R-V1636: Eneolithic steppe > Kura-Araxes?

Ancient samples from the Wang et al. preprint on the genetic prehistory of the Greater Caucasus are now available as BAM files at the European Nucleotide Archive (see here). I've requested the genotype data from the authors and I'm eagerly awaiting their response.

But various online genetic genealogy communities are already studying in detail the Y-chromosome data from the BAM files. One interesting outcome is that both of the Eneolithic steppe males, PG2001 and PG2004, apparently belong to Y-haplogroup R-V1636 (see here). This extremely rare subclade of R1b has apparently also been found in an ancient individual from what is now Armenia associated with the Kura-Araxes culture: Armenia_EBA I1635.

Importantly, the Eneolithic steppe males are dated to 4336-4047 calBCE, and don't show any recent genome-wide ancestry from south of the Caucasus, while the Kura-Araxes individual is dated to just 2619-2465 calBCE.

It'll be interesting to see whether Armenia_EBA I163 shows any genome-wide admixture from north of the Caucasus when I can test this with these new Wang et al. Eneolithic samples from the southernmost steppes. But in any case, if the R-V1636 link between the Eneolithic steppe and Kura-Araxes is real, then this is more evidence of migrations from the steppe across the Greater Caucasus into the Near East during the Eneolithic and/or Bronze Age.

Such population movements could potentially explain the appearance of Hittite and other closely related Indo-European languages in Anatolia during the Bronze Age.

See also...

Steppe ancestry in Chalcolithic Transcaucasia (aka Armenia_ChL explained)

Likely Yamnaya incursion(s) into Northwestern Iran

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

The Hajji Firuz fiasco

The specter of Hajji_Firuz_ChL I2327 still haunts us. Judging by some recent comments that I've seen here and elsewhere, it seems that a good number of confused souls haven't yet given up hope that this ancient sample represents a Near Eastern population ancestral to the Yamnaya people of Early Bronze Age Eastern Europe. But the chances of this are slim to none, because...

- Hajji_Firuz_ChL I2327 is the only (supposedly) pre-Yamnaya individual to date in the now ample West Asian ancient DNA record who belongs to Y-haplogroup R1b-Z2103, R1b-M269, or even R1b, which has got to tell you something about the reliability of his early dating

- overall the genome-wide structure of Hajji_Firuz_ChL I2327 most certainly doesn't fit the profile of the Near Eastern-related half of the Yamnaya genotype

- in fact, practically every analysis that I've run with Hajji_Firuz_ChL I2327 suggests that he harbors Yamnaya or Yamnaya-related genome-wide ancestry, which makes sense considering his Yamnaya-specific Y-haplogroup, don't you think?

Heck, even if Hajji_Firuz_ChL I2327 is more or less accurately dated, and really was alive during the Chalcolithic period, then considering the points I've made above, the only honest explanation for his presence that early in what is now Iran is that there was a migration of a Yamnaya-like people from the steppes across the Caucasus during the Chalcolithic.

I already wrote a post on this topic back in April, and a lengthy discussion ensued, with most of the commentators agreeing with my stance. But my efforts haven't had much of an impact outside of this blog. It's possible that my post was too confusing, so I went back today and rewrote it, also adding new stats and mixture models to help me drive home my point. Here's the link...

Likely Yamnaya incursion(s) into Northwestern Iran

Of course, no matter how strong my arguments are, many people will choose to disagree with me nevertheless and believe what they want to believe, because this is such an emotional issue for them. I don't want to get into the details about that here, but suffice to say that it's imperative for many people, particularly those of Near Eastern and Southern European backgrounds, that the origin of Yamnaya is somehow, by hook or by crook, put south of the Caucasus. I'm not kidding. It's a pointless cause though, especially now considering all of the new ancient DNA data from Eastern Europe that make this scenario about as likely as Out-of-India (see here).

See also...

Yamnaya: home-grown

Big deal of 2018: Yamnaya not related to Maykop

Ahead of the pack

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

Italians are interesting people (Raveane et al. 2018 preprint)

Over at bioRxiv at this LINK. As far as I can see from skimming through the preprint, it's a thorough effort with conclusions that make good sense. But, needless to say, it'll be very useful to plug the dataset from this study into the Global25 to see what these new Italian samples are really made of. Here's the abstract, emphasis is mine.

European populations display low genetic diversity as the result of long term blending of the small number of ancient founding ancestries. However it is still unclear how the combination of ancient ancestries related to early European foragers, Neolithic farmers and Bronze Age nomadic pastoralists can fully explain genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the overall continental diversity, but to date have been systematically understudied. Here we characterised the ancestry profiles of modern-day Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe and the rest of the world. Italian genomes captured several ancient signatures, including a non-steppe related substantial ancestry contribution ultimately from the Caucasus. Differences in ancestry composition as the result of migration and admixture generated in Italy the largest degree of population structure detected so far in the continent and shaped the amount of Neanderthal DNA present in modern-day populations.

Raveane et al., Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe, Posted December 13, 2018, bioRxiv, doi: https://doi.org/10.1101/494898

See also...

Greeks in a Longobard cemetery

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...

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

Y-haplogroup N1c probably entered Europe from Siberia during the Bronze Age or the Eneolithic period. 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 Siberian genome-wide 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)

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 a 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...

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

The Uralic cline in the Global25

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

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)

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

The mystery of the Sintashta people

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 Eneolithic 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

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

Update 17/02/2019: I basically managed to confirm my analysis with samples from the Wang et al. Caucasus paper. See here.

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...

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

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)

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

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...

Mediterranean PCA update

Celtic vs Germanic Europe

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 probably not from the west

Celtic vs Germanic Europe

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

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

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 presumably Celtic-speaking Hallstatt samples from Bylany, Czechia, clustering with the Belgians.

Update 14/12/2019: Pictured below is a new version of my Celtic vs Germanic genetic map. It's based on the same Principal Component Analysis (PCA) as the original, but more focused on Northwestern Europe and produced with a different program.

To see the interactive online version, navigate to Vahaduo Custom PCA and copy paste the text from here into the empty space under the PCA DATA tab. Then press the PLOT PCA button under the PCA PLOT tab. For more guidance, refer to the screen caps here and here.

To include a wider range of populations in the key, just edit the data accordingly. For instance, to break up the ancient grouping into more specific populations, delete the Ancient: prefix in all of the relevant rows. This is what you should see:

Conversely, you can leave the ancient sample set intact and instead reorder the present-day linguistic groupings into, say, geographic groupings. To achieve this just delete all of the linguistic prefixes, such as Celtic:, Germanic:, and so on. You should end up with a datasheet like this and plot like this.

Of course, you can design your own plot by using any combination of the ancient and present-day individuals and populations that I've already run in this PCA. Their coordinates are listed here. Indeed, if you're in the possession of your own Celtic vs Germanic PCA coordinates, you can add yourself to the plot. And if you're not, see here.

It's also possible to re-process PCA data via the SOURCE tab. But I don't recommend doing this with the Celtic vs Germanic data, which are derived from a fine scale analysis and don't pack much variation. On the other hand, Global25 data are ideal for such re-processing. I made the plots below from subsets of Global25 coordinates available in a zip file here. To see how, refer to the screen caps here and here.

See also...

Modeling your ancestry has never been easier

Getting the most out of the Global25

Modeling genetic ancestry with Davidski: step by step

Avars and Longobards

Most of the "barbarians" from today's Amorim et al. paper have made it into the Global25 datasheets. Look for the samples with Collegno and Szolad in their labels. Same links as always...

Global25 datasheet ancient scaled

Global25 pop averages ancient scaled

Global25 datasheet ancient

Global25 pop averages ancient

Here's my usual Principal Component Analysis (PCA) of West Eurasian variation with the same individuals. As seen in the paper, the two females from Avar burials are very European indeed, with no hints of any recent Asian ancestry. The relevant datasheet is available here.

And this is my Global25-derived North European PCA featuring a subset of these samples that plotted firmly with present-day populations from north of the Alps, Balkans and Pyrenees. The aforementioned Avars (red dots) are sitting within the Polish cluster. The relevant datasheet is available here.

See also...

Greeks in a Longobard cemetery

First real foray into Migration Period Europe: the Gepid, Roman, Ostrogoth and others

Blast from the past: Yamnaya prediction from 2016

I wonder what's holding up the publication of the Wang et al. "Greater Caucasus" preprint? It was released back in May at the bioRxiv (see here). On a related note, I was looking back at some of the stuff that I wrote about the origin of the Yamnaya people (aka Steppe_EMBA), and found this...

But here's my prediction: Steppe_EMBA only has 10-15% admixture from the post-Mesolithic Near East not including the North Caucasus, and basically all of this comes via female mediated gene flow from farming communities in the Caucasus and perhaps present-day Ukraine.

The relevant blog post from 2016 is here. I totally forgot that I made such a bold prediction. But it actually has a very good chance now of being proven correct, more or less.

This, however, depends on the precise origin of the Yamnaya-like Eneolithic populations of the southernmost parts of the Pontic-Caspian steppe. But, considering the data in Wang et al., I think the possibility that they date back to the Pottery Neolithic period, and are thus indigenous to the region, looks quite high.

About a year later I made a prediction about the genetic structure of the Maykop people, and was basically proven right by Wang et al. (see here). Admittedly, my jaw dropped when I saw how the Steppe Maykop individuals came out in the preprint, with their Botai-like ancestry that is missing in all Yamnaya populations sampled to date. But it was an interesting outcome and nice to be surprised by ancient DNA yet again.

See also...

Genetic borders are usually linguistic borders too

Ahead of the pack

Open thread: What are the linguistic implications of Olalde et al. 2019?

Major horse paper coming soon

Horse domestication is an important and controversial topic, in large part because it's intimately tied to the debate over the location of the Proto-Indo-European (PIE) homeland. Based on the currently available genetic and archaeological data, it seems likely that all modern domesticated horse breeds ultimately derive from the Pontic-Caspian steppe in Eastern Europe (see here and here).

In the interview linked to below (click on the image) horse expert Alan Outram reveals that a new paper will be published within months that will test this theory, and either confirm or debunk it.

Outram also talks about the colonization of Central Asia during the Middle Bronze Age by groups from the west associated with the Sintashta culture. He says that this was probably an aggressive affair, akin to the more recent European colonization of North America, that may have pushed the Botai people, who were the indigenous inhabitants of the Kazakh steppe, and their horses far to the east. This, he suggests, might explain why the Przewalski horse of Mongolia appears to be derived from the Botai horse.

See also...

The mystery of the Sintashta people

Focus on Hittite Anatolia

Friendly Yeniseian steppe pastoralists

Focus on Hittite Anatolia

I computed a series of D-statistics on most of the currently available ancient samples from Central Anatolia - dating from almost the Epipaleolithic (Boncuklu_N) to the Hittite era (Anatolia_MLBA) - to try and get a better idea of who the Indo-European-speaking Hittites may have been. The full output as well as details about the key ancient samples used in this analysis are available here. See anything interesting? The most noteworthy statistics, I suppose, are those listed below, because they're significant (Z≥3) and organized chronologically.

However, the thing to keep in mind in regards to D-statistics, and the very similar f4-statistics, when looking for signals of mixture is that they may or may not produce significant Z scores because of several reasons, such as the choice of the outgroup, the choice of the reference samples and the phylogenetic relationship between them, or even the type, quality and density of the data being used.

Perhaps ironically, the D-statistics above suggest that the Neolithic Central Anatolians (Boncuklu_N and Tepecik_Ciftlik_N) were more European-like than those from the Bronze Age, and I suspect that this is one of the main reasons why the idea of Eastern European admixture (from the Pontic-Caspian steppe and/or Balkans) in Hittites is currently being rejected by the geneticists working on the problem. But this dilemma is easy to explain away by the fact that the Neolithic samples carry much higher ratios of Anatolian Epipaleolithic hunter-gatherer admixture and also other types of ancestry shared with and/or closely related to European hunter-gatherers and early farmers.

In other words, I'd say that most of the statistics are being confounded by deep phylogenetic relationships, and thus aren't very useful for solving the Hittite problem. Interestingly, though, that relationship to Europe is reversed somewhat in the D-statistics involving Anatolia_EBA and Anatolia_MLBA, with the latter showing significantly higher affinity to Eastern European Hunter-Gatherers (EHG) and Minoans.

Thus, in my opinion, to get a more complete picture it's also useful to look for patterns in the statistics, even those that, strictly speaking, don't reach significance. One way to do that is with linear models. So here are a few linear models based on some of my D-statistics. The relevant datasheet is available here.

Arguably, the most striking thing about these models is the position at the top of the graphs of the ancient populations from Central Asia and what is now Iran, and the gradually lower position of populations with progressively less of this type of ancestry. The most plausible explanation for this phenomenon is post-Boncuklu_N gene flow into Central Anatolia from the east, possibly as a continuation of something that was happening already since the Epipaleolithic, but becoming more intense during the Neolithic revolution, probably as a result of rapid population growth in and around the Fertile Crescent.

Indeed, I strongly suspect that one of the main reasons why we've been hearing so much lately about Iran as a likely candidate for the Indo-European homeland is this strong eastern signal in Bronze Age Anatolian DNA. If so, then this is likely to be a misunderstanding, because there are better explanations for it than the Indo-Europeans, such as the Hattians and Hurrians.

Another rather obvious outcome in my graphs is the relatively stronger affinity between the Bronze Age Anatolians and the ancient populations from Eastern Europe, including, and especially, those from the Pontic-Caspian steppe, compared to Tepecik_Ciftlik_N. In fact, looking at the Anatolia_EBA vs Tepecik_Ciftlik_N graph, I'd say that steppe admixture was already seeping into Central Anatolia during the Early Bronze Age.

If so, this is an important point that should be taken into account when modeling the ancestry of the Hittite era Anatolians. That's because if Anatolia_EBA already harbored some steppe ancestry, then we'd be shooting ourselves in the proverbial foot if we were to use it as the supposedly unadmixed reference population to try and determine whether Anatolia_MLBA was partly of steppe origin. Hence, to model the ancestry of Anatolia_MLBA, at least in the context of possible migrations from the steppe to Anatolia during the Bronze Age, it might be more useful to use Tepecik_Ciftlik_N as the likely unadmixed reference population.

Let's try that with qpAdm, first on the whole Anatolia_MLBA set, and then on one individual labeled MA2203, who, as far as I can tell, shows an elevated level of steppe ancestry in several different types of analyses. I chose Yamnaya_Kalmykia as the potential mixture source from the steppe because it's likely to be the closest available population in my dataset to the Eneolithic groups of the southern region of the Pontic-Caspian steppe.

Anatolia_MLBA
Seh_Gabi_ChL 0.200±0.043
Tepecik_Ciftlik_N 0.659±0.033
Yamnaya_Kalmykia 0.141±0.022
chisq: 11.425
tail prob: 0.408405
Full output

MA2203
Seh_Gabi_ChL 0.179±0.065
Tepecik_Ciftlik_N 0.622±0.049
Yamnaya_Kalmykia 0.199±0.036
chisq: 12.914
tail prob: 0.299004
Full output

Please note, however, that these mixture models are based on f4-statisctics. So, obviously, they're going to be affected by the same factors as described above that affect f4-statistics. Hence, despite the seemingly statistically sound output, the steppe admixture that you see there might not actually be admixture from the steppe.

In fact, there's a good reason why I'm not shouting from the rooftops that I've just uncovered the presence of steppe ancestry in Bronze Age Anatolia, and thus confirmed the steppe or kurgan hypothesis positing that the Hittite and indeed Indo-European homeland was located in the Pontic-Caspian steppe. That's because I used a mixed bag of UDG-treated capture data and non-UDG-treated shotgun data. This is known to be a serious problem, which can skew the results of even the most robust analyses, and produce spurious statistics and Z scores.

Nevertheless, I'm reasonably confident that my findings will eventually be confirmed with more and higher quality data from ancient Anatolia. Let's wait and see.

See also...

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