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 170 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.

So, here we have the explanation for the “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.

Related

Expansion of haplogroup G2a in Anatolia possibly associated with the Mature Aceramic period

anatolian-hunter-gatherer-sampling

Preprint Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia, by Feldman et al. bioRxiv (2018).

Interesting excerpts (emphasis mine):

Anatolian hunter-gatherers experienced climatic changes during the last glaciation and inhabited a region that connects Europe to the Near East. However, interactions between Anatolia and Southeastern Europe in the later Upper Palaeolithic/Epipalaeolithic are so far not well documented archaeologically. Interestingly, a previous genomic study showed that present-day Near-Easterners share more alleles with European hunter-gatherers younger than 14,000 BP (‘Later European HG’) than with earlier ones (‘Earlier European HG’). With ancient genomic data available, we could directly compare the Near-Eastern hunter-gatherers (AHG and Natufian) with the European ones. As is the case for present-day Near-Easterners, the Near-Eastern hunter-gatherers share more alleles with the Later European HG than with the Earlier European HG, shown by the significantly positive statistic D(Later European HG, Earlier European HG; AHG/Natufian, Mbuti). Among the Later European HG, recently reported Mesolithic hunter-gatherers from the Balkan peninsula, which geographically connects Anatolia and central Europe (‘Iron Gates HG’), are genetically closer to AHG when compared to all the other European hunter-gatherers, as shown in the significantly positive statistic D(Iron_Gates_HG, European hunter-gatherers; AHG, Mbuti/Altai). Iron Gates HG are followed by Epigravettian and Mesolithic individuals from Italy and France (Villabruna and Ranchot respectively) as the next two European hunter-gatherers genetically closest to AHG. Iron Gates HG have been suggested to be genetically intermediate between WHG and eastern European hunter-gatherers (EHG) with an additional unknown ancestral component.

anatolian-hunter-gatherer-pca
Ancient genomes (marked with color-filled symbols) projected onto the principal components 5 computed from present-day west Eurasians (grey circles) (fig. S4). The geographic location of each ancient group is marked in (A). Ancient individuals newly reported in this study are additionally marked with a black dot inside the symbol

We find that Iron Gates HG can be modeled as a three-way mixture of Near-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4 % or 78.0 ± 4.6 % respectively) and EHG (11.3 ± 3.3 % or 10.9 ± 3 % respectively). The affinity detected by the above D-statistic can be explained by gene flow from Near-Eastern hunter-gatherers into the ancestors of Iron Gates or by a gene flow from a population ancestral to Iron Gates into the Near-Eastern hunter-gatherers as well as by a combination of both. To distinguish the direction of the gene flow, we examined the Basal Eurasian ancestry 5 component (α), which is prevalent in the Near East but undetectable in European hunter-gatherers. Following a published approach, we estimated α to be 24.8 ± 5.5 % in AHG and 38.5 ± 5.0 % in Natufians, consistent with previous estimates for the latter. Under the model of unidirectional gene flow from Anatolia to Europe, 6.4 % is expected for α of Iron Gates by calculating (% AHG in Iron Gates HG) × (α in AHG). However, Iron Gates can be modeled without any Basal Eurasian ancestry or with a non-significant proportion of 1.6 ± 2.8 %, suggesting that unidirectional gene flow from the Near East to Europe alone is insufficient to explain the extra affinity between the Iron Gates HG and the Near-Eastern hunter-gatherers. Thus, it is plausible to assume that prior to 15,000 years ago there was either a bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East. Presumably, this Southeastern European ancestral population later spread into central Europe during the post-last-glacial maximum (LGM) period, resulting in the observed late Pleistocene genetic affinity between the Near East and Europe.

near-eastern-european-hg
Basal Eurasian ancestry proportions (α) as a marker for Near-Eastern gene flow. Mixture proportions inferred by qpAdm for AHG and the Iron Gates HG are schematically represented. The lower schematic shows the expected α in Iron Gates HG under 10 assumption of unidirectional gene flow, inferred from α in the AHG source population. The observed α for Iron Gates HG is considerably smaller than expected thus, the unidirectional gene flow from the Near East to Europe is not sufficient to explain the above affinity.

While ancestry is not always relevant to distinguish certain population movements (see here), especially – as in this case – when there are few samples (thus neither geographically nor chronologically representative) and no previous model to test, it seems that ancestry and Y-DNA show a great degree of continuity in Anatolia since the Palaeolithic until the Neolithic, at least in the sampled regions. C1a2 appears in Europe since ca. 40,000 years ago (viz. Kostenki, Goyet, Vestonice, etc., and later emerges again in the Balkans after the Anatolian Neolithic expansion, probably a resurge of European groups).

The potential transition of a G2a-dominated agricultural society – that is later prevalent in Anatolian and European farmers – may have therefore happened during the Aceramic III period (ca. 8000 BC), a process of haplogroup expansion probably continuing through the early part of the Pottery Neolithic, as the society based on kinship appeared (Rosenberg and Erim-Özdoğan 2011). There is still much to know about the spread of ceramic technology and southwestern Asia domesticate complex, though.

anatolian-palaeolithic-hg

Without a proper geographical sampling, representative of previous and posterior populations, it is impossible to say. But the expansion of R1b-L754 through Anatolia to form part of the Villabruna cluster (and also the Iron Gates HG) seems perfectly possible with this data, although this paper does not help clarify the when or how. We have seen significant changes in ancestry happen within centuries with expanding populations admixing with locals. Palaeolithic sampling – like this one – shows few individuals scattered geographically over thousands of km and chronologically over thousands of years…

Related

Neolithic and Bronze Age Anatolia, Urals, Fennoscandia, Italy, and Hungary (ISBA 8, 20th Sep)

jena-isba8

I will post information on ISBA 8 sesions today as I see them on Twitter (see programme in PDF, and sessions from yesterday).

Official abstracts are listed first (emphasis mine), then reports and images and/or link to tweets. Here is the list for quick access:

Russian colonization in Yakutia

Exploring the genomic impact of colonization in north-eastern Siberia, by Seguin-Orlando et al.

Yakutia is the coldest region in the northern hemisphere, with winter record temperatures below minus 70°C. The ability of Yakut people to adapt both culturally and biologically to extremely cold temperatures has been key to their subsistence. They are believed to descend from an ancestral population, which left its original homeland in the Lake Baykal area following the Mongol expansion between the 13th and 15th centuries AD. They originally developed a semi-nomadic lifestyle, based on horse and cattle breeding, providing transportation, primary clothing material, meat, and milk. The early colonization by Russians in the first half of the 17th century AD, and their further expansion, have massively impacted indigenous populations. It led not only to massive epidemiological outbreaks, but also to an important dietary shift increasingly relying on carbohydrate-rich resources, and a profound lifestyle transition with the gradual conversion from Shamanism to Christianity and the establishment of new marriage customs. Leveraging an exceptional archaeological collection of more than a hundred of bodies excavated by MAFSO (Mission Archéologique Française en Sibérie Orientale) over the last 15 years and naturally kept frozen by the extreme cold temperatures of Yakutia, we have started to characterize the (epi)genome of indigenous individuals who lived from the 16th to the 20th century AD. Current data include the genome sequence of approximately 50 individuals that lived prior to and after Russian contact, at a coverage from 2 to 40 fold. Combined with data from archaeology and physical anthropology, as well as microbial DNA preserved in the specimens, our unique dataset is aimed at assessing the biological consequences of the social and biological changes undergone by the Yakut people following their neolithisation by Russian colons.

NOTE: For another interesting study on Yakutian tribes, see Relationships between clans and genetic kin explain cultural similarities over vast distances.

Ancient DNA from a Medieval trading centre in Northern Finland

Using ancient DNA to identify the ancestry of individuals from a Medieval trading centre in Northern Finland, by Simoes et al.

Analyzing genomic information from archaeological human remains has proved to be a powerful approach to understand human history. For the archaeological site of Ii Hamina, ancient DNA can be used to infer the ancestries of individuals buried there. Situated approximately 30 km from Oulu, in Northern Finland, Ii Hamina was an important trade place since Medieval times. The historical context indicates that the site could have been a melting pot for different cultures and people of diversified genetic backgrounds. Archaeological and osteological evidence from different individuals suggest a rich diversity. For example, stable isotope analyses indicate that freshwater and marine fish was the dominant protein source for this population. However, one individual proved to be an outlier, with a diet containing relatively more terrestrial meat or vegetables. The variety of artefacts that was found associated with several human remains also points to potential differences in religious beliefs or social status. In this study, we aimed to investigate if such variation could be attributed to different genetic ancestries. Ten of the individuals buried in Ii Hamina’s churchyard, dating to between the 15th and 17th century AD, were screened for presence of authentic ancient DNA. We retrieved genome-wide data for six of the individuals and performed downstream analysis. Data authenticity was confirmed by DNA damage patterns and low estimates of mitochondrial contamination. The relatively recent age of these human remains allows for a direct comparison to modern populations. A combination of population genetics methods was undertaken to characterize their genetic structure, and identify potential familiar relationships. We found a high diversity of mitochondrial lineages at the site. In spite of the putatively distant origin of some of the artifacts, most individuals shared a higher affinity to the present-day Finnish or Late Settlement Finnish populations. Interestingly, different methods consistently suggested that the individual with outlier isotopic values had a different genetic origin, being more closely related to reindeer herding Saami. Here we show how data from different sources, such as stable isotopes, can be intersected with ancient DNA in order to get a more comprehensive understanding of the human past.

A closer look at the bottom left corner of the poster (the left columns are probably the new samples):

finland-medieval-admixture

Plant resources processed in HG pottery from the Upper Volga

Multiple criteria for the detection of plant resources processed in hunter-gatherer pottery vessels from the Upper Volga, Russia, by Bondetti et al.

In Northern Eurasia, the Neolithic is marked by the adoption of pottery by hunter-gatherer communities. The degree to which this is related to wider social and lifestyle changes is subject to ongoing debate and the focus of a new research programme. The use and function of early pottery by pre-agricultural societies during the 7th-5th millennia BC is of central interest to this debate. Organic residue analysis provides important information about pottery use. This approach relies on the identification and isotopic characteristics of lipid biomarkers, absorbed into the pores of the ceramic or charred deposits adhering to pottery vessel surfaces, using a combined methodology, namely GC-MS, GC-c-IRMS and EA-IRMS. However, while animal products (e.g., marine, freshwater, ruminant, porcine) have the benefit of being lipid-rich and well-characterised at the molecular and isotopic level, the identification of plant resources still suffers from a lack of specific criteria for identification. In huntergatherer contexts this problem is exacerbated by the wide range of wild, foraged plant resources that may have been potentially exploited. Here we evaluate approaches for the characterisation of terrestrial plant food in pottery through the study of pottery assemblages from Zamostje 2 and Sakhtysh 2a, two hunter-gatherer settlements located in the Upper Volga region of Russia.

GC-MS analysis of the lipids, extracted from the ceramics and charred residues by acidified methanol, suggests that pottery use was primarily oriented towards terrestrial and aquatic animal products. However, while many of the Early Neolithic vessels contain lipids distinctive of freshwater resources, triterpenoids are also present in high abundance suggesting mixing with plant products. When considering the isotopic criteria, we suggest that plants were a major commodity processed in pottery at this time. This is supported by the microscopic identification of Viburnum (Viburnum Opulus L.) berries in the charred deposits on several vessels from Zamostje.

The study of Upper Volga pottery demonstrated the importance of using a multidisciplinary approach to determine the presence of plant resources in vessels. Furthermore, this informs the selection of samples, often subject to freshwater reservoir effects, for 14C dating.

Studies on hunter-gatherer pottery – appearing in eastern Europe before Middle Eastern Neolithic pottery – may be important to understand the arrival of R1a-M17 lineages to the region before ca. 7000 BC. Or not, right now it is not very clear what happened with R1b-P297 and R1a-M17, and with WHG—EHG—ANE ancestry

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe, by Warinner et al.

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH), beginning in the Eneolithic (ca. 3300-2700 BCE), profoundly transformed the genes and cultures of Europe and Central Asia. Compared to Europe, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Bronze Age khirigsuur burials from Khövsgöl, Mongolia (ca. 1380-975 BCE). Only one individual showed evidence of WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. At the same time, LCMS/ MS analysis of dental calculus provides direct protein evidence of milk consumption from Western domesticated livestock in 7 of 9 individuals. Our results show that dairy pastoralism was adopted by Bronze Age Mongolians despite minimal genetic exchange with Western steppe herders.

Detail of the images:

mongol-bronze-age-pca

mongol-bronze-age-f4-ancestry

Evolution of Steppe, Neolithic, and Siberian ancestry in Eurasia (ISBA 8, 19th Sep)

jena-isba8

Some information is already available from ISBA 8 (see programme in PDF), thanks to the tweets from Alexander M. Kim.

Official abstracts are listed first (emphasis mine), then reports and images with link to Kim’s tweets. Here is the list for quick access:

Updates (17:00 CET):

Turkic and Hunnic expansions

Tracing the origin and expansion of the Turkic and Hunnic confederations, by Flegontov et al.

Turkic-speaking populations, now spread over a vast area in Asia, are highly heterogeneous genetically. The first confederation unequivocally attributed to them was established by the Göktürks in the 6th c. CE. Notwithstanding written resources from neighboring sedentary societies such as Chinese, Persian, Indian and Eastern Roman, earlier history of the Turkic speakers remains debatable, including their potential connections to the Xiongnu and Huns, which dominated the Eurasian steppe in the first half of the 1st millennium CE. To answer these questions, we co-analyzed newly generated human genome-wide data from Central Asia (the 1240K panel), spanning the period from ca. 3000 to 500 YBP, and the data published by de Barros Damgaard et al. (137 ancient human genomes from across the Eurasian steppes, Nature, 2018). Firstly, we generated a PCA projection to understand genetic affinities of ancient individuals with respect to present-day Tungusic, Mongolic, Turkic, Uralic, and Yeniseian-speaking groups. Secondly, we modeled hundreds of present-day and few ancient Turkic individuals using the qpAdm tool, testing various modern/ancient Siberian and ancient West Eurasian proxies for ancestry sources.

A majority of Turkic speakers in Central Asia, Siberia and further to the west share the same ancestry profile, being a mixture of Tungusic or Mongolic speakers and genetically West Eurasian populations of Central Asia in the early 1st millennium CE. The latter are themselves modelled as a mixture of Iron Age nomads (western Scythians or Sarmatians) and ancient Caucasians or Iranian farmers. For some Turkic groups in the Urals and the Altai regions and in the Volga basin, a different admixture model fits the data: the same West Eurasian source + Uralic- or Yeniseian-speaking Siberians. Thus, we have revealed an admixture cline between Scythians and the Iranian farmer genetic cluster, and two further clines connecting the former cline to distinct ancestry sources in Siberia. Interestingly, few Wusun-period individuals harbor substantial Uralic/Yeniseian-related Siberian ancestry, in contrast to preceding Scythians and later Turkic groups characterized by the Tungusic/Mongolic-related ancestry. It remains to be elucidated whether this genetic influx reflects contacts with the Xiongnu confederacy. We are currently assembling a collection of samples across the Eurasian steppe for a detailed genetic investigation of the Hunnic confederacies.

jeong-population-clines
Three distinct East/West Eurasian clines across the continent with some interesting linguistic correlates, as earlier reported by Jeong et al. (2018). Alexander M. Kim.
siberian-genetic-component-chronology
Very important observation with implication of population turnover is that pre-Turkic Inner Eurasian populations’ Siberian ancestry appears predominantly “Uralic-Yeniseian” in contrast to later dominance of “Tungusic-Mongolic” sort (which does sporadically occur earlier). Alexander M. Kim

New interesting information on the gradual arrival of the “Uralic-Yeniseian” (Siberian) ancestry in eastern Europe with Iranian and Turkic-speaking peoples. We already knew that Siberian ancestry shows no original relationship with Uralic-speaking peoples, so to keep finding groups who expanded this ancestry eastwards in North Eurasia should be no surprise for anyone at this point.

Central Asia and Indo-Iranian

The session The Genomic Formation of South and Central Asia, by David Reich, on the recent paper by Narasimhan et al. (2018).

bmac-reich
One important upside of dense genomic sampling at single localities – greater visibility of outliers and better constraints on particular incoming ancestries’ arrival times. Gonur Tepe as a great case study of this. Alexander M. Kim
ani-asi-steppe-cline
– Tale of three clines, with clear indication that “Indus Periphery” samples drawn from an already-cosmopolitan and heterogeneous world of variable ASI & Iranian ancestry. (I know how some people like to pore over these pictures – so note red dots = just dummy data for illustration.)
– Some more certainty about primary window of steppe ancestry injection into S. Asia: 2000-1500 BC
Alexander M. Kim

British Isles

Ancient DNA and the peopling of the British Isles – pattern and process of the Neolithic transition, by Brace et al.

Over recent years, DNA projects on ancient humans have flourished and large genomic-scale datasets have been generated from across the globe. Here, the focus will be on the British Isles and applying aDNA to address the relative roles of migration, admixture and acculturation, with a specific focus on the transition from a Mesolithic hunter-gatherer society to the Neolithic and farming. Neolithic cultures first appear in Britain ca. 6000 years ago (kBP), a millennium after they appear in adjacent areas of northwestern continental Europe. However, in Britain, at the margins of the expansion the pattern and process of the British Neolithic transition remains unclear. To examine this we present genome-wide data from British Mesolithic and Neolithic individuals spanning the Neolithic transition. These data indicate population continuity through the British Mesolithic but discontinuity after the Neolithic transition, c.6000 BP. These results provide overwhelming support for agriculture being introduced to Britain primarily by incoming continental farmers, with surprisingly little evidence for local admixture. We find genetic affinity between British and Iberian Neolithic populations indicating that British Neolithic people derived much of their ancestry from Anatolian farmers who originally followed the Mediterranean route of dispersal and likely entered Britain from northwestern mainland Europe.

british-isles
Millennium of lag between farming establishment in NW mainland Europe & British Isles. Only 25 Mesolithic human finds from Britain. Alexander M. Kim.
british-admixture
– Evidently no resurgence of hunter-gatherer ancestry across Neolithic
– Argument for at least two geographically distinct entries of Neolithic farmers
Alexander M. Kim.

MN Atlantic / Megalithic cultures

Genomics of Middle Neolithic farmers at the fringe of Europe, by Sánchez Quinto et al.

Agriculture emerged in the Fertile Crescent around 11,000 years before present (BP) and then spread, reaching central Europe some 7,500 years ago (ya.) and eventually Scandinavia by 6,000 ya. Recent paleogenomic studies have shown that the spread of agriculture from the Fertile Crescent into Europe was due mainly to a demic process. Such event reshaped the genetic makeup of European populations since incoming farmers displaced and admixed with local hunter-gatherers. The Middle Neolithic period in Europe is characterized by such interaction, and this is a time where a resurgence of hunter-gatherer ancestry has been documented. While most research has been focused on the genetic origin and admixture dynamics with hunter-gatherers of farmers from Central Europe, the Iberian Peninsula, and Anatolia, data from farmers at the North-Western edges of Europe remains scarce. Here, we investigate genetic data from the Middle Neolithic from Ireland, Scotland, and Scandinavia and compare it to genomic data from hunter-gatherers, Early and Middle Neolithic farmers across Europe. We note affinities between the British Isles and Iberia, confirming previous reports. However, we add on to this subject by suggesting a regional origin for the Iberian farmers that putatively migrated to the British Isles. Moreover, we note some indications of particular interactions between Middle Neolithic Farmers of the British Isles and Scandinavia. Finally, our data together with that of previous publications allow us to achieve a better understanding of the interactions between farmers and hunter-gatherers at the northwestern fringe of Europe.

megalithic-europe
-Novel genomic data from 21 individuals from 6 sites.
– “Megalithic” individuals not systematically diff. from geographically proximate “non-megalithic” burials
– Mild evidence for over-representation of males in some British Isles megalithic tombs
– Megalithic tombs in W & N Neolithic Europe may have link to kindred structures
Alexander M. Kim

Central European Bronze Age

Ancient genomes from the Lech Valley, Bavaria, suggest socially stratified households in the European Bronze Age, by Mittnik et al.

Archaeogenetic research has so far focused on supra-regional and long-term genetic developments in Central Europe, especially during the third millennium BC. However, detailed high-resolution studies of population dynamics in a microregional context can provide valuable insights into the social structure of prehistoric societies and the modes of cultural transition.

Here, we present the genomic analysis of 102 individuals from the Lech valley in southern Bavaria, Germany, which offers ideal conditions for such a study. Several burial sites containing rich archaeological material were directly dated to the second half of the 3rd and first half of the 2nd millennium BCE and were associated with the Final Neolithic Bell Beaker Complex and the Early and Middle Bronze Age. Strontium isotope data show that the inhabitants followed a strictly patrilocal residential system. We demonstrate the impact of the population movement that originated in the Pontic-Caspian steppe in the 3rd millennium BCE and subsequent local developments. Utilising relatedness inference methods developed for low-coverage modern DNA we reconstruct farmstead related pedigrees and find a strong association between relatedness and grave goods suggesting that social status is passed down within families. The co-presence of biologically related and unrelated individuals in every farmstead implies a socially stratified complex household in the Central European Bronze Age.

lech-bavaria
Diminishing steppe ancestry and resurgent Neolithic ancestry over time. Alexander M. Kim

Notice how the arrival of Bell Beakers, obviously derived from Yamna settlers in Hungary, and thus clearly identified as expanding North-West Indo-Europeans all over Europe, marks a decrease in steppe ancestry compared to Corded Ware groups, in a site quite close to the most likely East BBC homeland. Copenhagen’s steppe ancestry = Indo-European going down the toilet, step by step…

UPDATES

Russian Far East populations

Gene geography of the Russian Far East populations – faces, genome-wide profiles, and Y-chromosomes, by Balanovsky et al.

Russian Far East is not only a remote area of Eurasia but also a link of the chain of Pacific coast regions, spanning from East Asia to Americas, and many prehistoric migrations are known along this chain. The Russian Far East is populated by numerous indigenous groups, speaking Tungusic, Turkic, Chukotko-Kamchatka, Eskimo-Aleut, and isolated languages. This linguistic and geographic variation opens question about the patterns of genetic variation in the region, which was significantly undersampled and received minor attention in the genetic literature to date. To fill in this gap we sampled Aleuts, Evenks, Evens, Itelmens, Kamchadals, Koryaks, Nanais, Negidals, Nivkhs, Orochi, Udegeis, Ulchi, and Yakuts. We also collected the demographic information of local populations, took physical anthropological photos, and measured the skin color. The photos resulted in the “synthetic portraits” of many studied groups, visualizing the main features of their faces.

north-eurasia

far-east-pca
Impressive North Eurasian biobank including 30,500 individual samples with broad consent, some genealogical info, phenotypic data. Alexander M. Kim

Finland AD 5th-8th c.

Sadly, no information will be shared on the session A 1400-year transect of ancient DNA reveals recent genetic changes in the Finnish population, by Salmela et al. We will have to stick to the abstract:

Objectives: Our objective was to use aDNA to study the population history of Finland. For this aim, we sampled and sequenced 35 individuals from ten archaeological sites across southern Finland, representing a time transect from 5th to 18th century.

Methods: Following genomic DNA extraction and preparation of indexed libraries, the samples were enriched for 1,2 million genomewide SNPs using in-solution capture and sequenced on an Illumina HighSeq 4000 instrument. The sequence data were then compared to other ancient populations as well as modern Finns, their geographical neighbors and worldwide populations. Authenticity testing of the data as well as population history inference were based on standard computational methods for aDNA, such as principal component analysis and F statistics.

Results: Despite the relatively limited temporal depth of our sample set, we are able to see major genetic changes in the area, from the earliest sampled individuals – who closely resemble the present-day Saami population residing markedly further north – to the more recent ancient individuals who show increased affinity to the neighboring Circum-Baltic populations. Furthermore, the transition to the present-day population seems to involve yet another perturbation of the gene pool.

So, most likely then, in my opinion – although possibly Y-DNA will not be reported – Finns were in the Classical Antiquity period mostly R1a with secondary N1c in the Circum-Baltic region (similar to modern Estonians, as I wrote recently), while Saami were probably mostly a mix of R1a-Z282 and I1 in southern Finland. That’s what the first transition after the 5th c. probably reflects, the spread of Finns (with mainly N1c lineages) to the north, while the more recent transition shows probably the introduction of North Germanic ancestry (and thus also R1b-U106, R1a-Z284, and I1 lineages) in the west.

Dairying in ancient Mongolia

The History of Dairying in ancient Mongolia, by Wilkin et al.

The use of mass spectrometry based proteomics presents a novel method for investigating human dietary intake and subsistence strategies from archaeological materials. Studies of ancient proteins extracted from dental calculus, as well as other archaeological material, have robustly identified both animal and plant-based dietary components. Here we present a recent case study using shotgun proteomics to explore the range and diversity of dairying in the ancient eastern Eurasian steppe. Contemporary and prehistoric Mongolian populations are highly mobile and the ephemerality of temporarily occupied sites, combined with the severe wind deflation common across the steppes, means detecting evidence of subsistence can be challenging. To examine the time depth and geographic range of dairy use in Mongolia, proteins were extracted from ancient dental calculus from 32 individuals spanning burial sites across the country between the Neolithic and Mongol Empire. Our results provide direct evidence of early ruminant milk consumption across multiple time periods, as well as a dramatic increase in the consumption of horse milk in the late Bronze Age. These data provide evidence that dairy foods from multiple species were a key part of subsistence strategies in prehistoric Mongolia and add to our understanding of the importance of early pastoralism across the steppe.

The confirmation of the date 3000-2700 BC for dairying in the eastern steppe further supports what was already known thanks to archaeological remains, that the pastoralist subsistence economy was brought for the first time to the Altai region by expanding late Khvalynsk/Repin – Early Yamna pastoralists that gave rise to the Afanasevo culture.

Neolithic transition in Northeast Asia

Genomic insight into the Neolithic transition peopling of Northeast Asia, by C. Ning

East Asian representing a large geographic region where around one fifth of the world populations live, has been an interesting place for population genetic studies. In contrast to Western Eurasia, East Asia has so far received little attention despite agriculture here evolved differently from elsewhere around the globe. To date, only very limited genomic studies from East Asia had been published, the genetic history of East Asia is still largely unknown. In this study, we shotgun sequenced six hunter-gatherer individuals from Houtaomuga site in Jilin, Northeast China, dated from 12000 to 2300 BP and, 3 farming individuals from Banlashan site in Liaoning, Northeast China, dated around 5300 BP. We find a high level of genetic continuity within northeast Asia Amur River Basin as far back to 12000 BP, a region where populations are speaking Tungusic languages. We also find our Compared with Houtaomuga hunter-gatherers, the Neolithic farming population harbors a larger proportion of ancestry from Houtaomuga related hunter-gathers as well as genetic ancestry from central or perhaps southern China. Our finding further suggests that the introduction of farming technology into Northeast Asia was probably introduced through demic diffusion.

A detail of the reported haplogroups of the Houtaomuga site:

houtaomuga-site-y-dna-mtdna

Y-DNA in Northeast Asia shows thus haplogroup N1b1 ~5000 BC, probably representative of the Baikal region, with a change to C2b-448del lineages before the Xiongnu period, which were later expanded by Mongols.

Modern Sardinians show elevated Neolithic farmer ancestry shared with Basques

sardinia-europe-relation

New paper (behind paywall), Genomic history of the Sardinian population, by Chiang et al. Nature Genetics (2018), previously published as a preprint at bioRxiv (2016).

#EDIT (18 Sep 2018): Link to read paper for free shared by the main author.

Interesting excerpts (emphasis mine):

Our analysis of divergence times suggests the population lineage ancestral to modern-day Sardinia was effectively isolated from the mainland European populations ~140–250 generations ago, corresponding to ~4,300–7,000 years ago assuming a generation time of 30 years and a mutation rate of 1.25 × 10−8 per basepair per generation. (…) in terms of relative values, the divergence time between Northern and Southern Europeans is much more recent than either is to Sardinia, signaling the relative isolation of Sardinia from mainland Europe.

We documented fine-scale variation in the ancient population ancestry proportions across the island. The most remote and interior areas of Sardinia—the Gennargentu massif covering the central and eastern regions, including the present-day province of Ogliastra— are thought to have been the least exposed to contact with outside populations. We found that pre-Neolithic hunter-gatherer and Neolithic farmer ancestries are enriched in this region of isolation. Under the premise that Ogliastra has been more buffered from recent immigration to the island, one interpretation of the result is that the early populations of Sardinia were an admixture of the two ancestries, rather than the pre-Neolithic ancestry arriving via later migrations from the mainland. Such admixture could have occurred principally on the island or on the mainland before the hypothesized Neolithic era influx to the island. Under the alternative premise that Ogliastra is simply a highly isolated region that has differentiated within Sardinia due to genetic drift, the result would be interpreted as genetic drift leading to a structured pattern of pre-Neolithic ancestry across the island, in an overall background of high Neolithic ancestry.

sardinia-pca
PCA results of merged Sardinian whole-genome sequences and the HGDP Sardinians. See below for a map of the corresponding regions.

We found Sardinians show a signal of shared ancestry with the Basque in terms of the outgroup f3 shared-drift statistics. This is consistent with long-held arguments of a connection between the two populations, including claims of Basque-like, non-Indo-European words among Sardinian placenames. More recently, the Basque have been shown to be enriched for Neolithic farmer ancestry and Indo-European languages have been associated with steppe population expansions in the post-Neolithic Bronze Age. These results support a model in which Sardinians and the Basque may both retain a legacy of pre-Indo-European Neolithic ancestry. To be cautious, while it seems unlikely, we cannot exclude that the genetic similarity between the Basque and Sardinians is due to an unsampled pre-Neolithic population that has affinities with the Neolithic representatives analyzed here.

density-nuraghi-sardinia-genetics
Left: Geographical map of Sardinia. The provincial boundaries are given as black lines. The provinces are abbreviated as Cag (Cagliari), Cmp (Campidano), Car (Carbonia), Ori (Oristano), Sas (Sassari), Olb (Olbia-tempio), Nuo (Nuoro), and Ogl (Ogliastra). For sampled villages within Ogliastra, the names and abbreviations are indicated in the colored boxes. The color corresponds to the color used in the PCA plot (Fig. 2a). The Gennargentu region referred to in the main text is the mountainous area shown in brown that is centered in western Ogliastra and southeastern Nuoro.
Right: Density of Nuraghi in Sardinia, from Wikipedia.

While we can confirm that Sardinians principally have Neolithic ancestry on the autosomes, the high frequency of two Y-chromosome haplogroups (I2a1a1 at ~39% and R1b1a2 at ~18%) that are not typically affiliated with Neolithic ancestry is one challenge to this model. Whether these haplogroups rose in frequency due to extensive genetic drift and/or reflect sex-biased demographic processes has been an open question. Our analysis of X chromosome versus autosome diversity suggests a smaller effective size for males, which can arise due to multiple processes, including polygyny, patrilineal inheritance rules, or transmission of reproductive success. We also find that the genetic ancestry enriched in Sardinia is more prevalent on the X chromosome than the autosome, suggesting that male lineages may more rapidly trace back to the mainland. Considering that the R1b1a2 haplogroup may be associated with post-Neolithic steppe ancestry expansions in Europe, and the recent timeframe when the R1b1a2 lineages expanded in Sardinia, the patterns raise the possibility of recent male-biased steppe ancestry migration to Sardinia, as has been reported among mainland Europeans at large (though see Lazaridis and Reich and Goldberg et al.). Such a recent influx is difficult to square with the overall divergence of Sardinian populations observed here.

sardinian-admixture
Mixture proportions of the three-component ancestries among Sardinian populations. Using a method first presented in Haak et al. (Nature 522, 207–211, 2015), we computed unbiased estimates of mixture proportions without a parameterized model of relationships between the test populations and the outgroup populations based on f4 statistics. The three-component ancestries were represented by early Neolithic individuals from the LBK culture (LBK_EN), pre-Neolithic huntergatherers (Loschbour), and Bronze Age steppe pastoralists (Yamnaya). See Supplementary Table 5 for standard error estimates computed using a block jackknife.

Once again, haplogroup R1b1a2 (M269), and only R1b1a2, related to male-biased, steppe-related Indo-European migrations…just sayin’.

Interestingly, haplogroup I2a1a1 is actually found among northern Iberians during the Neolithic and Chalcolithic, and is therefore associated with Neolithic ancestry in Iberia, too, and consequently – unless there is a big surprise hidden somewhere – with the ancestry found today among Basques.

NOTE. In fact, the increase in Neolithic ancestry found in south-west Ireland with expanding Bell Beakers (likely Proto-Beakers), coupled with the finding of I2a subclades in Megalithic cultures of western Europe, would support this replacement after the Cardial and Epi-Cardial expansions, which were initially associated with G2a lineages.

I am not convinced about a survival of Palaeo-Sardo after the Bell Beaker expansion, though, since there is no clear-cut cultural divide (and posterior continuity) of pre-Beaker archaeological cultures after the arrival of Bell Beakers in the island that could be identified with the survival of Neolithic languages.

We may have to wait for ancient DNA to show a potential expansion of Neolithic ancestry from the west, maybe associated with the emergence of the Nuragic civilization (potentially linked with contemporaneous Megalithic cultures in Corsica and in the Balearic Islands, and thus with an Iberian rather than a Basque stock), although this is quite speculative at this moment in linguistic, archaeological, and genetic terms.

Nevertheless, it seems that the association of a Basque-Iberian language with the Neolithic expansion from Anatolia (see Villar’s latest book on the subject) is somehow strengthened by this paper. However, it is unclear when, how, and where expanding G2a subclades were replaced by native I2 lineages.

Related

Mitogenomes from Avar nomadic elite show Inner Asian origin

ring-pommel-swords

Inner Asian maternal genetic origin of the Avar period nomadic elite in the 7th century AD Carpathian Basin, by Csáky et al. bioRxiv (2018).

Abstract (emphasis mine):

After 568 AD the nomadic Avars settled in the Carpathian Basin and founded their empire, which was an important force in Central Europe until the beginning of the 9th century AD. The Avar elite was probably of Inner Asian origin; its identification with the Rourans (who ruled the region of today’s Mongolia and North China in the 4th-6th centuries AD) is widely accepted in the historical research.

Here, we study the whole mitochondrial genomes of twenty-three 7th century and two 8th century AD individuals from a well-characterised Avar elite group of burials excavated in Hungary. Most of them were buried with high value prestige artefacts and their skulls showed Mongoloid morphological traits.

The majority (64%) of the studied samples’ mitochondrial DNA variability belongs to Asian haplogroups (C, D, F, M, R, Y and Z). This Avar elite group shows affinities to several ancient and modern Inner Asian populations.

The genetic results verify the historical thesis on the Inner Asian origin of the Avar elite, as not only a military retinue consisting of armed men, but an endogamous group of families migrated. This correlates well with records on historical nomadic societies where maternal lineages were as important as paternal descent.

mds-ancient-avar-elite
MDS with 23 ancient populations. The Multidimensional Scaling plot is based on linearised Slatkin FST values that were calculated based on whole mitochondrial sequences (stress value is 0.1581). The MDS plot shows the connection of the Avars (AVAR) to the Central-Asian populations of the Late Iron Age (C-ASIA_LIAge) and Medieval period (C-ASIA_Medieval) along coordinate 1 and coordinate 2, which is caused by non-significant genetic distances between these populations. The European ancient populations are situated on the left part of the plot, where the Iberian (IB_EBRAge), Central-European (C-EU_BRAge) and British (BRIT_BRAge) populations from Early Bronze Age and Bronze Age are clustered along coordinate 2, while the Neolithic populations from Germany (GER_Neo), Hungary (HUN_Neo), Near-East (TUR_ _Neo) and Baltic region (BALT_Neo) are located on the skirt of the plot along coordinate 1. The linearised Slatkin FST values, abbreviations and references are presented in Table S4.

Interesting excerpts:

The mitochondrial genome sequences can be assigned to a wide range of the Eurasian haplogroups with dominance of the Asian lineages, which represent 64% of the variability: four samples belong to Asian macrohaplogroup C (two C4a1a4, one C4a1a4a and one C4b6); five samples to macrohaplogroup D (one by one D4i2, D4j, D4j12, D4j5a, D5b1), and three individuals to F (two F1b1b and one F1b1f). Each haplogroup M7c1b2b, R2, Y1a1 and Z1a1 is represented by one individual. One further haplogroup, M7 (probably M7c1b2b), was detected (sample AC20); however, the poor quality of its sequence data (2.19x average coverage) did not allow further analysis of this sample.

European lineages (occurring mainly among females) are represented by the following haplogroups: H (one H5a2 and one H8a1), one J1b1a1, three T1a (two T1a1 and one T1a1b), one U5a1 and one U5b1b (Table S1).

We detected two identical F1b1f haplotypes (AC11 female and AC12 male) and two identical C4a1a4 haplotypes (AC13 and AC15 males) from the same cemetery of Kunszállás; these matches indicate the maternal kinship of these individuals. There is no chronological difference between the female and the male from Grave 30 and 32 (AC11 and AC12), but the two males buried in Grave 28 and 52 (AC13 and AC15) are not contemporaries; they lived at least 2-3 generations apart.

ward-clustering-ancient-populations
Ward type clustering of 44 ancient populations. The Ward type clustering shows separation of Asian and European populations. The Avar elite group (AVAR) is situated on an Asian branch and clustered together with Central Asian populations from Late Iron Age (C-ASIA_LIAge) and Medieval period (C-ASIA_Medieval), furthermore with Xiongnu period population from Mongolia (MON_Xiongnu) and Scythians from the Altai region (E-EU_IAge_Scyth). P values are given in percent as red numbers on the dendogram, where red rectangles indicate clusters with significant p values. The abbreviations and references are presented in Table S2.

The Avar period elite shows the lowest and non-significant genetic distances to ancient Central Asian populations dated to the Late Iron Age (Hunnic) and to the Medieval period, which is displayed on the ancient MDS plot (Fig. 4); these connections are also reflected on the haplogroup based Ward-type clustering tree (Fig. 3). Building of these large Central Asian sample pools is enabled by the small number of samples per cultural/ethnic group. Further mitogenomic data from Inner Asia are needed to specify the ancient genetic connections; however, genomic analyses are also set back by the state of archaeological research, i.e. the lack of human remains from the 4th-5th century Mongolia, which would be a particularly important region in the study of the Avar elite’s origin.

The investigated elite group from the Avar period elite also shows low genetic distances and phylogenetic connections to several Central and Inner Asian modern populations. Our results indicate that the source population of the elite group of the Avar Qaganate might have existed in Inner Asia (region of today’s Mongolia and North China) and the studied stratum of the Avars moved from there westwards towards Europe. Further genetic connections of the Avars to modern populations living to East and North of Inner Asia (Yakuts, Buryats, Tungus) probably indicate common source populations.

mds-eurasian-avar-elite-group
MDS with the 44 modern populations and the Avar elite group. The Multidimensional Scaling plot is displayed based on linearised Slatkin FST values calculated based on whole mitochondrial sequences (stress value is 0.0677). The MDS plot shows differentiation of European, Near-Eastern, Central- and East-Asian populations along coordinates 1 and 2. The Avar elite (AVAR) is located on the Asian part of plot and clustered with Uyghurs from Northwest-China (NW-CHIN_UYG) and Han Chinese (CHIN), as well as with Burusho and Hazara populations from the Central-Asian Highland (Pakistan). The linearised Slatkin FST values, abbreviations and references are presented in Table S5.

Sadly, no Y-DNA is available from this paper, although haplogroups Q, C2, or R1b (xM269) are probably to be expected, given the reported mtDNA. A replacement of the male population with subsequent migrations is obvious from the current distribution of Y-DNA haplogroups in the Carpathian Basin.

Hungarians and Corded Ware

Ancient Hungarians are important to understand the evolution, not only of Ugric, but also of Finno-Ugric peoples and their origin, since they show a genetic picture before more recent population expansions, genetic drift, and bottlenecks in eastern Europe.

By now it is evident that the migration of Magyar clans from their homeland in the Cis-Urals region (from the 4th century AD on) happened after the first waves of late and gradual expansion of N1c subclades among Finno-Ugric peoples, but before the bottlenecks seen in modern populations of eastern Europe.

In Ob-Ugric peoples, from the scarce data found in Pimenoff et al. (2018), we can see how Siberian N subclades expanded further after the separation of Magyars, evidenced by the inverted proportion of haplogroups R1a and N in modern Khantys and Mansis compared to Hungarians, and the diversity of N subclades compared to modern Fennic peoples.

Similarly to Hungarians, the situation of modern Estonians (where R1a and N subclades show approximately the same proportion, ca. 33%) is probably closer to Fennic peoples in Antiquity, not having undergone the latest strong founder effect evident in modern Finns after their expansion to the north.

middle-age-hungarian
Hungarian expansion from the 4th to the 10th century AD.

Modern Hungary

This is data from recent papers, summed up in Wikipedia:

  • In Semino et al. (2001) they found among 45 Palóc from Budapest and northern Hungary: 60% R1a, 13% R1b, 11% I, 9% E, 2% G, 2% J2.
  • In Csányi et al. (2008) Among 100 Hungarian men, 90 of whom from the Great Hungarian Plain: 30% R1a, 15% R1b, 13% I2a1, 13% J2, 9% E1b1b1a, 8% I1, 3% G2, 3% J1, 3% I*, 1% E*, 1% F*, 1% K*. Among 97 Székelys, in Romania: 20% R1b, 19% R1a, 17% I1, 11% J2, 10% J1, 8% E1b1b1a, 5% I2a1, 5% G2, 3% P*, 1% E*, 1% N.
  • In Pamjav et al. (2011), among 230 samples expected to include 6-8% Gypsy peoples: 26% R1a, 20% I2a, 19% R1b, 7% I, 6% J2, 5% H, 5% G2a, 5% E1b1b1a1, 3% J1, <1% N, <1% R2.
  • In Pamjav et al. (2017), from the Bodrogköz population: R1a-M458 (20.4%), I2a1-P37 (19%), R1b-M343 (15%), R1a-Z280 (14.3%), E1b-M78 (10.2%), and N1c-Tat (6.2%).

NOTE. The N1c-Tat found in Bodrogköz belongs to the N1c-VL29 subgroup, more frequent among Balto-Slavic peoples, which may suggest (yet again) an initial stage of the expansion of N subclades among Finno-Ugric peoples by the time of the Hungarian migration.

This is the data from FTDNA group on Hungary (copied from a Wikipedia summary of 2017 data):

  • 26.1% R1a (15% Z280, 6.5% M458, 0.9% Z93=>S23201, 3.7% unknown)
  • 19.2% R1b (6% L11-P312/U106, 5.3% P312, 4.2% L23/Z2103, 3.7% U106)
  • 16.9% I2 (15.2% CTS10228, 1.4% M223, 0.5% L38)
  • 8.3% I1
  • 8.1% J2 (5.3% M410, 2.8% M102)
  • 6.9% E1b1b1 (6% V13, 0.3% V22, 0.3% M123, 0.3% M81)
  • 6.9% G2a
  • 3.2% N (1.4% Z9136, 0.5% M2019/VL67, 0.5% Y7310, 0.9% Z16981)- note: only unrelated males are sampled
  • 2.3% Q (1.2% YP789, 0.9% M346, 0.2% M242)
  • 0.9% T
  • 0.5% J1
  • 0.2% L
  • 0.2% C

R1a-Z280 stands out in FDNA (which we have to assume has no geographic preference among modern Hungarians), while R1a-M458 is prevalent in the north, which probably points to its relationship with (at least West) Slavic populations.

Ancient Hungarians

We already knew that Hungarians show similarities with Srubna and Hunnic peoples, and this paper shows a good reason for the similarities with the Huns.

Also, recent population movements in the region (before the Avars) probably increased the proportion of R1b-L23 and I1 subclades (related to Roman and Germanic peoples) as well as possibly R1a-Z283 (mainly M458, related to the expansion of Slavs). From Understanding 6th-century barbarian social organization and migration through paleogenomics, by Amorim et al. (2018):

szolad-collegno
Y-chromosome haplogroup attribution for 37 medieval and 1 Bronze age individuals.

NOTE. The sample SZ15, of haplogroup R1a1a1b1a3a (S200), belongs to the Germanic branch Z284, which has a completely different history with its integration into the Nordic Bronze Age community.

Interesting is the Szólád Bronze Age sample of R1a1a1b2a2a (Z2123) subclade (ca. 2100-1700 BC), which is possibly the same haplogroup found in King Béla III [Z93+ (80.6%), Z2123+ (10.8%)]. Nevertheless, Z2123 refers to an upper clade, found also in East Andronovo sites in Narasimhan et al. (2018), as well as in the modern population of the Tarim Basin.

Bronze Age R1a-Z93 samples of central-east Europe – like the Balkans BA sample (ca. 1750-1625 BC) from Merichleri, of R1a1a1b2 subclade – correspond most likely to the expansion of Iranian-speaking peoples in the early 2nd millennium BC, probably to the westward expansion of the Srubna culture.

The specific subclade of King Béla III, on the other hand, probably corresponds to the more recent expansion of Magyar tribes settled in the region during the 9th century AD, so the specific subclade must have separated from those found in central-east Europe and in Andronovo during the Corded Ware expansion.

r1a-z282-z93-distribution
Modified image, from Underhill et al. (2015). Spatial frequency distributions of Z282 (green) and Z93 (blue) affiliated haplogroups. Notice the potential Finno-Ugric-associated distribution of Z282 (including M558, a Z280 subclade) according to ancient maps; the northern Eurasian finds of Z2125 (upper clade of Z2123); and the potential of M458 subclades representing a west-east expansion of Balto-Slavic as a western outgroup of an original Fenno-Ugric population, equivalent to Z284 in Scandinavia.

The study by Csányi et al. (2008), where the Tat C allele was found in 2 of 4 ancient samples, showed thus a potential 50:50 relationship of N1c in ancient Magyars, which is striking given the modern 1-3% a mere 1,000 years later, without any relevant population movement in between. This result remains to be reproduced with the current technology.

In fact, recent studies of ancient Magyars, from the 10th to the 12th century, have not shown any N1c sample, and have confirmed instead the ancient presence of R1a (two other samples, interred near Béla III), R1b (four samples), I2a (two samples) J1, and E1b, a mixed genetic picture which is more in line with what is expected.

So the question that I recently posed about east Corded Ware groups remains open: were Proto-Ugric peoples mainly of R1a-Z282 or R1a-Z93 subclades? Without ancient DNA from Middle Dnieper, Fatyanovo, Afanasevo, and the succeeding cultures (like Netted Ware) in north-eastern Europe, it is difficult to say.

It is very likely that they are going to show mainly a mixture of both R1a-Z282 and R1a-Z93 lineages, with later populations showing a higher proportion of R1a-Z280 subclades. Whether this mixture happened already during the Corded Ware period, or is the result of later developments, is still unknown. What is certain is that Hungarian N1a1a1a-L708 subclades belong to more recent additions of Siberian haplogroups to the Ugric stock, probably during the Iron Age, just centuries before the Magyar expansion.

Related

A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP

indo-european-indo-iranian-migrations

New open access paper (in Chinese) A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP, by liu et al. Acta Anthropologica Sinitica (2018)

Abstract:

The Keriyan, Lopnur and Dolan peoples are isolated populations with sparse numbers living in the western border desert of our country. By sequencing and typing the complete Y-chromosome of 179 individuals in these three isolated populations, all mutations and SNPs in the Y-chromosome and their corresponding haplotypes were obtained. Types and frequencies of each haplotype were analyzed to investigate genetic diversity and genetic structure in the three isolated populations. The results showed that 12 haplogroups were detected in the Keriyan with high frequencies of the J2a1b1 (25.64%), R1a1a1b2a (20.51%), R2a (17.95%) and R1a1a1b2a2 (15.38%) groups. Sixteen haplogroups were noted in the Lopnur with the following frequencies: J2a1 (43.75%), J2a2 (14.06%), R2 (9.38%) and L1c (7.81%). Forty haplogroups were found in the Dolan, noting the following frequencies: R1b1a1a1 (9.21%), R1a1a1b2a1a (7.89%), R1a1a1b2a2b (6.58%) and C3c1 (6.58%). These data show that these three isolated populations have a closer genetic relationship with the Uygur, Mongolian and Sala peoples. In particular, there are no significant differences in haplotype and frequency between the three isolated populations and Uygur (f=0.833, p=0.367). In addition, the genetic haplotypes and frequencies in the three isolated populations showed marked Eurasian mixing illustrating typical characteristics of Central Asian populations.

population-distribution-map
Figure 1. The populations distribution map. Left: Uluru. Center: Dali Yabuyi. Right: Kaerqu.

My knowledge of written Chinese is almost zero, so here are some excerpts with the help of Google Translate:

The source of 179 blood samples used in the study is shown in Figure 1. The Keriyan blood samples were collected from Dali Yabuyi Township, Yutian County (39 samples). The blood samples of the Lopnur people were collected from Kaerqu Township, Yuli County (64 cases); the blood samples of the Dolan people were collected from the town of Uluru, Awati County (76).

haplotype-frequency-uighur
Columns one and two are the Keriyan haplotypes and frequencies, respectively; the third and fourth columns are the Lopnur haplotypes and frequencies; the last four columns are the Daolang haplotypes and frequencies.

The composition and frequency of the Keriyan people’s haplogroup are closest to those of the Uighurs, and both Principal Component Analysis and Phylogenetic Tree Analysis show that their kinship is recent. We initially infer that the Keriyan are local desert indigenous people. They have a connection with the source of the Uighurs. Chen et al. [42] studied the patriarchal and maternal genetic analysis of the Keriyan people and found that they are not descendants of the Tibetan ethnic group in the West. The Keriyan people are a mixed group of Eastern and Western Europeans, which may originate from the local Vil group. Duan Ranhui [43] and other studies have shown that the nucleotide variability and average nucleotide differences in the Keriyan population are between the reported Eastern and Western populations. The phylogenetic tree also shows that the populations in Central Asia are between the continental lineage of the eastern population and the European lineage of the western population, and the genetic distance between the Keriyan and the Uighurs is the closest, indicating that they have a close relationship.

y-chromosome-pca

Regarding the origin of the Lopnur people, Purzhevski judged that it was a mixture of Mongolians and Aryans according to the physical characteristics of the Lopnur people. In 1934, the Sino-Swiss delegation discovered the famous burials of the ancient tombs in the Peacock River. After research, they were the indigenous people before the Loulan period; the researcher Yang Lan, a researcher at the Institute of Cultural Relics of the Chinese Academy of Social Sciences, said that the Lopnur people were descendants of the ancient “Landan survivors”. However, the Loulan people speaking an Indo-European language, and the Lopnur people speaking Uyghur languages contradict this; the historical materials of the Western Regions, “The Geography of the Western Regions” and “The Western Regions of the Ming Dynasty” record the Uighurs who lived in Cao Cao in the late 17th and early 18th centuries. Because of the occupation of the land by the Junggar nobles and their oppression, they fled. Some of them were forced to move to the Lop Nur area. There are many similar archaeological discoveries and historical records. We have no way to determine their accuracy, but they are at different times, and there is a great difference in what is heard in the same region. (…) The genetic characteristics of modern Lopnur people are the result of the long-term ethnic integration of Uyghurs, Mongols, and Europeans. This is also consistent with the similarity of the genetic structure of the Y chromosome of Lopnur in this study with the Uighurs and Mongolians. For example, the frequency of J haplogroup is as high as 59.37%, while J and its downstream sub-haplogroup are mainly distributed in western Europe, West Asia and Central Asia; the frequency of O, R haplogroup is close to that of Mongolians.

y-chromosome-frequency
1) KA: Keriya, LB: Rob, DL: Daolang, HTW: Hetian Uygur, HTWZ: and Uygur, TLFW: Turpan Uighur, HZ: Hui, HSKZ: Kazakh, WZBKZ: Wuhuan Others, TJKZ: Tajik, KEKZZ: Kirgiz, TTEZ: Tatar, ELSZ: Russian XBZ: Xibo, MGZ: Mongolian, SLZ: Salar, XJH: Xinjiang Han, GSH: Gansu Han, GDH: Guangdong Han SCH: Sichuan Han. 2) Reference population data source literature 19-22. After the population names in the table have been marked, all the shorthands in the text are referred to in this table. 3) Because the degree of haplotypes of each reference population is different to each sub-group branch, the sub-group branches under the same haplogroup are merged when the population haplogroup data is aggregated, for example: for haplogroup G Some people are divided into G1a and G2a levels, others are assigned to G1, G2, and G3, while some people can only determine G this time. Therefore, each subgroup is merged into a single group G.

According to Ming History·Western Biography, the Mongolians originated from the Mobei Plateau and later ruled Asia and Eastern Europe. Mongolia was established, and large areas of southern Xinjiang and Central Asia were included. Later, due to the Mongolian king’s struggle for power, it fell into a long-term conflict. People of the land fled to avoid the war, and the uninhabited plain of the lower reaches of the Yarkant River naturally became a good place to live. People from all over the world gathered together and called themselves “Dura” and changed to “Dang Lang”. The long-term local Uyghur exchanges that entered the southern Mongolian monks and “Dura” were gradually assimilated [44]. According to the report, locals wore Mongolian clothes, especially women who still maintained a Mongolian face [45]. In 1976, the robes and waistbands found in the ancient time of the Daolang people in Awati County were very similar to those of the ancients. Dalang Muqam is an important part of Daolang culture. It is also a part of the Uyghur Twelve Muqam, and it retains the ancient Western culture, but it also contains a larger Mongolian culture and relics. The above historical records show that the Daolang people should appear in the Chagatai Khanate and be formed by the integration of Mongolian and Uighur ethnic groups. Through our research, we also found that the paternal haplotype of the Daolang people is contained in both Uygur and Mongolian, and the main haplogroups are the same, whereas the frequencies are different (see Table 3). The principal component analysis and the NJ analysis are also the same. It is very close to the Uyghur and the Mongolian people, which establishes new evidence for the “mixed theory” in molecular genetics.

main-haplogroup-uighur
Genetic relationship between the three isolated populations: the Uygur and the Mongolian is the closest, and the main haplogroup can more intuitively compare the source composition of the genetic structure of each population. Haplogroups C, D, and O are mainly distributed in Asia as the East Asian characteristic haplogroup; haplogroups G, J, and R are mainly distributed in continental Europe, and the high frequency distribution is in Europe and Central Asia.

If the nomenclature follows a recent ISOGG standard, it appears that:

The presence of exclusively R1a-Z93 subclades and the lack of R1b-M269 samples is compatible with the expansion of R1a-Z93 into the area with Proto-Tocharians, at the turn of the 3rd-2nd millennium BC, as suggested by the Xiaohe samples, supposedly R1a(xZ93).

Now that it is obvious from ancient DNA (as it was clear from linguistics) that Pre-Tocharians separated earlier than other Late PIE peoples, with the expansion of late Khvalynsk/Repin into the Altai, at the end of the 4th millennium, these prevalent R1a (probably Z93) samples may be showing a replacement of Pre-Tocharian Y-DNA with the Andronovo expansion already by 2000 BC.

Lacking proper assessment of ancient DNA from Proto-Tocharians, this potential early Y-DNA replacement is still speculative*. However, if that is the case, I wonder what the Copenhagen group will say when supporting this, but rejecting at the same time the more obvious Y-DNA replacement in East Yamna / Poltavka in the mid-3rd millennium with incoming Corded Ware-related peoples. I guess the invention of an Indo-Tocharian group may be near…

*NOTE. The presence of R1b-M269 among Proto-Tocharians, as well as the presence of R1b-M269 among Tarim Basin peoples in modern and ancient times is not yet fully discarded. The prevalence of R1a-Z93 may also be the sign of a more recent replacement by Iranian peoples, before the Mongolian and Turkic expansions that probably brought R1b(xM269).

Also, the presence of R1b (xM269) samples in east Asia strengthens the hypothesis of a back-migration of R1b-P297 subclades, from Northern Europe to the east, into the Lake Baikal area, during the Early Mesolithic, as found in the Botai samples and later also in Turkic populations – which are the most likely source of these subclades (and probably also of Q1a2 and N1c) in the region.

Related

Migrations in the Levant region during the Chalcolithic, also marked by distinct Y-DNA

halaf-ubaid-migrations

Open access Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation, by Harney et al. Nature Communications (2018).

Interesting excerpts (emphasis mine, reference numbers deleted for clarity):

Introduction

The material culture of the Late Chalcolithic period in the southern Levant contrasts qualitatively with that of earlier and later periods in the same region. The Late Chalcolithic in the Levant is characterized by increases in the density of settlements, introduction of sanctuaries, utilization of ossuaries in secondary burials, and expansion of public ritual practices as well as an efflorescence of symbolic motifs sculpted and painted on artifacts made of pottery, basalt, copper, and ivory. The period’s impressive metal artifacts, which reflect the first known use of the “lost wax” technique for casting of copper, attest to the extraordinary technical skill of the people of this period.

The distinctive cultural characteristics of the Late Chalcolithic period in the Levant (often related to the Ghassulian culture, although this term is not in practice applied to the Galilee region where this study is based) have few stylistic links to the earlier or later material cultures of the region, which has led to extensive debate about the origins of the people who made this material culture. One hypothesis is that the Chalcolithic culture in the region was spread in part by immigrants from the north (i.e., northern Mesopotamia), based on similarities in artistic designs. Others have suggested that the local populations of the Levant were entirely responsible for developing this culture, and that any similarities to material cultures to the north are due to borrowing of ideas and not to movements of people.

Previous genome-wide ancient DNA studies from the Near East have revealed that at the time when agriculture developed, populations from Anatolia, Iran, and the Levant were approximately as genetically differentiated from each other as present-day Europeans and East Asians are today. By the Bronze Age, however, expansion of different Near Eastern agriculturalist populations — Anatolian, Iranian, and Levantine — in all directions and admixture with each other substantially homogenized populations across the region, thereby contributing to the relatively low genetic differentiation that prevails today. Showed that the Levant Bronze Age population from the site of ‘Ain Ghazal, Jordan (2490–2300 BCE) could be fit statistically as a mixture of around 56% ancestry from a group related to Levantine Pre-Pottery Neolithic agriculturalists (represented by ancient DNA from Motza, Israel and ‘Ain Ghazal, Jordan; 8300–6700 BCE) and 44% related to populations of the Iranian Chalcolithic (Seh Gabi, Iran; 4680–3662 calBCE). Suggested that the Canaanite Levant Bronze Age population from the site of Sidon, Lebanon (~1700 BCE) could be modeled as a mixture of the same two groups albeit in different proportions (48% Levant Neolithic-related and 52% Iran Chalcolithic-related). However, the Neolithic and Bronze Age sites analyzed so far in the Levant are separated in time by more than three thousand years, making the study of samples that fill in this gap, such as those from Peqi’in, of critical importance.

This procedure produced genome-wide data from 22 ancient individuals from Peqi’in Cave (4500–3900 calBCE) (…)

Discussion

We find that the individuals buried in Peqi’in Cave represent a relatively genetically homogenous population. This homogeneity is evident not only in the genome-wide analyses but also in the fact that most of the male individuals (nine out of ten) belong to the Y-chromosome haplogroup T, a lineage thought to have diversified in the Near East. This finding contrasts with both earlier (Neolithic and Epipaleolithic) Levantine populations, which were dominated by haplogroup E, and later Bronze Age individuals, all of whom belonged to haplogroup J.

levant-chalcolithic-bronze-age
Detailed sample background data for each of the 22 samples from which we successfully obtained ancient DNA. Additionally, background information for all samples from Peqi’in that were screened is included in Supplementary Data 1. *Indicates that Y-chromosome haplogroup call should be interpreted with caution, due to low coverage data.

Our finding that the Levant_ChL population can be well-modeled as a three-way admixture between Levant_N (57%), Anatolia_N (26%), and Iran_ChL (17%), while the Levant_BA_South can be modeled as a mixture of Levant_N (58%) and Iran_ChL (42%), but has little if any additional Anatolia_N-related ancestry, can only be explained by multiple episodes of population movement. The presence of Iran_ChL-related ancestry in both populations – but not in the earlier Levant_N – suggests a history of spread into the Levant of peoples related to Iranian agriculturalists, which must have occurred at least by the time of the Chalcolithic. The Anatolian_N component present in the Levant_ChL but not in the Levant_BA_South sample suggests that there was also a separate spread of Anatolian-related people into the region. The Levant_BA_South population may thus represent a remnant of a population that formed after an initial spread of Iran_ChL-related ancestry into the Levant that was not affected by the spread of an Anatolia_N-related population, or perhaps a reintroduction of a population without Anatolia_N-related ancestry to the region. We additionally find that the Levant_ChL population does not serve as a likely source of the Levantine-related ancestry in present-day East African populations.

These genetic results have striking correlates to material culture changes in the archaeological record. The archaeological finds at Peqi’in Cave share distinctive characteristics with other Chalcolithic sites, both to the north and south, including secondary burial in ossuaries with iconographic and geometric designs. It has been suggested that some Late Chalcolithic burial customs, artifacts and motifs may have had their origin in earlier Neolithic traditions in Anatolia and northern Mesopotamia. Some of the artistic expressions have been related to finds and ideas and to later religious concepts such as the gods Inanna and Dumuzi from these more northern regions. The knowledge and resources required to produce metallurgical artifacts in the Levant have also been hypothesized to come from the north.

Our finding of genetic discontinuity between the Chalcolithic and Early Bronze Age periods also resonates with aspects of the archeological record marked by dramatic changes in settlement patterns, large-scale abandonment of sites, many fewer items with symbolic meaning, and shifts in burial practices, including the disappearance of secondary burial in ossuaries. This supports the view that profound cultural upheaval, leading to the extinction of populations, was associated with the collapse of the Chalcolithic culture in this region.

levant-chalcolithic-pca
Genetic structure of analyzed individuals. a Principal component analysis of 984 present-day West Eurasians (shown in gray) with 306 ancient samples projected onto the first two principal component axes and labeled by culture. b ADMIXTURE analysis of 984 and 306 ancient samples with K = 11
ancestral components. Only ancient samples are shown

Comments

I think the most interesting aspect of this paper is – as usual – the expansion of peoples associated with a single Y-DNA haplogroup. Given that the expansion of Semitic languages in the Middle East – like that of Anatolian languages from the north – must have happened after ca. 3100 BC, coinciding with the collapse of the Uruk period, these Chalcolithic north Levant peoples are probably not related to the posterior Semitic expansion in the region. This can be said to be supported by their lack of relationship with posterior Levantine migrations into Africa. The replacement of haplogroup E before the arrival of haplogroup J suggests still more clearly that Natufians and their main haplogroup were not related to the Afroasiatic expansions.

semitic-languages
Distribution of Semitic languages. From Wikipedia.

On the other hand, while their ancestry points to neighbouring regional origins, their haplogroup T1a1a (probably T1a1a1b2) may be closely related to that of other Semitic peoples to the south, as found in east Africa and Arabia. This may be due either to a northern migration of these Chalcolithic Levantine peoples from southern regions in the 5th millennium BC, or maybe to a posterior migration of Semitic peoples from the Levant to the south, coupled with the expansion of this haplogroup, but associated with a distinct population. As we know, ancestry can change within certain generations of intense admixture, while Y-DNA haplogroups are not commonly admixed in prehistoric population expansions.

Without more data from ancient DNA, it is difficult to say. Haplogroup T1a1 is found in Morocco (ca. 3780-3650 calBC), which could point to a recent expansion of a Berbero-Semitic branch; but also in a sample from Balkans Neolithic ca. 5800-5400 calBCE, which could suggest an Anatolian origin of the specific subclades encountered here. In any case, a potential origin of Proto-Semitic anywhere near this wide Near Eastern region ca. 4500-3500 BC cannot be discarded, knowing that their ancestors came probably from Africa.

haplogroup-t-levant
Distribution of haplogroup T of Y-chromosome. From Wikipedia.

Interesting from this paper is also that we are yet to find a single prehistoric population expansion not associated with a reduction of variability and expansion of Y-DNA haplogroups. It seems that the supposedly mixed Yamna community remains the only (hypothetical) example in history where expanding patrilineal clans will not share Y-DNA haplogroup…

Related

Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component

invasion-from-the-steppe-yamnaya

Good timing for the publication of two interesting papers, that a lot of people should read very carefully:

ADMIXTURE

Open access A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots, by Daniel J. Lawson, Lucy van Dorp & Daniel Falush, Nature Communications (2018).

Interesting excerpts (emphasis mine):

Experienced researchers, particularly those interested in population structure and historical inference, typically present STRUCTURE results alongside other methods that make different modelling assumptions. These include TreeMix, ADMIXTUREGRAPH, fineSTRUCTURE, GLOBETROTTER, f3 and D statistics, amongst many others. These models can be used both to probe whether assumptions of the model are likely to hold and to validate specific features of the results. Each also comes with its own pitfalls and difficulties of interpretation. It is not obvious that any single approach represents a direct replacement as a data summary tool. Here we build more directly on the results of STRUCTURE/ADMIXTURE by developing a new approach, badMIXTURE, to examine which features of the data are poorly fit by the model. Rather than intending to replace more specific or sophisticated analyses, we hope to encourage their use by making the limitations of the initial analysis clearer.

The default interpretation protocol

Most researchers are cautious but literal in their interpretation of STRUCTURE and ADMIXTURE results, as caricatured in Fig. 1, as it is difficult to interpret the results at all without making several of these assumptions. Here we use simulated and real data to illustrate how following this protocol can lead to inference of false histories, and how badMIXTURE can be used to examine model fit and avoid common pitfalls.

admixture-protocol
A protocol for interpreting admixture estimates, based on the assumption that the model underlying the inference is correct. If these assumptions are not validated, there is substantial danger of over-interpretation. The “Core protocol” describes the assumptions that are made by the admixture model itself (Protocol 1, 3, 4), and inference for estimating K (Protocol 2). The “Algorithm input” protocol describes choices that can further bias results, while the “Interpretation” protocol describes assumptions that can be made in interpreting the output that are not directly supported by model inference

Discussion

STRUCTURE and ADMIXTURE are popular because they give the user a broad-brush view of variation in genetic data, while allowing the possibility of zooming down on details about specific individuals or labelled groups. Unfortunately it is rarely the case that sampled data follows a simple history comprising a differentiation phase followed by a mixture phase, as assumed in an ADMIXTURE model and highlighted by case study 1. Naïve inferences based on this model (the Protocol of Fig. 1) can be misleading if sampling strategy or the inferred value of the number of populations K is inappropriate, or if recent bottlenecks or unobserved ancient structure appear in the data. It is therefore useful when interpreting the results obtained from real data to think of STRUCTURE and ADMIXTURE as algorithms that parsimoniously explain variation between individuals rather than as parametric models of divergence and admixture.

For example, if admixture events or genetic drift affect all members of the sample equally, then there is no variation between individuals for the model to explain. Non-African humans have a few percent Neanderthal ancestry, but this is invisible to STRUCTURE or ADMIXTURE since it does not result in differences in ancestry profiles between individuals. The same reasoning helps to explain why for most data sets—even in species such as humans where mixing is commonplace—each of the K populations is inferred by STRUCTURE/ADMIXTURE to have non-admixed representatives in the sample. If every individual in a group is in fact admixed, then (with some exceptions) the model simply shifts the allele frequencies of the inferred ancestral population to reflect the fraction of admixture that is shared by all individuals.

Several methods have been developed to estimate K, but for real data, the assumption that there is a true value is always incorrect; the question rather being whether the model is a good enough approximation to be practically useful. First, there may be close relatives in the sample which violates model assumptions. Second, there might be “isolation by distance”, meaning that there are no discrete populations at all. Third, population structure may be hierarchical, with subtle subdivisions nested within diverged groups. This kind of structure can be hard for the algorithms to detect and can lead to underestimation of K. Fourth, population structure may be fluid between historical epochs, with multiple events and structures leaving signals in the data. Many users examine the results of multiple K simultaneously but this makes interpretation more complex, especially because it makes it easier for users to find support for preconceptions about the data somewhere in the results.

In practice, the best that can be expected is that the algorithms choose the smallest number of ancestral populations that can explain the most salient variation in the data. Unless the demographic history of the sample is particularly simple, the value of K inferred according to any statistically sensible criterion is likely to be smaller than the number of distinct drift events that have practically impacted the sample. The algorithm uses variation in admixture proportions between individuals to approximately mimic the effect of more than K distinct drift events without estimating ancestral populations corresponding to each one. In other words, an admixture model is almost always “wrong” (Assumption 2 of the Core protocol, Fig. 1) and should not be interpreted without examining whether this lack of fit matters for a given question.

admixture-pitfalls
Three scenarios that give indistinguishable ADMIXTURE results. a Simplified schematic of each simulation scenario. b Inferred ADMIXTURE plots at K= 11. c CHROMOPAINTER inferred painting palettes.

Because STRUCTURE/ADMIXTURE accounts for the most salient variation, results are greatly affected by sample size in common with other methods. Specifically, groups that contain fewer samples or have undergone little population-specific drift of their own are likely to be fit as mixes of multiple drifted groups, rather than assigned to their own ancestral population. Indeed, if an ancient sample is put into a data set of modern individuals, the ancient sample is typically represented as an admixture of the modern populations (e.g., ref. 28,29), which can happen even if the individual sample is older than the split date of the modern populations and thus cannot be admixed.

This paper was already available as a preprint in bioRxiv (first published in 2016) and it is incredible that it needed to wait all this time to be published. I found it weird how reviewers focused on the “tone” of the paper. I think it is great to see files from the peer review process published, but we need to know who these reviewers were, to understand their whiny remarks… A lot of geneticists out there need to develop a thick skin, or else we are going to see more and more delays based on a perceived incorrect tone towards the field, which seems a rather subjective reason to force researchers to correct a paper.

PCA of SNP data

Open access Effective principal components analysis of SNP data, by Gauch, Qian, Piepho, Zhou, & Chen, bioRxiv (2018).

Interesting excerpts:

A potential hindrance to our advice to upgrade from PCA graphs to PCA biplots is that the SNPs are often so numerous that they would obscure the Items if both were graphed together. One way to reduce clutter, which is used in several figures in this article, is to present a biplot in two side-by-side panels, one for Items and one for SNPs. Another stratagem is to focus on a manageable subset of SNPs of particular interest and show only them in a biplot in order to avoid obscuring the Items. A later section on causal exploration by current methods mentions several procedures for identifying particularly relevant SNPs.

One of several data transformations is ordinarily applied to SNP data prior to PCA computations, such as centering by SNPs. These transformations make a huge difference in the appearance of PCA graphs or biplots. A SNPs-by-Items data matrix constitutes a two-way factorial design, so analysis of variance (ANOVA) recognizes three sources of variation: SNP main effects, Item main effects, and SNP-by-Item (S×I) interaction effects. Double-Centered PCA (DC-PCA) removes both main effects in order to focus on the remaining S×I interaction effects. The resulting PCs are called interaction principal components (IPCs), and are denoted by IPC1, IPC2, and so on. By way of preview, a later section on PCA variants argues that DC-PCA is best for SNP data. Surprisingly, our literature survey did not encounter even a single analysis identified as DC-PCA.

The axes in PCA graphs or biplots are often scaled to obtain a convenient shape, but actually the axes should have the same scale for many reasons emphasized recently by Malik and Piepho [3]. However, our literature survey found a correct ratio of 1 in only 10% of the articles, a slightly faulty ratio of the larger scale over the shorter scale within 1.1 in 12%, and a substantially faulty ratio above 2 in 16% with the worst cases being ratios of 31 and 44. Especially when the scale along one PCA axis is stretched by a factor of 2 or more relative to the other axis, the relationships among various points or clusters of points are distorted and easily misinterpreted. Also, 7% of the articles failed to show the scale on one or both PCA axes, which leaves readers with an impressionistic graph that cannot be reproduced without effort. The contemporary literature on PCA of SNP data mostly violates the prohibition against stretching axes.

pca-how-to
DC-PCA biplot for oat data. The gradient in the CA-arranged matrix in Fig 13 is shown here for both lines and SNPs by the color scheme red, pink, black, light green, dark green.

The percentage of variation captured by each PC is often included in the axis labels of PCA graphs or biplots. In general this information is worth including, but there are two qualifications. First, these percentages need to be interpreted relative to the size of the data matrix because large datasets can capture a small percentage and yet still be effective. For example, for a large dataset with over 107,000 SNPs for over 6,000 persons, the first two components capture only 0.3693% and 0.117% of the variation, and yet the PCA graph shows clear structure (Fig 1A in [4]). Contrariwise, a PCA graph could capture a large percentage of the total variation, even 50% or more, but that would not guarantee that it will show evident structure in the data. Second, the interpretation of these percentages depends on exactly how the PCA analysis was conducted, as explained in a later section on PCA variants. Readers cannot meaningfully interpret the percentages of variation captured by PCA axes when authors fail to communicate which variant of PCA was used.

Conclusion

Five simple recommendations for effective PCA analysis of SNP data emerge from this investigation.

  1. Use the SNP coding 1 for the rare or minor allele and 0 for the common or major allele.
  2. Use DC-PCA; for any other PCA variant, examine its augmented ANOVA table.
  3. Report which SNP coding and PCA variant were selected, as required by contemporary standards in science for transparency and reproducibility, so that readers can interpret PCA results properly and reproduce PCA analyses reliably.
  4. Produce PCA biplots of both Items and SNPs, rather than merely PCA graphs of only Items, in order to display the joint structure of Items and SNPs and thereby to facilitate causal explanations. Be aware of the arch distortion when interpreting PCA graphs or biplots.
  5. Produce PCA biplots and graphs that have the same scale on every axis.

I read the referenced paper Biplots: Do Not Stretch Them!, by Malik and Piepho (2018), and even though it is not directly applicable to the most commonly available PCA graphs out there, it is a good reminder of the distorting effects of stretching. So for example quite recently in Krause-Kyora et al. (2018), where you can see Corded Ware and BBC samples from Central Europe clustering with samples from Yamna:

NOTE. This is related to a vertical distorsion (i.e. horizontal stretching), but possibly also to the addition of some distant outlier sample/s.

pca-cwc-yamna-bbc
Principal Component Analysis (PCA) of the human Karsdorf and Sorsum samples together with previously published ancient populations projected on 27 modern day West Eurasian populations (not shown) based on a set of 1.23 million SNPs (Mathieson et al., 2015). https://doi.org/10.7554/eLife.36666.006

The so-called ‘Yamnaya’ ancestry

Every time I read papers like these, I remember commenters who kept swearing that genetics was the ultimate science that would solve anthropological problems, where unscientific archaeology and linguistics could not. Well, it seems that, like radiocarbon analysis, these promising developing methods need still a lot of refinement to achieve something meaningful, and that they mean nothing without traditional linguistics and archaeology… But we already knew that.

Also, if this is happening in most peer-reviewed publications, made by professional geneticists, in journals of high impact factor, you can only wonder how many more errors and misinterpretations can be found in the obscure market of so many amateur geneticists out there. Because amateur geneticist is a commonly used misnomer for people who are not geneticists (since they don’t have the most basic education in genetics), and some of them are not even ‘amateurs’ (because they are selling the outputs of bioinformatic tools)… It’s like calling healers ‘amateur doctors’.

NOTE. While everyone involved in population genetics is interested in knowing the truth, and we all have our confirmation (and other kinds of) biases, for those who get paid to tell people what they want to hear, and who have sold lots of wrong interpretations already, the incentives of ‘being right’ – and thus getting involved in crooked and paranoid behaviour regarding different interpretations – are as strong as the money they can win or loose by promoting themselves and selling more ‘product’.

As a reminder of how badly these wrong interpretations of genetic results – and the influence of the so-called ‘amateurs’ – can reflect on research groups, yet another turn of the screw by the Copenhagen group, in the oral presentations at Languages and migrations in pre-historic Europe (7-12 Aug 2018), organized by the Copenhagen University. The common theme seems to be that Bell Beaker and thus R1b-L23 subclades do represent a direct expansion from Yamna now, as opposed to being derived from Corded Ware migrants, as they supported before.

NOTE. Yes, the “Yamna → Corded Ware → Únětice / Bell Beaker” migration model is still commonplace in the Copenhagen workgroup. Yes, in 2018. Guus Kroonen had already admitted they were wrong, and it was already changed in the graphic representation accompanying a recent interview to Willerslev. However, since there is still no official retraction by anyone, it seems that each member has to reject the previous model in their own way, and at their own pace. I don’t think we can expect anyone at this point to accept responsibility for their wrong statements.

So their lead archaeologist, Kristian Kristiansen, in The Indo-Europeanization of Europé (sic):

kristiansen-migrations
Kristiansen’s (2018) map of Indo-European migrations

I love the newly invented arrows of migration from Yamna to the north to distinguish among dialects attributed by them to CWC groups, and the intensive use of materials from Heyd’s publications in the presentation, which means they understand he was right – except for the fact that they are used to support a completely different theory, radically opposed to those defended in Heyd’s model

Now added to the Copenhagen’s unending proposals of language expansions, some pearls from the oral presentation:

  • Corded Ware north of the Carpathians of R1a lineages developed Germanic;
  • R1b borugh [?] Italo-Celtic;
  • the increase in steppe ancestry on north European Bell Beakers mean that they “were a continuation of the Yamnaya/Corded Ware expansion”;
  • Corded Ware groups [] stopped their expansion and took over the Bell Beaker package before migrating to England” [yep, it literally says that];
  • Italo-Celtic expanded to the UK and Iberia with Bell Beakers [I guess that included Lusitanian in Iberia, but not Messapian in Italy; or the opposite; or nothing like that, who knows];
  • 2nd millennium BC Bronze Age Atlantic trade systems expanded Proto-Celtic [yep, trade systems expanded the language]
  • 1st millennium BC expanded Gaulish with La Tène, including a “Gaulish version of Celtic to Ireland/UK” [hmmm, dat British Gaulish indeed].

You know, because, why the hell not? A logical, stable, consequential, no-nonsense approach to Indo-European migrations, as always.

Also, compare still more invented arrows of migrations, from Mikkel Nørtoft’s Introducing the Homeland Timeline Map, going against Kristiansen’s multiple arrows, and even against the own recent fantasy map series in showing Bell Beakers stem from Yamna instead of CWC (or not, you never truly know what arrows actually mean):

corded-ware-migrations
Nørtoft’s (2018) maps of Indo-European migrations.

I really, really loved that perennial arrow of migration from Volosovo, ca. 4000-800 BC (3000+ years, no less!), representing Uralic?, like that, without specifics – which is like saying, “somebody from the eastern forest zone, somehow, at some time, expanded something that was not Indo-European to Finland, and we couldn’t care less, except for the fact that they were certainly not R1a“.

This and Kristiansen’s arrows are the most comical invented migration routes of 2018; and that is saying something, given the dozens of similar maps that people publish in forums and blogs each week.

NOTE. You can read a more reasonable account of how haplogroup R1b-L51 and how R1-Z645 subclades expanded, and which dialects most likely expanded with them.

We don’t know where these scholars of the Danish workgroup stand at this moment, or if they ever had (or intended to have) a common position – beyond their persistent ideas of Yamnaya™ ancestral component = Indo-European and R1a must be Indo-European – , because each new publication changes some essential aspects without expressly stating so, and makes thus everything still messier.

It’s hard to accept that this is a series of presentations made by professional linguists, archaeologists, and geneticists, as stated by the official website, and still harder to imagine that they collaborate within the same professional workgroup, which includes experienced geneticists and academics.

I propose the following video to close future presentations introducing innovative ideas like those above, to help the audience find the appropriate mood:

Related

On the origin and spread of haplogroup R1a-Z645 from eastern Europe

indo-european-uralic-migrations-corded-ware

In my recent post about the origin and expansion of haplogroup R1b-L51, Chetan made an interesting comment on the origin and expansion of R1a-Z645. Since this haplogroup is also relevant for European history and dialectal North-West Indo-European and Indo-Iranian expansion, I feel compelled to do a similar post, although the picture right now is more blurry than that of R1b-L51.

I find it interesting that many geneticists would question the simplistic approach to the Out of Africa model as it is often enunciated, but they would at the same time consider the current simplistic model of Yamna expansion essentially right; a model – if anyone is lost here – based on proportions of the so-called Yamnaya™ ancestral component, as found in a small number of samples, from four or five Eneolithic–Chalcolithic cultures spanning more than a thousand years.

The “75% Yamnaya ancestry of Corded Ware”, which has been given so much publicity since 2015, made geneticists propose a “Yamna → Corded Ware → Únětice / Bell Beaker” migration model, in order of decreasing Yamnaya proportions. Y-DNA and solid archaeological models suggested that this model was wrong, and recent findings have proven it was. In fact, the CWC sample closest to Yamna was a late outlier of Esperstedt in Central Europe, whose ancestry is most likely directly related to Yamna settlers from Hungary.

These wrong interpretations have been now substituted by data from two new early samples from the Baltic, which cluster closely to Yamna, and which – based on the Y-DNA and PCA cluster formed by all Corded Ware samples – are likely the product of female exogamy with Yamna peoples from the neighbouring North Pontic region (as we are seeing, e.g. in the recent Nikitin et al. 2018).

NOTE. There is also another paper from Nikitin et al. (2017), with more ancient mtDNA, “Subdivisions of haplogroups U and C encompass mitochondrial DNA lineages of Eneolithic-Early Bronze Age Kurgan populations of western North Pontic steppe”. Link to paper (behind paywall). Most interesting data is summarized in the following table:

yamna-corded-ware-mtdna

Even after the publication of Olalde et al. (2018) and Wang et al. (2018) – where expanding Yamna settlers and Bell Beakers are clearly seen highly admixed within a few generations, and are found spread across a wide Eurasian cline (sharing one common invariable trait, the paternally inherited haplogroup, as supported by David Reich) – fine-scale studies of population structure and social dynamics is still not a thing for many, even though it receives more and more advocates among geneticists (e.g. Lazaridis, or Veeramah).

NOTE. I have tried to explain, more than once, that the nature and origin of the so-called “Yamnaya ancestry” (then “steppe ancestry”, and now subdivided further as Steppe_EMBA and Steppe_MLBA) is not known with precision before Yamna samples of ca. 3000 BC, and especially that it is not necessarily a marker of Indo-European speakers. Why some people are adamant that steppe ancestry and thus R1a must be Indo-European is mostly related to a combination of grandaddy’s haplogroup, the own modern ethnolinguistic attribution, and an aversion to sharing grandpa with other peoples and cultures.

In the meantime, we are seeing the “Yamnaya proportion” question often reversed: “how do we make Corded Ware stem from Yamna, now that we believed it?”. This is a funny circular reasoning, akin to the one used by proponents of the Franco-Cantabrian origin of R1b, when they look now at EEF proportions in Iberian R1b-L23 samples. It seems too comic to be true.

R1a and steppe ancestry

The most likely origin of haplogroup R1a-Z645 is to be found in eastern Europe. Samples published in the last year support this region as a sort of cradle of R1a expansions:

  • I1819, Y-DNA R1a1-M459, mtDNA U5b2, Ukraine Mesolithic ca. 8825-8561 calBCE, from Vasilievka.
  • I5876, Y-DNA R1a, mtDNA U5a2a, Ukraine Mesolithic 7040-6703 calBCE, from Dereivka.
  • I0061, hg R1a1-M459 (xR1a1a-M17), mtDNA C1, ca. 6773-6000 calBCE (with variable dates), from Yuzhnyy Oleni Ostrov in Karelia.
  • Samples LOK_1980.006 and LOK_1981.024.01, of hg MR1a1a-M17, mtDNA F, Baikalic cultures, dated ca. 5500-5000 BC.
  • Sample I0433, hg R1a1-M459(xM198), mtDNA U5a1i, from Samara Eneolithic, ca. 5200-4000 BCE
  • Samples A3, A8, A9, of hg R1a1-M459, mtDNA H, from sub-Neolithic cultures (Comb Ware and Zhizhitskaya) at Serteyea, although dates (ca. 5th-3rd millennium BC) need possibly a revision (from Chekunova 2014).

NOTE. The fact that Europe is better sampled than North Asia, coupled with the finding of R1a-M17 in Baikalic cultures, poses some problems as to the precise origin of this haplogroup and its subclades. While the first (Palaeolithic or Mesolithic) expansion was almost certainly from Northern Eurasia to the west – due to the Mal’ta sample – , it is still unknown if the different subclades of R1a in Europe are the result of local developments, or rather different east—west migrations through North Eurasia.

Y-Full average estimates pointed to R1a-M417 formation ca. 6500 BC, TMRCA ca. 3500 BC, and R1a-Z645 formation ca. 3300 BC, TMRCA ca. 2900 BC, so the most likely explanation was that R1a-Z645 and its subclades – similar to R1b-L23 subclades, but slightly later) expanded quickly with the expansion of Corded Ware groups.

The presence of steppe ancestry in Ukraine Eneolithic sample I6561, of haplogroup R1a-M417, from Alexandria, dated ca. 4045-3974 calBCE, pointed to the forest steppe area and late Sredni Stog as the most likely territory from where the haplogroup related to the Corded Ware culture expanded.

However, the more recent Y-SNP call showing R1a-Z93 (L657) subclade rendered Y-Full’s (at least formation) estimates too young, so we have to rethink the actual origin of both subclades, R1a-Z93 (formation ca. 2900 BC, TMRCA ca 2700 BC), and R1a-Z283 (formation ca. 2900 BC, TMRCA ca. 2800 BC).

Contrary to what we thought before this, then, it is possible that the expansion of Khvalynsk-Novodanilovka chieftains through the steppes, around the mid-5th millennium BC, had something to do with the expansion of R1a-Z645 to the north, in the forest steppe.

We could think that the finding of Z93 in Alexandria after the expansion of Khvalynsk-Novodanilovka chiefs would make it more likely that R1a-Z645 will be found in the North Pontic area. However, given that Lower Mikhailovka and Kvitjana seem to follow a steppe-related cultural tradition, different to forest steppe cultures (like Dereivka and Alexandria), and that forest steppe cultures show connections to neighbouring northern and western forest regions, the rest of the expanding R1a-Z645 community may not be related directly to the steppe at all.

Adding a hypothetical split and expansion of Z645 subclades to the mid-/late-5th millennium could place the expansion of this haplogroup to the north and west, pushed by expanding Middle PIE-speaking steppe peoples from the east:

distribution-horse-scepters
Schematic depiction of the spread of horse-head scepters in the Middle Eneolithic, representing expanding Khvalynsk-Novodanilovka chieftains. See a full version with notes here.

The Złota culture

I have already written about the Podolia-Volhynia region: about the North Pontic steppe cultures in contact with this area, and about the chaotic period of migrations when Corded Ware seem to have first emerged there among multi-directional and multi-ethnic migrants.

This is what Włodarczak (2017) says about the emergence of Corded Ware with ‘steppe features’ after the previous expansion of such features in Central Europe with Globular Amphorae peoples. He refers here to the Złota culture (appearing ca. 2900-2800 BC) in Lesser Poland, believed to be the (or a) transitional stage between GAC and Corded Ware, before the emergence of the full-fledged “Corded Ware package”.

So far, to the north of the Carpathian Mountains, including Polish lands, no graves indicating their relationship with communities of the steppe zone have been found. On the contrary, the funeral rites always display a local, central European nature. However, individual elements typical of steppe communities do appear, such as the “frog-like” arrangement of the body (Fig. 20), or items associated with Pit Grave milieux (cf. Klochko, Kośko 2009; Włodarczak 2014). A spectacular example of the latter is the pointed-base vessel of Pit Grave culture found at the cemetery in Święte, site 11 near Jarosław (Kośko et al. 2012). These finds constitute a confirmation of the importance of the relationships between communities of Pit Grave culture and Corded Ware culture. They are chronologically diverse, although most of them are dated to 2600-2400 BC – that is, to the “classic” period of Corded Ware culture.

funnelbeaker-trypillia-corded-ware
Map of territorial ranges of Funnel Beaker Culture (and its settlement concentrations in Lesser Poland), local Trypillian groups and early Corded Ware Culture settlements (◼) at the turn of the 4th/3rd millennia BC.

However, when discussing the relationships with the steppe communities, Polish lands deserve particular attention since part of the groups inhabiting it belonged to the eastern province of Corded Ware culture (cf. Häusler 2014), which neighboured Pit Grave culture both from the east and south. In addition, there was a tradition of varied relationships with the north Pontic zone, which began to intensify from the second half of the 4th millennium BC (Kośko, Szmyt, 2009; Kośko, Klochko, 2009). These connections are especially readable in Małopolska and Kujawy (Kośko 2014; Włodarczak 2014). The emergence of the community of Globular Amphora culture in the north Pontic zone at the end of the 4th and the beginnings of the 3rd millennium BC (Szmyt 1999) became a harbinger of a cultural closening between the worlds of central Europe and the steppe.

The second important factor taking place at that time was the expansion of the people of Pit Grave culture in a westerly direction, along the Danube thoroughfare. As a result of this, also to the south of the Carpathian Mountains, e.g., along the upper Tisza River, a new “kurgan” cultural system was formed. As one outcome, the areas of central Europe, above all Małopolska, found themselves in the vicinity of areas inhabited by communities characterized by new principles of social organization and a new funeral rite. Around 2800 BC these changes became evident in different regions of Poland, with the most numerous examples being documented in south-eastern Poland and Kujawy. The nature of the funeral rite and the features of the material culture perceptible at that time do not have straight forward analogies in the world of north Pontic communities. In this respect, the “A-horizon” is a phenomenon of local, central European origin. The events preceding the emergence of the said horizon (that is, the expansion of the people of Pit Grave culture into the area north of the arc of the Carpathians) are nowadays completely unidentifiable and remain merely an interesting theoretical matter (cf. e.g., Kośko 2000). Therefore, analysis of the archaeological sources cannot confirm the first archaeogenetic analysis suggesting a bond between the communities of the Pit Grave culture and Corded Ware culture (e.g., Haak et al. 2015).

Artefacts of the “A-horizon”, i.e., shaft-hole axes, amphorae (Fig. 21), beakers, and pots with a plastic wavy strip (Fig. 7) are found in different funerary and settlement contexts, sometimes jointly with finds having characteristics of various cultures (e.g., in graves of Złota culture, or at settlements of Rzucewo culture). Hence, they primarily represent a chronological phase (c. 2800-2600 BC), one obviously related to the expansion of a new ideology.

Eastern CWC expansion

Before continuing tracing the Corded Ware culture’s main features, it is worth it to trace first their movement forward in time, as Corded Ware settlers, from Poland to the east.

Circum-Baltic CWC

According to Klochko and Kośko (1998):

The colonizing Neolithic waves are continued by the Circum-Baltic Corded Ware culture, closely related to the traditions of the Single Grave culture and traditions of the Northern European Lowlands. After ca. 2900 BC, certain cultural systems with ‘corded’ traits –genetically related to the catchment area of the south-western Baltic – appear in the drainages of the Nemen, Dvina, Upper Dnieper, and even the Volga. These communities are considered the vector of Neolithisation in the Forest Zone.

east-european-fatyanovocwc
East European movement directions (arrows) of the representatives of the Central European Corded Ware Culture. Modified from I.I. Artemenko.

The picture in the Baltic (Pamariu / Rzucewo) and Finland (Battle Axe) is thus more or less clearly connected with early dates ca. 2900-2800 BC:

There is a clear interaction sphere between the eastern Gulf of Finland area – reaching from Estonia to the areas of present-day Finland and the Karelian Isthmus in Russia –, evidenced e.g. by the sharp-butted axes, derived from the Estonian Karlova axe.

Interesting in this regard is the expansion of the Corded Ware culture in Finland, into a far greater territory than previously thought, that is poorly represented in most maps depicting the extent of the culture in Europe. Here is summary of CWC findings in Finland, using images from Nordqvist and Häkäla (2014):

finland-cwc
Corded Ware culture remains in Finland, excluding the so-called ‘imitations’. [Notice in the top left image the often depicted border of the culture]. Combination of maps from Nordqvist & Häkälä (2014)

Middle Dnieper and Fatyanovo

The earliest Middle Dnieper remains are related to CWC graves between the Upper Vistula and the Bug, containing pottery with Middle Dnieper traits, dated probably ca. 2700 BC, which links it with the expansion of the A-horizon. In fact, during the period ca. 2800-2400 BC, the area of Lesser Poland (with its numerous kurgans and catacomb burials) is considered the western fringe of an area spreading to the east, to the middle Dniester and middle Dnieper river basins, i.e. regions bordering the steppe oecumene. This ‘eastern connection’ of funeral ritual, raw materials, and stylistic traits of artefacts is also identified in some graves of the Polish Lowlands (Włodarczak 2017).

gac-cwc-baltic-dnieper
Cultural situation in Eastern Europe in approximately the middle of the III mill. BC. Key: 1 – areas settled by Globular Amphora culture populations; 2 – areas penetrated by Globular Amphora culture populations; 3 – border between central and eastern group; 4 – Pamariu/Rzucewo culture area; 5 – zone of Pamariu/Rzucewo culture influences; 6 – directions of Comb Pottery culture influence; 7 – Zhizhitskaya culture; 8 – eastern border of “pure” Corded Ware site; 9 – North Belarussian culture; 10 – Middle Dnieper culture; 11 – Fatyanovo culture; 12 – Yamnaya culture; 13 – eastern border of Dniester group; 14 – Kemi-Oba culture and influences; 15 – Foltesti culture; 16 – syncretic sites with evidence of Globular Amphora culture traits (1 – Nida; 2 – Butinge; 3 – Palanga; 4 – Juodkrante; 5 – Azyarnoye; 6 – Mali Rogi; 7 – Prorva; 8 – Strumen/Losha; 9 – Syabrovichi; 10 – Luchin-Zavale; 11 – Lunevo (?); 12 – Belynets; 13 – Losiatyn; 14 – Corpaci; 15 – Ocnita; 16-17 – Camenca; 18 – Marculesti; 19 – Orhei; 20 – Efimovka; 21 – Tatarbunary; 22 – Novoselitsa; 23 – Primorskoye; 24 – Sanzhiyka; 25 – Akkermen; 26 – Maydanetskoye; 27 – Grigorevka; 28 – Kholmskoye; 29 – Purcari; 30 – Roscani; 31 – Semenovka; 32 – Grishevka; 33 – Durna Skela; 34 – Iskovshchina; 35 – Primorskoye); 17 – borders of ecological zones. From Szmyt (2010)

The Fatyanovo (or Fatyanovo-Balanovo) culture was the easternmost group of the Corded Ware culture, and occupied the centre of the Russian Plain, from Lake Ilmen and the Upper Dnieper drainage to the Wiatka River and the middle course of the Volga. From the few available dates, the oldest ones from the plains of the Moskva river, and from the late Volosovo culture containing also Fatyanovo materials, and in combination they show a date of ca. 2700 BC for its appearance in the region. The Volosovo culture of foragers eventually disappeared when the Fatyanovo culture expanded into the Upper and Middle Volga basin.

The origin of the culture is complicated, because it involves at its earliest stage different Corded Ware influences in neighbouring sites, at least on the Moskva river plains (Krenke et al. 2013): some materials (possibly earlier) show Circum-Baltic and Polish features; other sites show a connection to western materials, in turn a bridge to the Middle Dnieper culture. This suggests that groups belonging to different groups of the corded ware tradition penetrated the Moscow region.

The split of subclades Z93 – Z283

If we take into account that the split between R1-Z93 and R1a-Z283 must have happened during the 5th millennium BC, we have R1a-Z93 likely around the middle Dnieper area (as supported by the Alexandria sample), and R1a-Z283 possibly to the north(-west), so that it could have expanded easily into Central Europe, and – through the northern, Baltic region – to the east.

Where exactly lies the division is unclear, but for the moment all reported Circum-Baltic samples with Z645 subclades seem to belong to Z282, while R1a samples from Sintashta/Potapovka (including the Poltavka outlier) point to Abashevo being dominated by R1a-Z93 subclades.

We have to assume, then, that an original east-west split betwen R1a-Z283 and R1a-Z93 turned, in the eastern migrations, into a north-south split between Z282 and Z93, where Finland and Battle Axe in general is going to show Z282, and Middle Dnieper – Abashevo Z93 subclades.

copper-age-early-cwc
Early Copper Age migrations ca. 3100-2600 BC.

I can think of two reasons why this is important:

  1. Depending on how Proto-Corded Ware peoples expanded, we may be talking about one community overcoming the other and imposing its language. Because either
    • clans of both Z93 and Z283 were quite close and kept intense cultural contacts around Dnieper-Dniester area; or
    • if the split is as early as the 5th millennium BC, and both communities separated then without contact, we are probably going to see a difference in the language spoken by both of them.
  2. In any case, the main north-south division of eastern Corded Ware groups is pointing to an important linguistic division within the Uralic-speaking communities, specifically between a Pre-Finno-Ugric and a Pre-Samoyedic one, and potentially between Pre-Finno-Permic and Pre-Ugric.

These may seem irrelevant questions – especially for people interested only in Indo-European migrations. However, for those interested in the history of Eurasian peoples and languages as a whole, they are relevant: even those who support an ‘eastern’ origin of Proto-Uralic, like Häkkinen, or Parpola (who are, by the way, in the minority, because most Uralicists would point to eastern Europe well before the Yamna expansion), place the Finno-Ugric expansion with the Netted Ware culture as the latest possible Finno-Ugric immigrants in Fennoscandia.

The Netted Ware culture

The image below shows the approximate expansion of Corded Ware peoples of Battle Axe traditions in Finland, as well as neighbouring Fennoscandian territories, from ca. 2800 BC until the end of the 3rd millennium. A controversial 2nd (late) wave of the so-called Estonian Corded Ware is popular in texts about this region, but has not been substantiated, and it seems to be a regional development, rather than the product of migrations.

finland-corded-ware
Left: Corded Ware remains in Finland from ca. 2800 BC, according to Nordqvist & Häkälä (2014), combined in a single image. Right: Distribution of the Corded Ware culture within Finland. Mapped (black dots) are finds of typical stone battle axes, used as a proxy (data from [8]). The red isolines indicate average permanent snow cover period from 1981 to 2010 (data from [9]). A recent study estimates the snow cover period ca 4500 years ago would have been 40–50 days less than today [10]. Overlying coloration refers to the lactose persistance (LP) allele gradient in modern northeastern Europe (see the electronic supplementary material, appendix B: Material and methods and table 1, for details); lozenge dots specify the dataset mean points for the triangulation. From Cramp et al. (2014).

As we have seen, Fatyanovo represents the most likely cultural border zone between Circum-Baltic peoples reaching from the Russian Battle Axe to the south, and Middle Dnieper peoples reaching from Abashevo to the north. In that sense, it also represents the most likely border culture between north-western (mainly R1a-Z282) and south-eastern (R1a-Z93) subclades.

With worsening climatic conditions (cooler seasons) at the end of the 3rd millennium, less settlements are apparent in the archaeological record in Finland. After ca. 2000 BC, two CWC-related cultures remain: in the coast, the Kiukainen culture, derived from the original Circum-Baltic Corded Ware settlers, reverts to a subsistence economy which includes hunting and fishing, and keeps mainly settlements (from the best territories) along the coast. In the inland, Netted Ware immigrants eventually appear from the south.

cultures-western-finland
Image modified from Cramp et al. (2014) “The timeline shows the archaeological cultures
discussed here alongside actual sherds sampled and typical vessel forms (after [26–28]) (latter not shown to scale). Distribution maps show the geographical range of (f) Typical Comb Ware, (g) Corded Ware, (h) Kiukainen Ware and (i) Bronze Age cultures in the region (after [10,20,29]).”

The Netted Ware culture emerged in the Upper Volga–Oka region, derived from the Abashevo culture and its interaction with the Seima-Turbino network, and spread ca. 1900-1800 BC to the north into Finland, spreading into eastern regions previously occupied by cultures producing asbestos and organic-tempered wares (Parpola 2018).

NOTE. Those ‘contaminated’ by the Copenhagen fantasy map series may think that Volosovo hunter-gatherers somehow survived the expansion of Fatyanovo-Balanovo and Abashevo, hidden for hundreds of years in the forest, and then reappeared and expanded the Netted Ware culture. Well, they didn’t. At least not in archaeological terms, and certainly not with the genetic data we have.

If we combine all this information, and we think about these peoples in terms of Pre-Finno-Permic and Pre-Ugric languages developing side by side, we get a really interesting picture (see here for Proto-Fennic estimates):

  • The Battle Axe around the Baltic Sea – including the Gulf of Finland and Scandinavia – would be the area of expansion of Pre-Finno-Permic peoples, of R1a-Z283 subclades, which became later concentrated mainly on coastal regions;
  • the southern areas may correspond to Pre-Ugric peoples, which expanded later to the north with Netted Ware (see image below) – their precise subclades may be dependent on what will be found in Fatyanovo;
  • and Pre-Samoyedic peoples (of R1a-Z93 subclades) would have become isolated somewhere in the Cis- or (more likely) Trans-Urals region after 2000 BC, possibly from the interaction of the latest Balanovo stages and the Seima-Turbino phenomenon.
netted-ware-parpola
Distribution of the Netted Ware according to Carpelan (2002: 198). A: Emergence of the Netted Ware on the Upper Volga c. 1900 calBC. B: Spread of Netted Ware by c. 1800 calBC. C: Early Iron Age spread of Netted Ware. (After Carpelan 2002: 198 > Parpola 2012a: 151.)

These communities in contact would have allowed for:

  • the known Indo-Iranian loanwords in Finno-Ugric to spread through a continuum of early dialects formed by Abashevo – Fatyanovo – Battle Axe groups;
  • the Finno-Saamic substrate of Germanic to be associated with Battle Axe groups in Scandinavia;
  • the important Palaeo-Germanic loanwords in Finno-Saamic spreading with long-term contacts (from Pre-Germanic to the Proto-Germanic, and later North Germanic period) through the Baltic Sea, between Scandinavia and the Gulf of Finland;
  • and Tocharian contacts with Samoyedic (although limited, and in part controversial), which point to its early expansion to the east of the Ural Mountains.

On the other hand, if one is inclined to believe that R1a and steppe ancestry do represent Indo-European speakers… which language was spoken from the Gulf of Finland well into the north, the inland, and Karelia, and in Northern Russia, by Corded Ware peoples and their cultural heirs (like Kiukainen or Netted Ware) for almost three thousand years?

Because we know that no other peoples of different haplogroups dominated over eastern Fennoscandia until the Iron Age, and N1c and Siberian ancestry expanded separately, and probably due to late bottlenecks, especially with Fennic peoples expanding recently to the north at the expense of the Saami population.

After the expansion of Bell Beaker peoples, the geographic distribution of late Corded Ware groups in the second half of the 3rd millennium, just before their demise – and before the expansion of Netted Ware to the north – , can be depicted thus as follows:

bronze_age_early_cut
Early Bronze Age Europe.

Territories in cyan must then represent, for some people who believe in an archaic Indo-Slavonic of sorts, the famous Fennoscandian Balto-Slavic to the north (before they were displaced by incoming Finno-Saamic peoples of hg N1c during the Iron Age and up to the Middle Ages); and the also famous Tundra-Forest Indo-Iranian in the Upper Volga area, a great environment for the development of the two-wheeled chariot…

But let’s leave the discussion on imaginary IE dialects for another post, and continue with the real question at hand.

A steppe funerary connection?

Back to Złota as a transitional culture, we have already seen how the corded ware vessels characteristic of the Classic CWC are related to Globular Amphora tradition, and show no break with this culture. It is usually believed that the funerary rites were adopted from steppe influence, too. That is probably right; but it does not mean that it came from Yamna or other coeval (or previous) steppe culture; at least not directly.

NOTE. A similar problem is seen when we read that Mierzanowice or Trzciniec show “Corded Ware” traits from a neighbouring CWC group, when CWC groups disappeared long before these cultures emerged. For cultural groups that are separated centuries from each other, an assertion as to their relationship needs specifics in terms of dates and material connection, or it is plainly wrong.

These are the funerary ritual features from Złota (later specialized in Corded Ware), as described by Włodarczak (2017):

  • Single burial graves; along with the habit of interring the deceased in multiple burial graves, but emphasizing their individual character by careful deposition of the body and personal nature of the grave goods.
  • Grave goods with materials and stylistiscs belonging to an older system (e.g. amber products); and others correlated to the ‘new world’ of the CWC, such as flint products made of the raw materials tipical of Lesser Poland’s CWC, copper ornaments, stone shaft-hole axes, bone and shell ornaments, and characteristic forms of vessels like beakers and amphoras.
  • Military goods, which would become prevalent in later periods, are present in a moderate number, compatible with their lesser importance.
  • There are also cases of the characteristic catacomb (“niche”) graves – with an entrance pit, a more extensive niche, and a narrow corridor leading to a vault – , as well as some individual cases of application of ochre and deformation of skulls.
catacomb-grave-ksiaznice
Catacomb grave no. 2a/06 from Książnice, Złota culture (acc. to Wilk 2013). Image from Włodarczak (2017)

It seems that the Złota funerary tradition was also “transitional”, like corded ware vessels, into the classical Corded Ware ideology. But “transitional” from what exactly? Yamna? Probably not.

The Lublin-Volhynia culture

One needs not look for a too distant culture to find similarities. Włodarczak (2017) points to CWC in south-eastern Poland and Kuyavia showing, by the time of the Yamna expansion, a funeral rite and features of the material culture without straightforward analogies in the world of north Pontic communities, and thus suggests that the “A-horizon” is a local phenomenon of central European origin.

This assertion is interesting, in so far as most Corded Ware samples investigated to date seem to come precisely from an East-Central territory near the Ukraine forest steppe, with a cluster already established by the end of the 5th millennium:

PCA-caucasus-lola-ane-chg
Image modified from Wang et al. (2018). Samples projected in PCA of 84 modern-day West Eurasian populations (open symbols). Previously known clusters have been marked and referenced. An EHG and a Caucasus ‘clouds’ have been drawn, leaving Pontic-Caspian steppe and derived groups between them.See the original file here.

The following text is from Stanisław Wilk (2018), about the Lublin-Volhynian (and related) cemeteries at Wyciąże and Książnice:

lublin-volhynia-culture
A reach of the Wyciąże-Złotniki group and Lublin-Volhynian culture in the south-eastern Poland and western Ukraine: 1. Area of the Wyciąże-Złotniki group; 2. Area of the Lublin-Volhynian culture. A. Cemetery of the Lublin-Volhynian culture at site 2 in Książnice; B. Cemetery of the Wyciąże-Złotniki group at site 5 in Kraków Nowa Huta-Wyciąże (drawing by S. Wilk based on Zakościelna 2006 and Nowak 2014, on a background downloaded from https://maps-for-free.com/).

Regardless of the differences between the two necropolises (such as the number of burials, the area which has been explored, the orientation and layout of burials), it seems that they have several key elements in common:

  • concentration of graves in separate cemeteries;
  • differentiation of burials with regard to sex (the principle of the ‘left ̶ right’ side, different burial goods for males and females);
  • stratification of graves with regard to the richness of their inventories (this mainly applied to copper artefacts);
  • occurrence of indicators of the richest male burials (a copper dagger in Wyciąże, a copper battle axe, a small axe and a chisel in Książnice);
  • allocation of a separate area for elite burials (the eastern burial area in Książnice, and the southeastern and north-central part of the necropolis in Wyciąże), as well as one for egalitarian burials (the western area in Książnice, and the south-central and western part of the cemetery in Wyciąże).
lublin-volhynian-eneolithic-cemetery
Plan of the Lublin-Volhynian culture cemetery at site 2 in Książnice: 1. female graves; 2. man graves; 3. copper traces; 4. cenothap; 5. cremation grave; 6. partial grave; 7. estimated area of the L-VC cemetery; 8. estimated area of an elite and poor burial fields; 9. area of burials containing copper artefacts (drawing by S. Wilk).

The above-mentioned characteristics prove that the patterns of social and religious behaviours from areas lying beyond the Carpathian Mountains exerted a strong influence on the two societies living in Lesser Poland.

Anna Zakościelna, while describing the similarities between the burial ritual of the late Polgár groups and cultures from areas on the Tisza river and the Lublin-Volhynia culture, claimed that:

a characteristic feature of the burial ritual of both cultures was practicing various group norms, which required different treatment of the deceased depending on their sex, age and social rank. As in the Lublin-Volhynia culture, the opposition ‘male – female’ can the most clearly be observed ̶ particularly, in the consistent positioning of males on the right, and females, on the left side. And, there is much indication that this ritual norm divided the deceased from early childhood (Sofaer Derevensky 1997: 877, Tab. 1; Lichter 2001: 276- 280, 322-323) (Zakościelna 2010: 227-228).

It seems that these observations can also be extended to the Wyciąże-Złotniki group.

Another question is whether the evidence of the influences of the copper civilization observed in both cemeteries emerged as a result of the literal copying of patterns from the south, or whether the latter were only a source of inspiration for local solutions.

Looking at this problem form the perspective of the details of burial ritual, between the Carpathian Basin and Lesser Poland, we can observe clear differences, among others, in the size of cemeteries and orientation of burials. While, in the Carpathian Basin there were large necropolises, consisting of several dozen burials located in rows, with the dominant orientation along the SE-NW and E-W axis (Lichter 2001: Abb. 123, 143; Kadrow 2008: 87); in Lesser Poland there were small cemeteries of several to a dozen or so burials, mostly oriented along the S-N axis (in the Lublin-Volhynia culture; Zakościelna 2010: 66), as well as S-E and NE-SW (in the Wyciąże-Złotniki group; Kaczanowska 2009: 77). Similarly, there are differences in the details of the burial goods. North of the Carpathians, there is a much smaller frequency of copper artefacts, particularly in the group of prestigious, heavy items (battle axes, axes and daggers), as well as a complete lack of objects made of gold. Want is more, the pottery found in the graves has a distinct local character, only supplemented by imitating or imports from areas beyond the Carpathians (Zakościelna 2006: 85; Nowak 2014: 273; a different opinion Kozłowski 2006: 57). Therefore, the suggestion made by Nowak seems right ̶ namely, that these influences were not caused by migrations of groups of the population living on the Tisza river to Lesser Poland, but were rather due to processes of selective cultural transmission (Nowak 2014: 273).

Therefore, the sharing of a similar funerary rite (as happened later between Lublin-Volhynia and Złota), although it shows a strong cultural connection with autochthonous cultures, is obviously not the same as sharing ancestors; and even if it were so, they would not need to be paternal ancestors. But it shows that important Corded Ware cultural traits are local developments, and it disconnects thus still more supposed CWC ‘steppe traits’ from steppe cultures, and connects them with the first steppe-related cultural wave that reached central Europe in the 5th millennium BC.

Prehistoric Pontic—Caspian links

How would a Lublin-Volhynia culture be related to the North Pontic area ca. 4500-3000 BC? We can enjoy the map series of Baltic—Pontic migrations by Viktor Klochko (2009), and make a wild guess:

baltic-pontic-routes
Pontic—Baltic routes of migrations during the Eneolithic. Top left: Linear Pottery expansion. Top right: Funnel Beaker expansion. Bottom left: late Trypillia expansion. Bottom right: GAC expansion.

And then read the account of Sławomir Kadrow, in Exchange of People, Ideas and Things between Cucuteni-Trypillian Complex and Areas of South-Eastern Poland (2016):

In the second half of the 5th millennium BC (horizon 1), communities of the Tripolye culture, phases BI-BII, had contacts with the population of the late (IIa) phase of the Malice culture. The areas settled by both cultural complexes were located at a great distance from each other. The communities of the Tripolye culture adopted selected features of Malice ceramic production (fig 2). This seems to have resulted from marital exchange: on a moderate scale, Tripolye men sought out their wives in the area of the Malice culture and, according to patrilocal marriage customs, the women then moved to the Tripolye settlements, sporadically transferring ready-made ceramic products, so-called imports, to the Tripolye culture. Thus, the wives were responsible for the considerably more numerous imitations of the Malice ceramics and the long-lasting, though selective, traditions of Malice pottery passed down in their new environment. The patrilocal marriage customs involving the Malice women and the Tripolye men (never the other way round), and the fact that pottery was women’s domain, led to the unidirectional transfer of vessels, technology and norms of ceramic production from the Malice culture to the Tripolye culture.

The turn of the 5th and the 4th millennia and the early 4th millennium BC (horizon 2) witnessed the deepening interaction between the populations of the youngest (IIb) phase of the Malice culture and the classic (II) phase of the Lublin-Volhynia culture on the one hand and the communities of phase BII of the Tripolye culture on the other. The Danube and the Tripolye settlement complexes came into contact on the upper Dniester and between the Styr and the Horyn rivers in Volhynia. This helped to continue the previous forms of marital exchange, which resulted in further popularisation of the ceramics and the traditions of ceramic production typical of the Danube cultures, i.e. the Malice and the Lublin-Volhynia cultures, and also the Polgár culture, in the areas settled by the Tripolye cultural complex.

As the civilizational norms of the Eneolithic (Copper) Age became widespread in that period, the forms of interaction described above acquired new elements. The deepening internal diversification of the early Eneolithic communities of the Lublin-Volhynia culture led to a growing demand for prestige objects, which was met with import or imitation of copper artefacts, mainly those from the Carpathian Basin, and with flint tools produced from long blades. That type of flint production depended largely on new technologies derived from the Tripolye culture, as proven by such borrowings as troughlike retouch or the very idea and technology for the production of long flint blades in the Lublin-Volhynia culture. It seems that the influx of Tripolye settlers into flintbearing areas in Volhynia and on the upper Dniester, adjacent to the settlement centres of the late phase of the Malice culture and the Lublin-Volhynia culture, created sufficient conditions for the expanding influence of the Tripolye flint working on the communities of the Eneolithic Lublin-Volhynia culture.

In the mid-4th millennium BC (horizon 3), those forms of interaction between the Danube communities (the late phase of the Lublin-Volhynian culture) and the Tripolye communities (phase CI)were continued. Elements of the Danube pottery still grew in popularity in the Tripolye population, while selected features of the Tripolye flint working were adopted by the Lublin-Volhynia culture.

In that period, the population of the Funnel Beaker culture of the pre-classic and early classic phases (the beginnings of Gródek 1 and Bronocice III), until then absent from those areas, quite quickly drove out and replaced the Danube population in western Volhynia and the upper Dniester basin. This caused significant changes in the forms and intensity of the intercultural interaction, which became fully apparent already in the 2nd half of the 4th millennium BC.

In the following period (horizon 4), the population of the classic phase of the Funnel Beaker culture (Gródek 1, Bronocice III) settled more and more intensively the upper Dniester basin, up to the Hnyla Lypa river, and western Volhynia, up to the Styr river. East of those rivers, the Funnel Beaker settlers created considerable areas where they mixed with settlers from early phase CII of the Tripolye culture. Their coexistence, lasting there for many generations, resulted in deepening the interactions between members of both cultural complexes and in developing entirely new forms of relationships.

(…)

The intensifying interaction between the communities of the Funnel Beaker culture and the Tripolye culture, early phase CII, in the 2nd half of the 4th millennium BC (horizon 4) was an introduction to, and perhaps a condition for, even more frequent contacts in the next period, the first centuries of the 3rd millennium BC (horizon 5). In that case, the interaction was mainly triggered by multidirectional migrations of larger human groups, involving a significant part of the population of all cultures from the areas discussed here. The Tripolye communities of younger phase CII settled Volhynia, its eastern areas in particular, from the south and the south-east, while groups representing the younger phases of the Funnel Beaker culture (Gródek 2), often with Baden features (Bronocice IV and V), moved increasingly into the western part of that region. The Yamna communities expanded along the lower and central Danube to the west, whereas the populations of the late phase of the Baden culture took the opposite direction, reaching as far as Kiev in the northeast, and contributed to the cultural character of the Sofievka group.

The communities of the Globular Amphora culture migrated from the north-west, from eastern Poland, towards the Danube Delta and as far as the Dnieper in the east, while the multicultural population from the areas around the mouth of the Danube moved in the opposite direction, carrying with them cultural elements from Thrace, or even from Anatolia. Some of them returned to the starting point (to south-eastern Poland), bringing with them a new form of pottery, so-called Thuringian amphora, borrowed from the late Trypillian Usatovo group. This resulted in origins of the Złota culture, a cultural phenomenon that gave beginnings to the oldest Corded Ware culture. Inventories of both cultures contained the already mentioned Thuringian amphorae.

lublin-volhynia-alexandria
Graves and cemeteries with gender differentiated burial rites in Europe; A — Hamangia and Varna cultures; B — Tiszapolgar and Bodrogkeresztur cultures; C — Lublin-Volhynia culture; D — Brześć Kujawski culture. Added star symbol with approximate location of the Alexandria site. Modified image from Sławomir Kadrow (2016)

Here is a more recent assessment (2017) of the latest radiocarbon analyses of the available settlements of cultures in the area, published by Marek Novak (announced in a previous post), which gives the following data on Wyciąże-Złotniki, Lublin-Volhynia, and Wyciąże/Niedźwiedź:

This scheme unambiguously suggests both the overlapping and contiguous nature of cultural development in western Lesser Poland within the Middle Neolithic. The basic elements of this development are: 1) the Wyciąże-Złotniki group and the Lublin-Volhynian culture, until c. 3650–3550 cal BC; 2) the Funnel Beaker culture proper, which appeared c. 3750–3700c al BC, and existed until c. 3300–3250 cal BC, perhaps accompanied by the Wyciąże/Niedźwiedź materials from c. 3650–3550 cal BC; and 3) the Baden culture and the Funnel Beaker/Baden assemblages from 3100 and 3300–3100 cal BC, respectively, until 2850–2750 and 2850 cal BC, with – possibly – later Funnel Beaker culture and Wyciąże/ Niedźwiedź materials, existing until c. 3100 cal BC.

The final scheme shows that the Lublin-Volhynian culture could have coincided with the Wyciąże-Złotniki group. In view of the territorial relationship between them, relations from the point of view of material culture, primarily in the field of pottery, become particularly interesting. It is relatively easy to see clear similarities between these units. However, the most evident similarities apply only to some categories of ceramics, including, for example, vessels with Scheibenhenkel handles. What is more, in the period between the late 38th and early 36th centuries BC, the early Funnel Beaker and possibly early Baden influences are superimposed on this Lublin-Volhynian/Wyciąże-Złotniki ‘mix’.

[About Corded Ware: The] development of this unit in central Europe, including western Lesser Poland, [] usually point to c. 2800 cal BC (Włodarczak 2006a). (…) the calibration curve makes it possible to alternatively refer several dates earlier than c. 3100 to c. 2850–2800 cal BC.

Conclusion

There is no direct archaeological link of Lublin-Volhynia-related groups with Corded Ware, beyond the fact that they shared homeland and Central European (‘steppe-related’) traits, as found in the Złota culture. But there is no direct link of Yamna with Corded Ware, either, whether in terms of culture or population.

So, given the evident link of R1a-Z93 and steppe ancestry with the forest steppe ca. 4000 BC, the surrounding North Pontic areas in contact along the Dniester, Dnieper, Bug, and Prut are the best candidates for the appearance of R1a-Z283: steppe cultures to the south and south-west; sub-Neolithic (Comb Ware) groups to the north in the forest zone; and Eneolithic groups to the west and north-west.

Seeing how ‘ancestral components’ and PCA cluster can change within a few generations, the question of the spread of R1a-Z645 subclades is still not settled by a single sample in Alexandria. However, based on the explosive expansions we are seeing from small territories, it would not be surprising to find R1a-Z93 and R1a-Z283 side by side in the same small area within the forest steppe.

NOTE. An archaeological link may not mean anything relevant in genetics, especially – as in this case – when no clear migration event has been traced to date. We have seen exactly that with Kristiansen’s proposal of a long-term genetic admixture of Yamna with Trypillia and GAC to form Corded Ware, which didn’t happen. The cultural and ideological connection of CWC peoples with Lublin-Volhynian tradition may be similar to the already known connection with GAC, and not mean anything in genetic finds; at least in terms of Y-DNA haplogroup.

We believed in the 2000s that Corded Ware represented the expansion of Late Proto-Indo-European, because the modern map of haplogroup R1a showed a distribution similar to how we thought the European and Indo-Iranian languages could have expanded. This has been proven wrong, and that’s what ancient DNA is for; not to confirm the own ideas or models, or to support modern ideologies.

It is impossible to know if R1a-Z645 comes from the steppe, forest steppe, or forest zone, until more samples are published. I don’t think there will be any big surprise, no matter where it is eventually found. By now, adding linguistic reconstruction to archaeological traits, and to the genetic data from Yamna and Corded Ware settlers, the only clear pattern is that patrilineal clans expanded, during the Final Eneolithic / Chalcolithic:

  • Late Proto-Indo-European with Yamna and R1b-L23 subclades, given the known genomic data from Khvalynsk, Yamna, Afanasevo, Bell Beaker, Catacomb, and Poltavka—Sintashta/Potapovka.
  • Uralic with Corded Ware and R1a-Z645 subclades, given the known genomic data from Fennoscandia and the Forest Zone.

Everything else is just wishful thinking at this moment.

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