Genetic landscape and past admixture of modern Slovenians

slovenes-snp

Open access Genetic Landscape of Slovenians: Past Admixture and Natural Selection Pattern, by Maisano Delser et al. Front. Genet. (2018).

Interesting excerpts (emphasis mine):

Samples

Overall, 96 samples ranging from Slovenian littoral to Lower Styria were genotyped for 713,599 markers using the OmniExpress 24-V1 BeadChips (Figure 1), genetic data were obtained from Esko et al. (2013). After removing related individuals, 92 samples were left. The Slovenian dataset has been subsequently merged with the Human Origin dataset (Lazaridis et al., 2016) for a total of 2163 individuals.

Y chromosome

First, Y chromosome genetic diversity was assessed. A total of 52 Y chromosomes were analyzed for 195 SNPs. The majority of individuals (25, 48.1%) belong to the haplogroup R1a1a1a (R-M417) while the second major haplogroup is represented by R1b (R-M343) including 15 individuals (28.8%). Twelve samples are assigned to haplogroup I (I M170): five and two samples belong to haplogroup I2a (I L460) and I1 (I M253), respectively, while the remaining five samples did not have enough information to be further assigned.

pca-slovenes
PCA of Slovenian samples with European populations (Slovenian_HO_EU dataset). For details regarding the populations included, see Supplementary Table 1.

PCA

Considering the unbalanced sample size of the Slovenian population compared to the other populations included in the dataset, a subset of 20 Slovenian individuals randomly sampled was used.

All Slovenian samples group together with Hungarians, Czechs, and some Croatians (“Central-Eastern European” cluster) as also suggested by the PCA. All Basque individuals with few French and Spanish cluster together (“Basque” cluster) while a “Northern-European” cluster is made of the majority of French, English, Icelanders, Norwegians, and Orcadians. Five populations contributed to the “Eastern-European” cluster including Belarusians, Estonians, Lithuanians, Mordovians, and Russians. Western and South Europe is split into two cluster: the first (“Western European” cluster) includes all Spanish individuals, few French, and some Italians (North Italy) while the second (“Southern-European” cluster) groups Sicilians, Greeks, some Croatians, Romanians, and some Italians (North Italy).

Admixture Pattern and Migration

admixture-slovenians
Modified image, from the paper (Central-East Europeans marked). Unsupervised admixture analysis of Slovenians. Results for K = 5 are showed as it represents the lowest cross-validation error. Slovenian samples show an admixture pattern similar to the neighboring populations such as Croatians and Hungarians. The major ancestral components are: the blue one which is shared with Lithuanians and Russians, followed by the dark green one that is mostly present in Greek samples and the light blue which characterizes Orcadians and English. For population acronyms see Supplementary Table 1.

All Slovenian individuals share common pattern of genetic ancestry, as revealed by ADMIXTURE analysis. The three major ancestry components are the North East and North West European ones (light blue and dark blue, respectively, Figure 3), followed by a South European one (dark green, Figure 3). Contribution from the Sardinians and Basque are present in negligible amount. The admixture pattern of Slovenians mimics the one suggested by the neighboring Eastern European populations, but it is different from the pattern suggested by North Italian populations even though they are geographically close.

Using ALDER, the most significant admixture event was obtained with Russians and Sardinians as source populations and it happened 135 ± 9.31 generations ago (Z-score = 11.54). (…) When tested for multiple admixture events (MALDER), we obtained evidence for one admixture event 165.391 ± 17.1918 generations ago corresponding to ∼2620 BCE (CI: 3101–2139) considering a generation time of 28 years (Figure 4), with Kalmyk and Sardinians as sources.

We then modeled the Slovenian population as target of admixture of ancient individuals from Haak et al. (2015) while computing the f3(Ancient 1, Ancient 2, Slovenian) statistic. The most significant signal was obtained with Yamnaya and HungaryGamba_EN (Z-score = -10.66), followed by MA1 with LBK_EN (Z-score -9.7) and Yamnaya with Stuttgart (Z-score = -8.6) used as possible source populations (Supplementary Figure 5).

We found a significant signal of admixture by using both pairs as ancient sources. Specifically, for the pair Yamnaya and Hungary_EN the admixture event is dated at 134.38 ± 23.69 generations ago (Z-score = 5.26, p-value of 1.5e-07) while for Yamnaya and LBK_EN at 153.65 ± 22.19 generations ago (Z-score = 6.92, p-value 4.4e-12). Outgroup f3 with Yamnaya put Slovenian population close to Hungarians, Czechs, and English, indicating a similar shared drift between these population with the Steppe populations (Supplementary Figure 6).

admixture-events-slovenes
Admixture events identified with ALDER and MALDER. The gray dots represent significant admixture events detected with ALDER using Slovenians as target, the solid line represents the single admixture event detected using MALDER, dashed lines represent the confidence interval. Only the significant results after multiple testing correction are plotted. For ALDER results see Supplementary Table 5.

Not that any of this would come as a surprise, but:

  • R1a-M458 and some R1a-Z280 (xR1a-Z92) lineages (found among Slovenes) were associated with the Slavic expansion, likely with the Prague-Korchak culture, originally stemming probably from peoples of the Lusatian culture. Other R1a-Z280 lineages remained associated with Uralic peoples, and some became Slavicized only recently.
  • PCA keeps supporting the common cluster of certain West, South, and East Slavs in a “Central-Eastern European” cluster, distinct from the “North-Eastern European” cluster formed by modern Finno-Ugrians, as well as ancient Finno-Ugrians of north-eastern Europe who were only recently Slavicized.
  • Admixture supports the same ancient ‘western’ (a core West+South+East Slavic) cluster, and the admixture event with Yamna + Hungary_EN is logically a proxy for Yamna Hungary being at the core of ancestral Central-East population movements related to Bell Beakers in the mid- to late 3rd millennium.

The theory that East Slavs are at the core of the Slavic expansion makes no sense, in terms of archaeology (see Florin Curta’s dismissal of those recent eastern ‘Slavic’ finds, his commentary on 19th century Pan-Slavic crap, or his book on Slavic migrations), in terms of ancient DNA (the earliest Slavs sampled cluster with modern West Slavs, distant from the steppe cluster, unlike Finno-Ugrians), or in terms of modern DNA.

I don’t know where exactly this impulse for the theory of Russia being the cradle of Slavs comes from today (although there are some obvious political trends to revive 19th c. ideas), but it was always clear for everyone, including Russians, that East Slavs had migrated to the east and north and assimilated indigenous Finno-Ugrians, apart from Turkic-, Iranian-, and Caucasian-speaking peoples to the east. Genetics is only confirming what was clear from other disciplines long ago.

Related

“Steppe ancestry” step by step: Khvalynsk, Sredni Stog, Repin, Yamna, Corded Ware

dzudzuana_pca-large

Wang et al. (2018) is obviously a game changer in many aspects. I have already written about the upcoming Yamna Hungary samples, about the new Steppe_Eneolithic and Caucasus Eneolithic keystones, and about the upcoming Greece Neolithic samples with steppe ancestry.

An interesting aspect of the paper, hidden among so many relevant details, is a clearer picture of how the so-called Yamnaya or steppe ancestry evolved from Samara hunter-gatherers to Yamna nomadic pastoralists, and how this ancestry appeared among Proto-Corded Ware populations.

anatolia-neolithic-steppe-eneolithic
Image modified from Wang et al. (2018). Marked are in orange: equivalent Steppe_Maykop ADMIXTURE; in red, approximate limit of Anatolia_Neolithic ancestry found in Yamna populations; in blue, Corded Ware-related groups. “Modelling results for the Steppe and Caucasus cluster. Admixture proportions based on (temporally and geographically) distal and proximal models, showing additional Anatolian farmer-related ancestry in Steppe groups as well as additional gene flow from the south in some of the Steppe groups as well as the Caucasus groups.”

Please note: arrows of “ancestry movement” in the following PCAs do not necessarily represent physical population movements, or even ethnolinguistic change. To avoid misinterpretations, I have depicted arrows with Y-DNA haplogroup migrations to represent the most likely true ethnolinguistic movements. Admixture graphics shown are from Wang et al. (2018), and also (the K12) from Mathieson et al. (2018).

1. Samara to Early Khvalynsk

The so-called steppe ancestry was born during the Khvalynsk expansion through the steppes, probably through exogamy of expanding elite clans (eventually all R1b-M269 lineages) originally of Samara_HG ancestry. The nearest group to the ANE-like ghost population with which Samara hunter-gatherers admixed is represented by the Steppe_Eneolithic / Steppe_Maykop cluster (from the Northern Caucasus Piedmont).

Steppe_Eneolithic samples, of R1b1 lineages, are probably expanded Khvalynsk peoples, showing thus a proximate ancestry of an Early Eneolithic ghost population of the Northern Caucasus. Steppe_Maykop samples represent a later replacement of this Steppe_Eneolithic population – and/or a similar population with further contribution of ANE-like ancestry – in the area some 1,000 years later.

PCA-caucasus-steppe-samara

This is what Steppe_Maykop looks like, different from Steppe_Eneolithic:

steppe-maykop-admixture

NOTE. This admixture shows how different Steppe_Maykop is from Steppe_Eneolithic, but in the different supervised ADMIXTURE graphics below Maykop_Eneolithic is roughly equivalent to Eneolithic_Steppe (see orange arrow in ADMIXTURE graphic above). This is useful for a simplified analysis, but actual differences between Khvalynsk, Sredni Stog, Afanasevo, Yamna and Corded Ware are probably underestimated in the analyses below, and will become clearer in the future when more ancestral hunter-gatherer populations are added to the analysis.

2. Early Khvalynsk expansion

We have direct data of Khvalynsk-Novodanilovka-like populations thanks to Khvalynsk and Steppe_Eneolithic samples (although I’ve used the latter above to represent the ghost Caucasus population with which Samara_HG admixed).

We also have indirect data. First, there is the PCA with outliers:

PCA-khvalynsk-steppe

Second, we have data from north Pontic Ukraine_Eneolithic samples (see next section).

Third, there is the continuity of late Repin / Afanasevo with Steppe_Eneolithic (see below).

3. Proto-Corded Ware expansion

It is unclear if R1a-M459 subclades were continuously in the steppe and resurged after the Khvalynsk expansion, or (the most likely option) they came from the forested region of the Upper Dnieper area, possibly from previous expansions there with hunter-gatherer pottery.

Supporting the latter is the millennia-long continuity of R1b-V88 and I2a2 subclades in the north Pontic Mesolithic, Neolithic, and Early Eneolithic Sredni Stog culture, until ca. 4500 BC (and even later, during the second half).

Only at the end of the Early Eneolithic with the disappearance of Novodanilovka (and beginning of the steppe ‘hiatus’ of Rassamakin) is R1a to be found in Ukraine again (after disappearing from the record some 2,000 years earlier), related to complex population movements in the north Pontic area.

NOTE. In the PCA, a tentative position of Novodanilovka closer to Anatolia_Neolithic / Dzudzuana ancestry is selected, based on the apparent cline formed by Ukraine_Eneolithic samples, and on the position and ancestry of Sredni Stog, Yamna, and Corded Ware later. A good alternative would be to place Novodanilovka still closer to the Balkan outliers (i.e. Suvorovo), and a source closer to EHG as the ancestry driven by the migration of R1a-M417.

PCA-sredni-stog-steppe

The first sample with steppe ancestry appears only after 4250 BC in the forest-steppe, centuries after the samples with steppe ancestry from the Northern Caucasus and the Balkans, which points to exogamy of expanding R1a-M417 lineages with the remnants of the Novodanilovka population.

steppe-ancestry-admixture-sredni-stog

4. Repin / Early Yamna expansion

We don’t have direct data on early Repin settlers. But we do have a very close representative: Afanasevo, a population we know comes directly from the Repin/late Khvalynsk expansion ca. 3500/3300 BC (just before the emergence of Early Yamna), and which shows fully Steppe_Eneolithic-like ancestry.

afanasevo-admixture

Compared to this eastern Repin expansion that gave Afanasevo, the late Repin expansion to the west ca. 3300 BC that gave rise to the Yamna culture was one of colonization, evidenced by the admixture with north Pontic (Sredni Stog-like) populations, no doubt through exogamy:

PCA-repin-yamna

This admixture is also found (in lesser proportion) in east Yamna groups, which supports the high mobility and exogamy practices among western and eastern Yamna clans, not only with locals:

yamnaya-admixture

5. Corded Ware

Corded Ware represents a quite homogeneous expansion of a late Sredni Stog population, compatible with the traditional location of Proto-Corded Ware peoples in the steppe-forest/forest zone of the Dnieper-Dniester region.

PCA-latvia-ln-steppe

We don’t have a comparison with Ukraine_Eneolithic or Corded Ware samples in Wang et al. (2018), but we do have proximate sources for Abashevo, when compared to the Poltavka population (with which it admixed in the Volga-Ural steppes): Sintashta, Potapovka, Srubna (with further Abashevo contribution), and Andronovo:

sintashta-poltavka-andronovo-admixture

The two CWC outliers from the Baltic show what I thought was an admixture with Yamna. However, given the previous mixture of Eneolithic_Steppe in north Pontic steppe-forest populations, this elevated “steppe ancestry” found in Baltic_LN (similar to west Yamna) seems rather an admixture of Baltic sub-Neolithic peoples with a north Pontic Eneolithic_Steppe-like population. Late Repin settlers also admixed with a similar population during its colonization of the north Pontic area, hence the Baltic_LN – west Yamna similarities.

NOTE. A direct admixture with west Yamna populations through exogamy by the ancestors of this Baltic population cannot be ruled out yet (without direct access to more samples), though, because of the contacts of Corded Ware with west Yamna settlers in the forest-steppe regions.

steppe-ancestry-admixture-latvia

A similar case is found in the Yamna outlier from Mednikarovo south of the Danube. It would be absurd to think that Yamna from the Balkans comes from Corded Ware (or vice versa), just because the former is closer in the PCA to the latter than other Yamna samples. The same error is also found e.g. in the Corded Ware → Bell Beaker theory, because of their proximity in the PCA and their shared “steppe ancestry”. All those theories have been proven already wrong.

NOTE. A similar fallacy is found in potential Sintashta→Mycenaean connections, where we should distinguish statistically that result from an East/West Yamna + Balkans_BA admixture. In fact, genetic links of Mycenaeans with west Yamna settlers prove this (there are some related analyses in Anthrogenica, but the site is down at this moment). To try to relate these two populations (separated more than 1,000 years before Sintashta) is like comparing ancient populations to modern ones, without the intermediate samples to trace the real anthropological trail of what is found…Pure numbers and wishful thinking.

Conclusion

Yamna and Corded Ware show a similar “steppe ancestry” due to convergence. I have said so many times (see e.g. here). This was clear long ago, just by looking at the Y-chromosome bottlenecks that differentiate them – and Tomenable noticed this difference in ADMIXTURE from the supplementary materials in Mathieson et al. (2017), well before Wang et al. (2018).

This different stock stems from (1) completely different ancestral populations + (2) different, long-lasting Y-chromosome bottlenecks. Their similarities come from the two neighbouring cultures admixing with similar populations.

If all this does not mean anything, and each lab was going to support some pre-selected archaeological theories from the 1960s or the 1980s, coupled with outdated linguistic models no matter what – Anthony’s model + Ringe’s glottochronological tree of the early 2000s in the Reich Lab; and worse, Kristiansen’s CWC-IE + Germano-Slavonic models of the 1940s in the Copenhagen group – , I have to repeat my question again:

What’s (so much published) ancient DNA useful for, exactly?

Related

Palaeolithic Caucasus samples reveal the most important component of West Eurasians

dzudzuana-ancestry-europe

Preprint Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry, by Lazaridis et al. bioRxiv (2018).

Interesting excerpts:

We analyzed teeth from two individuals 63 recovered from Dzudzuana Cave, Southern Caucasus, from an archaeological layer previously dated to ~27-24kya (…). Both individuals had mitochondrial DNA sequences (U6 and N) that are consistent with deriving from lineages that are rare in the Caucasus or Europe today. The two individuals were genetically similar to each other, consistent with belonging to the same population and we thus analyze them jointly.

(…) our results prove that the European affinity of Neolithic Anatolians does not necessarily reflect any admixture into the Near East from Europe, as an Anatolian Neolithic-like population already existed in parts of the Near East by ~26kya. Furthermore, Dzudzuana shares more alleles with Villabruna-cluster groups than with other ESHG (Extended Data Fig. 5b), suggesting that this European affinity was specifically related to the Villabruna cluster, and indicating that the Villabruna affinity of PGNE populations from Anatolia and the Levant is not the result of a migration into the Near East from Europe. Rather, ancestry deeply related to the Villabruna cluster was present not only in Gravettian and Magdalenian-era Europeans but also in the populations of the Caucasus, by ~26kya. Neolithic Anatolians, while forming a clade with Dzudzuana with respect to ESHG, share more alleles with all other PGNE (Extended Data Fig. 5d), suggesting that PGNE share at least partially common descent to the exclusion of the much older samples from Dzudzuana.

dzudzuana-anatolia-pca
Ancient West Eurasian population structure. PCA of key ancient West Eurasians, including additional populations (shown with grey shells), in the space of outgroup f4-statistics (Methods).

Our co-modeling of Epipaleolithic Natufians and Ibero-Maurusians from Taforalt confirms that the Taforalt population was mixed, but instead of specifying gene flow from the ancestors of Natufians into the ancestors of Taforalt as originally reported, we infer gene flow in the reverse direction (into Natufians). The Neolithic population from Morocco, closely related to Taforalt is also consistent with being descended from the source of this gene flow, and appears to have no admixture from the Levantine Neolithic (Supplementary Information 166 section 3). If our model is correct, Epipaleolithic Natufians trace part of their ancestry to North Africa, consistent with morphological and archaeological studies that indicate a spread of morphological features and artifacts from North Africa into the Near East. Such a scenario would also explain the presence of Y-chromosome haplogroup E in the Natufians and Levantine farmers, a common link between the Levant and Africa.

(…) we cannot reject the hypothesis that Dzudzuana and the much later Neolithic Anatolians form a clade with respect to ESHG (P=0.286), consistent with the latter being a population largely descended from Dzudzuana-like pre-Neolithic populations whose geographical extent spanned both Anatolia and the Caucasus. Dzudzuana itself can be modeled as a 2-way mixture of Villabruna-related ancestry and a Basal Eurasian lineage.

In qpAdm modeling, a deeply divergent hunter-gatherer lineage that contributed in relatively unmixed form to the much later hunter-gatherers of the Villabruna cluster is specified as contributing to earlier hunter-gatherer groups (Gravettian Vestonice16: 35.7±11.3% and Magdalenian ElMiron: 60.6±11.3%) and to populations of the Caucasus (Dzudzuana: 199 72.5±3.7%, virtually identical to that inferred using ADMIXTUREGRAPH). In Europe, descendants of this lineage admixed with pre-existing hunter-gatherers related to Sunghir3 from Russia for the Gravettians and GoyetQ116-1 from Belgium for the Magdalenians, while in the Near East it did so with Basal Eurasians. Later Europeans prior to the arrival of agriculture were the product of re-settlement of this lineage after ~15kya in mainland Europe, while in eastern Europe they admixed with Siberian hunter-gatherers forming the WHG-ANE cline of ancestry [See PCA above]. In the Near East, the Dzudzuana-related population admixed with North African-related ancestry in the Levant and with Siberian hunter-gatherer and eastern non-African-related ancestry in Iran and the Caucasus. Thus, the highly differentiated populations at the dawn of the Neolithic were primarily descended from Villabruna Cluster and Dzudzuana-related ancestors, with varying degrees of additional input related to both North Africa and Ancient North/East Eurasia whose proximate sources may be clarified by future sampling of geographically and temporally intermediate populations.

qpgraph-dzudzuana
An admixture graph model of Paleolithic West Eurasians. An automatically generated admixture graph models fits populations (worst Z-score of the difference between estimated and fitted f-statistics is 2.7) or populations (also including South_Africa_HG, worst Z-score is 3.5). This is a simplified model assuming binary admixture events and is not a unique solution (Supplementary Information section 2). Sampled populations are shown with ovals and select labeled internal nodes with rectangles.

Interesting excerpts from the supplementary materials:

From our analysis of Supplementary Information section 3, we showed that these sources are indeed complex, and only one of these (WHG, represented by Villabruna) appears to be a contributor to all the remaining sources. This should not be understood as showing that hunter-gatherers from mainland Europe migrated to the rest of West Eurasia, but rather that the fairly homogeneous post-15kya population of mainland Europe labeled WHG appear to represent a deep strain of ancestry that seems to have contributed to West Eurasians from the Gravettian era down to the Neolithic period.

Villabruna is representative of the WHG group. We also include ElMiron, the best sample from the Magdalenian era as we noticed that within the WHG group there were individuals that could not be modeled as a simple clade with Villabruna but also had some ElMiron-related ancestry. Ddudzuana is representative of the Ice Age Caucasus population, differentiated from Villabruna by Basal Eurasian ancestry. AG3 represents ANE/Upper Paleolithic Siberian ancestry, sampled from the vicinity of Lake Baikal, while Russia_Baikal_EN related to eastern Eurasians and represents a later layer of ancestry from the same region of Siberia as AG3 Finally, Mbuti are a deeply diverged African population that is used here to represent deep strains of ancestry (including Basal Eurasian) prior to the differentiation between West Eurasians and eastern non-Africans that are otherwise not accounted for by the remaining five sources. Collectively, we refer to this as ‘Basal’ or ‘Deep’ ancestry, which should be understood as referring potentially to both Basal Eurasian and African ancestry.

It has been suggested that there is an Anatolia Neolithic-related affinity in hunter-gatherers from the Iron Gates. Our analysis confirms this by showing that this population has Dzudzuana-related ancestry as do many hunter-gatherer populations from southeastern Europe, eastern Europe and Scandinavia. These populations cannot be modeled as a simple mixture of Villabruna and AG3 but require extra Dzudzuana-related ancestry even in the conservative estimates, with a positive admixture proportion inferred for several more in the speculative ones. Thus, the distinction between European hunter-gatherers and Near Eastern populations may have been gradual in pre-Neolithic times; samples from the Aegean (intermediate between those from the Balkans and Anatolia) may reveal how gradual the transition between Dzudzuana-like Neolithic Anatolians and mostly Villabruna-like hunter-gatherers was in southeastern Europe.

ancient-modern-european-admixture
Modified image (cut, with important samples marked). Modeling present-day and ancient West-Eurasians. Mixture proportions computed with qpAdm (Supplementary Information section 4). The proportion of ‘Mbuti’ ancestry represents the total of ‘Deep’ ancestry from lineages that split prior to the 365 split of Ust’Ishim, Tianyuan, and West Eurasians and can include both ‘Basal Eurasian’ and other (e.g., Sub-Saharan African) ancestry. (a) ‘Conservative’ estimates. Each population 367 cannot be modeled with fewer admixture events than shown.

Villabruna: This type of ancestry differentiates between present-day Europeans and non-Europeans within West Eurasia, attaining a maximum of ~20% in the Baltic in accordance with previous observations and with the finding of a later persistence of significant hunter-gatherer ancestry in the region. Its proportion drops to ~0% throughout the Near East. Interestingly, a hint of such ancestry is also inferred in all North African populations west of Libya in the speculative proportions, consistent with an archaeogenetic inference of gene flow from Iberia to North Africa during the Late Neolithic.

ElMiron: This type of ancestry is absent in present-day West Eurasians. This may be because most of the Villabruna-related ancestry in Europeans traces to WHG populations that lacked it (since ElMiron-related ancestry is quite variable within European hunter-gatherers). However, ElMiron ancestry makes up only a minority component of all WHG populations sampled to date and WHG-related ancestry is a minority component of present-day Europeans. Thus, our failure to detect it in present day people may be simply be too little of it to detect with our methods.

Dzudzuana: Our analysis identifies Dzudzuana-related ancestry as the most important component of West Eurasians and the one that is found across West Eurasian-North African populations at ~46-88% levels. Thus, Dzudzuana-related ancestry can be viewed as the common core of the ancestry of West Eurasian-North African populations. Its distribution reaches its minima in northern Europe and appears to be complementary to that of Villabruna, being most strongly represented in North Africa, the Near East (including the Caucasus) and Mediterranean Europe. Our results here are expected from those of Supplementary Information section 3 in which we modeled ancient Near Eastern/North African populations (the principal ancestors of present-day people from the same regions) as deriving much of their ancestry from a Dzudzuana-related source. Migrations from the Near East/Caucasus associated with the spread of the Neolithic, but also the formation of steppe population introduced most of the Dzudzuana-related ancestry present in Europe, although (as we have seen above) some such ancestry was already present in some pre-agricultural hunter-gatherers in Europe.

AG3: Ancestry related to the AG3 sample from Siberia has a northern distribution, being strongly represented in both central-northern Europe and the north Caucasus.

Russia_Baikal_EN: Ancestry related to hunter-gatherers from Lake Baikal in Siberia (postdating AG3) appears to have affected primarily northeastern European populations which have been previously identified as having East Eurasian ancestry; some such ancestry is also identified for a Turkish population from Balıkesir, likely reflecting the Central Asian ancestry of Turkic speakers which has been recently confirmed directly in an Ottoman sample from Anatolia.

Some comments

So, to try and sum up:

  • Dzudzuana shares ancestry with ‘Common West Eurasian’ (CWE). the ancestor cluster of Villabruna.
  • Dzudzuana diverges from CWE because of a Basal Eurasian ancestry contribution [which supports that Basal Eurasian ancestry was a deep Middle Eastern lineage].
  • Dzudzuana is closest to Anatolia Neolithic, and close to Gravettian.
palaeolithic-gravettian-villabruna
Palaeolithic migrations and clusters in Europe. See more maps.

Chronologically:

  1. Aurignacian: First West Eurasians arrive ca. 36,000 BP, Goyet cluster expands probably with C1a2 lineages.
  2. After that, the early or ‘unmixed’ Villabruna cluster (‘hidden’ somewhere probably east of Europe, either North Eurasia or South Eurasia), lineages unknown (possibly IJ), contributes to:
    1. Gravettian (ca. 30,000 BP): Věstonice cluster expands, probably with IJ lineages.
    2. A (hidden) ‘Common West Eurasian’ population.
    3. In turn:

      • Dzudzuana ca. 26,000 BP derived from Common West Eurasian (curiously, haplogroup G seems to split in today’s subclades ca. 26,000 BP).
      • During the Gravettian (ca. 26,000 BP), an Anatolian Neolithic-like population exists already in the Near East. Both Věstonice and this Anatolian HG are close to Dzudzuana; in turn, Dzudzuana from CWE.

    4. Magdalenian (ca. 20,000 BP): El Mirón cluster expands, probably with more specific I lineages.
  3. Bølling-Allerød warming period (ca. 14,000 BP): ‘late’ Villabruna cluster or WHG (=CWE with greater affinity to Near Eastern populations) expands, probably spreading with R1b in mainland Europe and to the east (admixing with Siberian HG), creating the WHG — ANE ancestry cline, as reflected in Iron Gates HG, Baltic HG, etc.

[Here we have the possible “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” inferred from Anatolian hunter-gatherers]

palaeolithic-gravettian-magdalenian-migrations
The Gravettian (30,000 to 20,000 years) is drawn in black and white; the subsequent Magdalenian (17,000 to 10,000 years) and Hamburgian (13,000-11,750 years) are in light blue and red. It is not known whether the spread of the Gravettian was a result of diffusion of people or cultures. This figure illustrates the possible monocentric origins of the Gravettian, in which the Gravettian is hypothesized to have its origin in the Middle Danube Basin, first spreading west (solid lines) and later spreading east and southeast (dashed lines). This scenario is largely based on the chronology of sites. Thus far, genome-wide data has been collected from only three of the ten< Gravettian regions indicated on the map. These regions are northern Austria (1 sample), the Czech Republic (6), southern Italy (3) and Belgium (3), indicating that they all share a genomic ancestry. However, it is unknown whether samples from the remaining regions also share a close genomic ancestry. Some skeletal remains associated with the Gravettian that could be investigated paleogenomically are from Sungir (Russia); Laghar Velho (central Portugal); Cussac Cave; Les Garennes, near Vilhonneur; and Level 2 at Abri Pataud116 (western France). Light blue and light red regions represent the approximate distributions of the Magdalenian Culture and the Hamburgian Culture (13,000-11,750 years). Figure adapted from Kozłowski. Image from Harris (2017)

The paper talks about possibilities for Common West Eurasian:

  1. Migration from mainland Europe to Near East or vice versa (not very likely);
  2. Migration from a geographically intermediate Ice Age refugium in southeast Europe, Anatolia, or the circum-Pontic region that explain post-glacial affinity of post-glacial Levantine and Anatolian populations.

It also re-states what was known:

  • EHG (ca. 8,000 BP) = between WHG — ANE (ca. 24,000 BP).
  • CHG (ca. 10,000 BP) = between EHG — Iran N.

I would say that the distinct CHG vs. Dzudzuana ancestry puts CHG probably to the south, within the Iranian Plateau, during the Gravettian, expanding probably later.

Also important, Ancestral North African probably accompanied by haplogroup E. Early expansion of North Africans into the Near East further confirms the impossibility of Afroasiatic (much younger) to be associated with these expansions, and confirms that the still unclear Green Sahara migrations are the key.

Related