called Eneolithic steppe people. But they can't be linked to Maykop or even the roughly contemporaneous nearby Eneolithic Caucasus population, and seem to have vanished, at least as a coherent genetic unit, just as Maykop got going. Wang et al. managed to sequence three Eneolithic steppe samples with the following mtDNA haplogroups: H2, I3a and T2a1b.

H2 is too broad a haplogroup to bother with, but here are the results for I3a and T2a1b from the recently launched AmtDB, the first database of ancient human mitochondrial genomes (see here).


In a database of 1,131 ancient samples, I3a shows up in just five individuals, all of them associated with Yamnaya-related archeological cultures and populations: Poltavka (BARu), Unetice (UNC), Corded Ware (CWC), and Bell Beaker (BBC). Similarly, T2a1b shows up in just four individuals, all of them associated with Corded Ware (CWC) and Bell Beaker-derived Bronze Age Britons (BABI). And if I go back a step to T2a1, then the list reveals two Yamnaya individuals from what is now Kalmykia, Russia.

Thus, using just two mtDNA haplotypes I'm able to corroborate the results from genome-wide genetic data showing a close relationship between Eneolithic steppe and Yamnaya. So like I said, useful stuff.

This obviously begs the question: what does the AmtDB reveal about Maykop mtDNA haplotypes, especially in the context of the genetic relationship, or rather lack of, between Yamnaya and Maykop? Yep, again, the AmtDB basically corroborates the results from genome-wide genetic data.

But don't take my word for it. Stick the currently available Maykop mtDNA haplogroups into the AmtDB and see what happens (for your convenience I've made a list available here). Considering the close geographic and temporal proximity of Maykop to Yamnaya, you won't see an overly high sharing rate with Yamnaya and closely related populations. Moreover, Maykop shows several haplogroups that appear highly unusual in the context of the Eneolithic and Bronze Age steppe mtDNA gene pool, and, instead, link its maternal ancestry to those of the early European farmers, West Asians or even Central Asians, such as HV, M52, U1b, U7b and X2f.

See also...

Yamnaya: home-grown

Yamnaya isn't from Iran just like R1a isn't from India

Big deal of 2016: the territory of present-day Iran cannot be the Indo-European homeland

Wednesday, October 24, 2018

Steppe Maykop: a buffer zone?


Unfortunately, the ancient data from the Wang et al. preprint still haven't been released online. As I've already pointed out many times, the manuscript conclusion looks horribly contrived (for instance, see here), but the data are awesome, and most of the preprint is quite solid.


One thing that I'd really like to do is to compare in detail each of the ancient populations from the preprint to groups of present-day and ancient speakers of Indo-European and Caucasian languages. What's the bet that, by and large, Eneolithic steppe will show strong links to Indo-Europeans, while Eneolithic Caucasus and Maykop to Caucasians?

But pending the release of the data, all I can do is look at what the authors have done with it.

Intriguingly, their analyses suggest that the Eneolithic steppe genotype may have vanished from the steppes abutting the Caucasus by at least 3500 BC. It seems to have been replaced there by a more heterogeneous gene pool, with both more easterly and southerly genetic affinities, associated with the Steppe Maykop archeological culture.

So who were the Steppe Maykop people and why did they show up, rather suddenly, in the North Caucasus steppes to seemingly clear out the Eneolithic steppe population from the region? I have a theory about that.

Both archeological and ancient DNA data show that the North Caucasus was being colonized by groups from Transcaucasia during the Eneolithic. But apparently this wasn't an entirely smooth and safe process, because these southern settlers were forced to build elaborate fortifications to keep the natives at bay. Indeed, at the site of Meshoko, in the Northwest Caucasus, there is evidence of such a fort being overrun and its community replaced, probably by a nearby indigenous group (see here).

On the other hand, during the Bronze Age Maykop period, the relations between the settlers from the south and the steppe peoples were apparently much more peaceful. So much so, in fact, that Maykop settlements weren't fortified. However, this was also the period when the North Caucasus steppes were home to the Steppe Maykop people.

So here's my theory: either by chance or design, Steppe Maykop territory was a buffer zone between Maykop and the potentially aggressive natives of the steppes to the north. I'm not necessarily suggesting that the Steppe Maykop people were foreign mercenaries hired by Maykop chiefs, but, in any case, they may have benefited economically in a variety of ways by keeping Maykop settlements safe.

Around 3000 BC, both Maykop and Steppe Maykop disappeared. The latter was replaced by the Yamnaya culture. I don't know much about this process. It may have been mostly driven by environmental impacts from climate change. But the fact that the Steppe Maykop population didn't contribute much, if any, ancestry to the Yamnaya people in the region suggests to me that it was a hostile takeover by Yamnaya.

Interestingly, the spread of Yamnaya into the North Caucasus steppes saw the return of the Eneolithic steppe genotype to the region, albeit in a modified form, with admixture from Middle Neolithic European farmers (see here).

See also...

Yamnaya: home-grown

A potentially violent end to the Kura-Araxes Culture (Alizadeh et al. 2018)

Monday, October 22, 2018

Y-haplogroup P1 in Pleistocene Siberia (Sikora et al. 2018 preprint)


Over at bioRxiv at this LINK. Below is the abstract, emphasis is mine. Two of the (unrelated) males from Yana RHS belong to Y-haplogroup P1 and mitochondrial haplogroup U2. Note that P1 is ancestral to Y-haplogroups Q and R.

Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we report 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of "Ancient North Siberians" (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry from East Asia, giving rise to ancestral Native Americans and "Ancient Paleosiberians" (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the "Neosiberians" from which many contemporary Siberians derive. We detect additional gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic, starting in the Late Pleistocene and continuing well into the Late Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

Sikora et al., The population history of northeastern Siberia since the Pleistocene, bioRxiv, posted October 22, 2018, doi: https://doi.org/10.1101/448829

See also...

Ust'-Ishim belongs to K-M526

Wednesday, October 17, 2018

A closer look at a couple of ancients from Hellenistic Anatolia


Not sure if anyone's mentioned or noticed this already, but the two currently available genomes from Hellenistic Anatolia (samples MA2197 and MA2198 from Damgaard et al. 2018) pack an impressive amount of steppe ancestry. Moreover, one of these individuals also shows obvious admixture from Central Asia.

This isn't particularly surprising, considering the well attested presence of Galatian Celts from deep in Europe and Cimmerians from the Eurasian steppe in Iron Age Anatolia. But it's worthy of note, because it's yet another example of ancient DNA correlating very strongly with archaeological data and historical records. Below are a couple qpAdm models for each of the two aforementioned Anatolians:

Anatolia_IA_MA2197
Anatolia_MLBA 0.429±0.073
Beaker_Hungary 0.571±0.073
chisq: 4.073
tail prob: 0.967727
Full output

Anatolia_IA_MA2197
Anatolia_MLBA 0.431±0.085
Hallstatt_Bylany 0.569±0.085
chisq: 4.056
tail prob: 0.968241
Full output

...

Anatolia_IA_MA2198
Anatolia_MLBA 0.469±0.037
Kangju 0.531±0.037
chisq: 12.091
tail prob: 0.356839
Full output

Anatolia_IA_MA2198
Anatolia_IA_MA2197 0.588±0.165
Cimmerian_Moldova 0.412±0.165
chisq: 11.657
tail prob: 0.390007
Full output

Hence, MA2197 can be modeled very successfully with more than 50% ancestry from a source closely related to the Bell Beakers from the Carpathian Basin and the presumably Celtic-speaking Hallstatt population of what is now Czechia. This almost certainly proves to me that MA2197 is largely of Galatian Celtic stock. The models for MA2198 aren't quite as statistically sound, but they still work, and indeed suggest that this individual might be in large part of Cimmerian origin.

See also...

Focus on Hittite Anatolia

Cimmerians, Scythians and Sarmatians came from...

Central Asian admixture in Hallstatt Celts

Monday, October 15, 2018

ASHG 2018 open thread


The American Society of Human Genetics (ASHG) annual meetings kicks off tomorrow in San Diego. Feel free to post anything near and far related to this event in the comment thread below.

You can explore this year's offerings via the online planner/abstract search located HERE. See anything really interesting? Here's what I found after a quick search using the term "ancient". Hopefully someone tweets from the South Asian talk.

Mount Lebanon provides an opportunity to study DNA from the ancient Near East

Reconstructing the peopling of old world south Asia: From modern to ancient genomes

Tracing the evolution of pigmentation-associated variants in Europe

Intriguingly, the Mount Lebanon abstract says this:

In addition, we found steppe-like ancestry in the Roman Period individuals which we have previously detected in present-day Lebanese but not in Bronze Age individuals. This supports our previous proposition that the steppe ancestry penetrated the region more than 2,000 years ago, and genetic continuity in Lebanon is substantial.

So what are we dealing with here exactly: admixture from the Hittites, Mittani, and/or Romans? Who does the Global25 point to?

See also...

The South Asian cline that no longer exists

Sunday, October 7, 2018

The resistance crumbles


Over the years some scientists from the Estonian Biocentre have been among the staunchest opponents of the idea that Bronze Age pastoralists originating in the steppes of Eastern Europe had a significant genetic and linguistic impact on South Asia (for instance, see here).

But this week they put out a review paper titled The genetic makings of South Asia [LINK] featuring the figure below. It's a nice visualization of the current state of understanding of the peopling of South Asia, and does acknowledge the major role that the said steppe pastoralists had in this process.


However, there's not a single mention of Y-haplogroup R1a in the review. This is surprising, considering the once common, but now no longer valid, claims that this paternal marker may have originated in India. I guess the grieving process will continue for a little longer for some.

My long-held opinion about the claims that R1a was native to India, Iran, Central Asia, or, indeed, anywhere but its actual homeland, which is certainly Eastern Europe, can be summarized as such: LOL!

See also...

Wednesday, October 3, 2018

Cimmerians, Scythians and Sarmatians came from...


Apparently they all came from the eastern Pontic-Caspian steppe. There's a new paper about that at Science Advances (see here). Below is the abstract, emphasis is mine:

For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.

Krzewinska et al., Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads, Science Advances, 03 Oct 2018: Vol. 4, no. 10, eaat4457, DOI: 10.1126/sciadv.aat4457

Update 04/10/2018: Twenty four of the ancient nomad samples made it into the Global25 datasheets. Look for the following population codes: Cimmerian_Moldova, Sarmatian_Urals, Scythian_Moldova, Scythian_Ukraine and Srubnaya-Alakulskaya_MLBA. Feel free to put them through their paces and share the results with us in the comments below.

Global 25 datasheet

Global 25 datasheet (scaled)

Global 25 pop averages

Global 25 pop averages (scaled)

See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Monday, October 1, 2018

Greeks in a Longobard cemetery


I designed a new Principal Component Analysis (PCA) to help me test the fine scale genetic affinities of post-Bronze Age ancient samples from Southern Europe and surrounds. Below is a version of this PCA with a selection of the most Southern European-related ancients from this year's Amorim et al. and Veeramah et al. papers (for background reading, see the posts and comments here and here). The relevant datasheet is available here.
A number of people in the comments at this blog and elsewhere were especially curious about the potential genetic origins of the three most Near Eastern-shifted individuals from the Amorim et al. dataset: CL25, CL30 and CL38. Judging from my new PCA, it seems likely to me that this trio came to North Italy from the pre-Slavic invasions Aegean region. In other words, I'd say they're probably Roman era Greeks or their descendants, who, unlike most present-day Greeks, don't harbor any Slavic ancestry. That's because they cluster very strongly with present-day Greeks from Crete, and also more or less sit on a cline running from present-day mainland Greeks to Cypriots.

See also...

Celtic vs Germanic Europe

Wednesday, September 26, 2018

The Hallstatt effect (?)


Just to see what would happen, I ran a subset of the highest coverage Bronze Age samples from what are now Britain and Ireland in my new Celtic vs Germanic Principal Component Analysis (PCA). Look for the Britain_&_Ireland_BA cluster. The relevant datasheet is available here.


Perhaps it's not a coincidence that the likely Celtic-speaking Iron Age individuals from present-day England (labeled England_IA) are positioned between these older British and Irish samples and the two ancients from Iron Age burials in present-day Bylany, Czechia, associated with the Hallstatt culture (marked with black stars). That's because the Hallstatt people are generally considered to have been the earliest speakers of Celtic languages.

Hence, what the PCA might be showing is a genetic shift in the British and Irish Isles caused by the arrival of Hallstatt Celts in Northwestern Europe.

Interestingly, the present-day English samples appear to be a mixture of Britain_&_Ireland_BA, England_IA and England_Anglo-Saxon. However, a subset of these samples is also heavily shifted "east" towards one of the Hallstatt individuals and present-day Dutch, suggesting that they harbor extra admixture from continental Europe.

This isn't easy to make out on my plot, because of the clutter, but I can assure you that it's true. Keep in mind that you can plug the datasheet into the PAST program (freely available here) to have a much closer look at the PCA and even change the color coding.

To check whether England_IA can be modeled as a mixture of Britain_&_Ireland_BA and Hallstatt with formal methods, I ran an analysis with the qpAdm software using all of the publicly available Bronze Age samples from present-day Britain and Ireland. The standard errors are high, likely because Britain_&_Ireland_BA and Hallstatt are closely related, but, overall, we can probably say that the model does limp across the line.

England_IA
Britain_&_Ireland_BA 0.555±0.172
Hallstatt 0.445±0.172
chisq 18.513
tail prob 0.100973
Full output

However, the really important thing about this output is that England_IA cannot be modeled as simply Britain_&_Ireland_BA (the chisq and tail prob are way off). Thus, even though the Hallstatt samples from Bylany don't appear to be ideal proxies for the admixture in England_IA that is lacking in Britain_&_Ireland_BA, the signal they produce does suggest that a closely related population arrived in the British Isles during or after the Bronze Age to give rise to England_IA.

See also...

Celtic vs Germanic Europe

Central Asian admixture in Hallstatt Celts

Tuesday, September 25, 2018

AmtDB: an interactive ancient human mitogenome database


A very useful resource called AmtDB has just come online. For background info, check out the relevant paper by Ehler et al. here. Below is the paper abstract:

Ancient mitochondrial DNA is used for tracing human past demographic events due to its population-level variability. The number of published ancient mitochondrial genomes has increased in recent years, alongside with the development of high-throughput sequencing and capture enrichment methods. Here, we present AmtDB, the first database of ancient human mitochondrial genomes. Release version contains 1107 hand-curated ancient samples, freely accessible for download, together with the individual descriptors, including geographic location, radiocarbon dating, and archaeological culture affiliation. The database also features an interactive map for sample location visualization. AmtDB is a key platform for ancient population genetic studies and is available at https://amtdb.org.

To give an example of how this thing works, I'll search for a very specific mitochondrial (mtDNA) haplogroup, H6a1b, which was recorded, perhaps unexpectedly, in a sample from Hittite era Anatolia (individual MA2208 from Damgaard et al. 2018). I say perhaps unexpectedly, because it's a marker that is today, by and large, restricted to Northern Europe. Here are the results...


Interestingly, H6a1b only pops up in Copper and Bronze Age individuals from what are now Czechia, Great Britain, Poland and Russia, with not a single instance from the Near East. Moreover, the oldest sample on the list is from an Yamnaya culture burial in Samara, Russia. Thus, if the presence of this marker in the Hittite sample isn't due to contamination or poor quality sequencing, then it's likely that some Hittites belonged to mtDNA haplogroups that arrived in Anatolia from the steppes of what is now Russia.

See also...

Focus on Hittite Anatolia

Saturday, September 22, 2018

Corded Ware people =/= Proto-Uralics (Tambets et al. 2018)


A new paper on the genetic structure of Uralic-speaking populations has appeared at Genome Biology (see here). It looks to me like the prelude to a forthcoming paleogenetics paper on the same topic that was discussed in the Estonian media recently (see here). Although not exactly ground breaking (because it basically argues what I've been saying at this blog for years, like here and here), it's a very nice effort all round and must be read by anyone with an interest in this topic. From the paper, emphasis is mine:

Background The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools. While the maternal lineages reflect by and large the geographic background of a given Uralic-speaking population, the frequency of Y chromosomes of Eastern Eurasian origin is distinctively high among European Uralic speakers. The autosomal variation of Uralic speakers, however, has not yet been studied comprehensively.

Results: Here, we present a genome-wide analysis of 15 Uralic-speaking populations which cover all main groups of the linguistic family. We show that contemporary Uralic speakers are genetically very similar to their local geographical neighbours. However, when studying relationships among geographically distant populations, we find that most of the Uralic speakers and some of their neighbours share a genetic component of possibly Siberian origin. Additionally, we show that most Uralic speakers share significantly more genomic segments identity-by-descent with each other than with geographically equidistant speakers of other languages. We find that correlated genome-wide genetic and lexical distances among Uralic speakers suggest co-dispersion of genes and languages. Yet, we do not find long-range genetic ties between Estonians and Hungarians with their linguistic sisters that would distinguish them from their non-Uralic-speaking neighbours.

Conclusions: We show that most Uralic speakers share a distinct ancestry component of likely Siberian origin, which suggests that the spread of Uralic languages involved at least some demic component.

...

Recent aDNA studies have shown that extant European populations draw ancestry form three main migration waves during the Upper Palaeolithic, the Neolithic and Early Bronze Age [2, 3, 45]. The more detailed reconstructions concerning NE Europe up to the Corded Ware culture agree broadly with this scenario and reveal regional differences [65–67]. However, to explain the demographic history of extant NE European populations, we need to invoke a novel genetic component in Europe—the Siberian. The geographic distribution of the main part of this component is likely associated with the spread of Uralic speakers but gene flow from Siberian sources in historic and modern Uralic speakers has been more complex, as revealed also by a recent study of ancient DNA from Fennoscandia and Northwest Russia [68]. Thus, the Siberian component we introduce here is not the perfect but still the current best candidate for the genetic counterpart in the spread of Uralic languages.


Citation...

Tambets et al., Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations, Genome Biology, (2018) 19:139 https://doi.org/10.1186/s13059-018-1522-1

See also...

Indo-European crackpottery

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Genetic and linguistic structure across space and time in Northern Europe

Friday, September 21, 2018

Dzudzuana Ice Age foragers: a different type of Caucasus hunter-gatherer (Lazaridis et al. 2018 preprint)


Over at bioRxiv at this LINK. Below is the abstract. Emphasis is mine.

The earliest ancient DNA data of modern humans from Europe dates to ~40 thousand years ago, but that from the Caucasus and the Near East to only ~14 thousand years ago, from populations who lived long after the Last Glacial Maximum (LGM) ~26.5-19 thousand years ago. To address this imbalance and to better understand the relationship of Europeans and Near Easterners, we report genome-wide data from two ~26 thousand year old individuals from Dzudzuana Cave in Georgia in the Caucasus from around the beginning of the LGM. Surprisingly, the Dzudzuana population was more closely related to early agriculturalists from western Anatolia ~8 thousand years ago than to the hunter-gatherers of the Caucasus from the same region of western Georgia of ~13-10 thousand years ago. Most of the Dzudzuana population's ancestry was deeply related to the post-glacial western European hunter-gatherers of the 'Villabruna cluster', but it also had ancestry from a lineage that had separated from the great majority of non-African populations before they separated from each other, proving that such 'Basal Eurasians' were present in West Eurasia twice as early as previously recorded. We document major population turnover in the Near East after the time of Dzudzuana, showing that the highly differentiated Holocene populations of the region were formed by 'Ancient North Eurasian' admixture into the Caucasus and Iran and North African admixture into the Natufians of the Levant. We finally show that the Dzudzuana population contributed the majority of the ancestry of post-Ice Age people in the Near East, North Africa, and even parts of Europe, thereby becoming the largest single contributor of ancestry of all present-day West Eurasians.

Lazaridis et al., Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry, bioRxiv, posted September 21, 2018, doi: https://doi.org/10.1101/423079

See also...

Villabruna cluster =/= Near Eastern migrants

Thursday, September 20, 2018

Early Anatolian farmers were overwhelmingly of local hunter-gatherer origin (Feldman et al. 2018 preprint)


Over at bioRxiv at this LINK. The dataset in this preprint includes just one Anatolian hunter-gatherer, but that's enough to make the point that in Anatolia, unlike in Europe, there was very strong genetic continuity between the local foragers and earliest farmers. His Y-chromosome haplogroup is an interesting one: C1a2, which has been recorded in European remains from the Upper Paleolithic. Below is the abstract and a pertinent quote. I think this preprint basically confirms what I argued about the origin of the so called Villabruna hunter-gatherer clade back in 2016 (see here). Emphasis is mine.

Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000 year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity between the hunter-gatherer and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago that extends to central Europe during the post-last-glacial maximum period. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

...

Among the Later European HG, recently reported Mesolithic hunter-gatherers from the Balkan peninsula, which geographically connects Anatolia and central Europe (‘Iron Gates HG’) [18], are genetically closer to AHG when compared to all the other European hunter-gatherers, as shown in the significantly positive statistic D(Iron_Gates_HG, European hunter-gatherers; AHG, Mbuti/Altai). Iron Gates HG are followed by Epigravettian and Mesolithic individuals from Italy and France (Villabruna [14] and Ranchot88 respectively [17]) as the next two European hunter-gatherers genetically closest to AHG [20] (Fig. 3A and data table S5). Iron Gates HG have been suggested to be genetically intermediate between WHG and eastern European hunter-gatherers (EHG) with an additional unknown ancestral component [18]. We find that Iron Gates HG can be modeled as a three-way mixture of Near-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4 % or 78.0 ± 4.6 % respectively) and EHG (11.3 ± 3.3 % or 10.9 ± 3 % respectively); (tables S4 and S9). The affinity detected by the above D-statistic can be explained by gene flow from Near-Eastern hunter-gatherers into the ancestors of Iron Gates or by a gene flow from a population ancestral to Iron Gates into the Near-Eastern hunter-gatherers as well as by a combination of both. To distinguish the direction of the gene flow, we examined the Basal Eurasian ancestry component (α), which is prevalent in the Near East [6] but undetectable in European hunter-gatherers [17]. Following a published approach [6], we estimated α to be 24.8 ± 5.5 % in AHG and 38.5 ± 5.0 % in Natufians (Fig. 3B, table S10), consistent with previous estimates for the latter [6]. Under the model of unidirectional gene flow from Anatolia to Europe, 6.4 % is expected for α of Iron Gates by calculating (% AHG in Iron Gates HG) × (α in AHG). However, Iron Gates can be modeled without any Basal Eurasian ancestry or with a non-significant proportion of 1.6 ± 2.8 % (Fig. 3B, table S10), suggesting that unidirectional gene flow from the Near East to Europe alone is insufficient to explain the extra affinity between the Iron Gates HG and the Near-Eastern hunter-gatherers. Thus, it is plausible to assume that prior to 15,000 years ago there was either a bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East. Presumably, this Southeastern European ancestral population later spread into central Europe during the post-last-glacial maximum (LGM) period, resulting in the observed late Pleistocene genetic affinity between the Near East and Europe.

Feldman et al., Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia, biRxiv, posted September 20, 2018, doi: https://doi.org/10.1101/422295

Sunday, September 16, 2018

Celtic vs Germanic Europe


I have a feeling that ancient DNA from post-Bronze Age Northwestern Europe will be coming thick and fast from now on. To get the most out of such data I've designed a new Principal Component Analysis (PCA) that does a better job of separating the Celtic- and Germanic-speaking populations of Europe than my previous efforts of this sort (see here and here). Below are two different versions of the same PCA. The relevant datasheet is available here.


And here's a Discrimination Analysis (LDA) plot based on the 25 principal components. It further differentiates many of the populations along the east > west cline of genetic diversity.


The difference between the Germanic Anglo-Saxons and the Celtic and Roman Britons of what is now eastern England is obvious. The Anglo-Saxons could pass for Scandinavians, while the Celts and Romans both cluster between the Irish and French. This makes good sense, and is exactly what I was looking for. It's also interesting to see the Hallstatt Celts from Bylany, Czechia, clustering with the Belgians. I'll add this PCA to the Eurogenes store if there's enough interest from the community.