The cradle of Russians, an obvious Finno-Volgaic genetic hotspot

pskov-novgorod-russia

First look of an accepted manuscript (behind paywall), Genome-wide sequence analyses of ethnic populations across Russia, by Zhernakova et al. Genomics (2019).

Interesting excerpts:

There remain ongoing discussions about the origins of the ethnic Russian population. The ancestors of ethnic Russians were among the Slavic tribes that separated from the early Indo-European Group, which included ancestors of modern Slavic, Germanic and Baltic speakers, who appeared in the northeastern part of Europe ca. 1,500 years ago. Slavs were found in the central part of Eastern Europe, where they came in direct contact with (and likely assimilation of) the populations speaking Uralic (Volga-Finnish and Baltic- Finnish), and also Baltic languages [11–13]. In the following centuries, Slavs interacted with the Iranian-Persian, Turkic and Scandinavian peoples, all of which in succession may have contributed to the current pattern of genome diversity across the different parts of Russia. At the end of the Middle Ages and in the early modern period, there occurred a division of the East Slavic unity into Russians, Ukrainians and Belarusians. It was the Russians who drove the colonization movement to the East, although other Slavic, Turkic and Finnish peoples took part in this movement, as the eastward migrations brought them to the Ural Mountains and further into Siberia, the Far East, and Alaska. During that interval, the Russians encountered the Finns, Ugrians, and Samoyeds speakers in the Urals, but also the Turkic, Mongolian and Tungus speakers of Siberia. Finally, in the great expanse between the Altai Mountains on the border with Mongolia, and the Bering Strait, they encountered paleo-Asiatic groups that may be genetically closest to the ancestors of the Native Americans. Today’s complex patchwork of human diversity in Russia has continued to be augmented by modern migrations from the Caucasus, and from Central Asia, as modern economic migrations take shape.

pskov-novgorod-pca-eurasia-yakut
Sample relatedness based on genotype data. Eurasia: Principal Component plot of 574 modern Russian genomes. Colors reflect geographical regions of collection; shapes reflect the sample source. Red circles show the location of Genome Russia samples.

In the current study, we annotated whole genome sequences of individuals currently living on the territory of Russia and identifying themselves as ethnic Russian or as members of a named ethnic minority (Fig. 1). We analyzed genetic variation in three modern populations of Russia (ethnic Russians from Pskov and Novgorod regions and ethnic Yakut from the Sakha Republic), and compared them to the recently released genome sequences collected from 52 indigenous Russian populations. The incidence of function-altering mutations was explored by identifying known variants and novel variants and their allele frequencies relative to variation in adjacent European, East Asian and South Asian populations. Genomic variation was further used to estimate genetic distance and relationships, historic gene flow and barriers to gene flow, the extent of population admixture, historic population contractions, and linkage disequilibrium patterns. Lastly, we present demographic models estimating historic founder events within Russia, and a preliminary HapMap of ethnic Russians from the European part of Russia and Yakuts from eastern Siberia.

pskov-novgorod-pca-finno-permic
Sample relatedness based on genotype data. Western Russia and neighboring countries: Principal Component plot of 574 modern Russian genomes. Colors reflect geographical regions of collection; shapes reflect the sample source. Red circles show the location of Genome Russia samples.

The collection of identified SNPs was used to inspect quantitative distinctions among 264 individuals from across Eurasia (Fig. 1) using Principal Component Analysis (PCA) (Fig. 2). The first and the second eigenvectors of the PCA plot are associated with longitude and latitude, respectively, of the sample locations and accurately separate Eurasian populations according to geographic origin. East European samples cluster near Pskov and Novgorod samples, which fall between northern Russians, Finno-Ugric peoples (Karelian, Finns, Veps etc.), and other Northeastern European peoples (Swedes, Central Russians, Estonian, Latvians, Lithuanians, and Ukrainians) (Fig. 2b). Yakut individuals map into the Siberian sample cluster as expected (Fig. 2a). To obtain an extended view of population relationships, we performed a maximum likelihood-based estimation of ancestry and population structure using ADMIXTURE [46](Fig. 2c). The Novgorod and Pskov populations show similar profiles with their Northeastern European ancestors while the Yakut ethnic group showed mixed ancestry similar to the Buryat and Mongolian groups.

pskov-novgorod-yakut-admixture
Population structure across samples in 178 populations from five major geographic regions (k=5). Samples are pooled across three different studies that covered the territory of Russian Federation (Mallick et al. 2016 [36], Pagani et al. 2016 [37], this study). The optimal k-value was selected by value of cross validation error. Russian samples from all studies (highlighted in bold dark blue) show a slight gradient from Eastern European (Ukrainian, Belorussian, Polish) to North European (Estonian Karelian, Finnish) structures, reflecting population history of northward expansion. Yakut samples from different studies (highlighted in bold red) also show a slight gradient from Mongolian to Siberian people (Evens), as expected from their original admixture and northward expansions. The samples originated from this study are highlighted, and plotted in separated boxes below.

Possible admixture sources of the Genome Russia populations were addressed more formally by calculating F3 statistics, which is an allele frequency-based measure, allowing to test if a target population can be modeled as a mixture of two source populations [48]. Results showed that Yakut individuals are best modeled as an admixture of Evens or Evenks with various European populations (Supplemental Table S4). Pskov and Novgorod showed admixture of European with Siberian or Finno-Ugric populations, with Lithuanian and Latvian populations being the dominant European sources for Pskov samples.

direction-expansion-russians
The heatmaps of gene flow barriers show for each point at the geographical map the interpolated differences in allele frequencies (AF) between the estimated AF at the point with AFs in the vicinity of this point. The direction of the maximal difference in allele frequencies is coded by colors and arrows.

So, Russians expanding in the Middle Ages as acculturaded Finno-Volgaic peoples.

Or maybe the true Germano-Slavonic™-speaking area was in north-eastern Europe, until the recent arrival of Finno-Permians with the totally believable Nganasan-Saami horde, whereas Yamna -> Bell Beaker represented Vasconic-Caucasian expanding all over Europe in the Bronze Age. Because steppe ancestry in Fennoscandia and Modern Basques in Iberia.

A really hard choice between equally plausible models.

Related

Sintashta diet and economy based on domesticated animal products and wild resources

indo-iranian-sintashta-uralic-migrations

New paper (behind paywall) Bronze Age diet and economy: New stable isotope data from the Central Eurasian steppes (2100-1700 BC), by Hanks et al. J. Arch. Sci (2018) 97:14-25.

Interesting excerpts (emphasis mine):

Previous research at KA-5 was carried out by A. V. Epimakhov in 1994–1995 and 2002–2003 and resulted in the excavation of three Sintashta culture barrows (kurgans) that produced 35 burial pits and a reported 100 skeletons (Epimakhov, 2002, 2005; Epimakhov et al., 2005; Razhev and Epimakhov, 2004). Seven AMS radiocarbon dates on human remains from the cemetery yielded a date range of 2040–1730 cal. BC (2 sigma), which placed the cemetery within the Sintashta phase of the regional Bronze Age (Hanks et al., 2007). Twelve recently obtained AMS radiocarbon dates, taken from short-lived wood and charcoal species recovered from the Kamennyi Ambar settlement, have provided a date range of 2050–1760 cal. BC (2 sigma). Importantly, these dates confirm the close chronological relationship between the settlement and cemetery for the Middle Bronze Age phase and discount the possibility of a freshwater reservoir effect influencing the earlier dating of the human remains from the Kamennyi Ambar 5 cemetery (Epimakhov and Krause, 2013).

Sintashta cemeteries frequently yield fewer than six barrow complexes and the number of skeletons recovered represents a fraction of the total population that would have inhabited the settlements (Judd et al., 2018; Johnson and Hanks, 2012). Scholars have suggested that only members of higher status were afforded interment in these cemeteries and that principles of social organization structured placement of individuals within central or peripheral grave pits (Fig. 2) (Koryakova and Epimakhov, 2007: 75–81). In comparison with other Sintashta cemeteries that have been excavated, KA-5 provides one of the largest skeletal inventories currently available for study.

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Upper – plan of Kamennyi Ambar settlement and cemetery; Lower – plan views of Kurgan 2 and Kurgan 4 from KA-5 Cemetery (kurgan plans redrawn from Epimakhov, 2005: 10, 79).

The KA-5 (MBA), Bestamak (MBA) and Lisakovsk (LBA) datasets exhibited a wide range of δ13C and δ15N values for both humans and herbivores (Figs. 5 and 6 & Table 8). This diversity in isotopic signals may be evident for a variety of reasons. For example, the range of values may be associated with a broad spectrum of C3 and C4 plant diversity in the ancient site biome or herbivore grazing patterns that included more diverse environmental niche areas in the microregion around the sampled sites. Herders also may have chosen to graze animals in niche areas due to recognized territorial boundaries between settlements and concomitant patterns of mobility. Importantly, data from Bolshekaragansky represents humans with lower δ15N values that are more closely associated with δ15N values of the sampled domestic herbivores (Fig. 6). When the archaeological evidence from associated settlement sites is considered, Bolshekaragansky, Bestamak, Lisakovsk and KA-5 have been assumed to represent populations that shared similar forms of pastoral subsistence economies with significant dietary reliance upon domesticated herbivore meat and milk. Human diets have δ13C values closely related to those of local herbivores in terms of the slope of the trendline and range of values (Fig. 6). Comparatively, the cemetery of Bolshekaragansky (associated with the Arkaim settlement) reflects individuals with trend lines closer to those of cattle and caprines and may indicate a stronger reliance on subsistence products from these species with less use of wild riverine and terrestrial resources. The site of Čiča is significantly different with elevated human δ15N isotopic values and depleted δ13C values indicative of a subsistence regime more closely associated with the consumption of freshwater resources, such as fish. The stable isotopic data in this instance is strongly supported by zooarchaeological evidence recovered from the Čiča settlement and also is indicative of significant diachronic changes from the LBA phases through the Iron Age (Fig. 6).

kamenniy-ambar-isotopic-chicha-lisakovsk-bestamark
Regional analysis and comparison of stable isotope results from humans (adults) and animals recovered from MBA and LBA cemeteries in the Southern Urals (Kamennyi Ambar 5 & Bolshekaragansky) northwestern Kazakhstan (Liskovsk & Bestamak) and southwestern Siberia (Čiča).

Conclusion

(…) The isotopic results from KA-5, and recent botanical and archaeological studies from the Kamennyi Ambar settlement, have not produced any evidence for the production or use of domesticated cereals. While this does not definitively answer the question as to whether Sintashta populations engaged in agriculture and/or utilized agricultural products, it does call into serious question the ubiquity of such practices across the region and correlates well with recent archaeological, bioarchaeological, and isotopic studies of human and animal remains from the Southwestern Urals region and Samara Basin (Anthony et al., 2016; Schulting and Richards, 2016). The results substantiate a broader spectrum subsistence diet that in addition to the use of domesticated animal products also incorporated wild flora, wild fauna and fish species. These findings further demonstrate the need to draw on multiple methods and datasets for the reconstruction of late prehistoric subsistence economies in the Eurasian steppes. When possible, this should include datasets from both settlements and associated cemeteries.

Variability in subsistence practices in the central steppes region has been highlighted by other scholars and appears to be strongly correlated with local environmental conditions and adaptations. More comprehensive isotopic studies of human, animal and fish remains are of fundamental importance to achieve more robust and empirically substantiated reconstructions of local biomes and to aid the refinement of regional and micro-regional economic subsistence models. This will allow for a fuller understanding of key diachronic shifts within dietary trends and highlight regional variation of such practices. Ultimately, this will more effectively index the diverse social and environmental variables that contributed to late prehistoric lifeways and the economic strategies employed by these early steppe communities.

Social organization of Sintashta-Petrovka

Interesting to remember now the recent article by Chechushkov et al. (2018) about the social stratificaton in Sintashta-Petrovka, and how it must have caused the long-lasting, peaceful admixture process that led to the known almost full replacement of R1b-L23 (mostly R1b-Z2103) by R1a-Z645 (mostly R1a-Z93) subclades in the North Caspian steppe, coinciding with the formation of the Proto-Indo-Iranian community and language (read my thoughts on this after Damgaard et al. 2018).

Here is another relevant excerpt from Chechushkov et al. (2018), translated from Russian:

settlement-kamenniy-ambar
The map of the settlement of Kamennyi Ambar with excavations, soil cores, and test pits. Legend: a — cuts of the sides of ravines; b — test pits of 2015—2017; c — test pits of 2004; d — soil-science samples with a cultural layer; e — soil-science samples without cultural layer; f — borders of archaeological sites (interpretation of the plan of magnetic anomalies); g — boundaries of excavated structures (1, 2, 4, 5, 7 — Sintashta-Petrovka culture; 3, 6 — Srubnaya-Alakul’ culture).

The analysis suggests that the Sintashta-Petrovka societies had a certain degree of social stratification, expressed both in selective funeral rituals and in the significant difference in lifestyle between the elite and the immediate producers of the product. The data obtained during the field study suggest that the elite lived within the fortifications, while a part of the population was outside their borders, on seasonal sites, and also in stationary non-fortified settlements. Probably, traces of winter settlements can be found near the walls, while the search for summer ones is a task of a separate study. From our point of view, the elite of the early complex societies of the Bronze Age of the Eurasian steppe originated as a response to environmental challenges that created risks for cattle farming. The need to adapt the team to the harsh and changing climatic conditions created a precedent in which the settled collectives of pastoralists – hunter-gatherers could afford the content and magnificent posthumous celebration of people and their families who were not engaged in the production or extraction of an immediate product. In turn, representatives of this social group directed their efforts to the adoption of socially significant decisions, the organization of collective labor in the construction of settlement-shelters and risked their lives, acting as military leaders and fighters.

Thus, in Bronze Age steppe societies, the formation, development and decline of social complexity are directly related to the intensity of pastoralism and the development of new territories, where collectives had to survive in part a new ecological niche. At the same time, some members of the collective took upon themselves the organization of the collective’s life, receiving in return a privileged status. As soon as the conditions of the environment and management changed, the need for such functions was virtually eliminated, as a result of which the privileged members of society dissolved into the general mass, having lost their lifetime status and the right to be allocated posthumously.

Also interesting for the MLBA haplogroup bottleneck in the region is the paper by Judd et al. (2017) about fast life history in Early Indo-Iranian territories.

On the arrival of haplogroup N1c1-L392

Regarding the special position of the Chicha-1 samples in the change of diet and economy during the Iron Age, it is by now well known that haplogroup N must have arrived quite late to North-East Europe, and possibly not linked with the expansion of Siberian ancestry – or linked only with some waves of Siberian ancestry in the region, but not all of them. See Lamnidis et al. (2018) for more on this.

Also, the high prevalence of haplogroup N among Fennic and Siberian (Samoyedic) peoples is not related: while the latter reflects probably the native (Palaeo-Siberian) population that acquired their Uralic branch during the MLBA expansions associated with Corded Ware groups, the former points to the expansion of Fennic peoples into Saamic territory (i.e. after the Fenno-Saamic split) as the most likely period of expansion of N1c1-L392 subclades (see known recent bottlenecks among Finns, and on Proto-Finnic dialectalization).

Probably related to these late incomers are the ancient DNA samples from the Sargat culture during the Iron Age, which show the arrival of N subclades in the region, replacing most – but not all – R1a lineages (see Pilipenko et al. (2017)). Regarding the site of Chicha-1, the following are relevant excerpts about the cultural situation that could have allowed for such stepped, diachronic admixture events in Northern Eurasia, from the paper Stages in the settlement history of Chicha-1: The Results of ceramic analysis, by Molodin et al. (2008):

The stratigraphic data allows us to make the following inference: originally, the settlement was inhabited by people bearing the Late Irmen culture. Later, the people of the Baraba trend of the Suzgun culture arrived at the site (Molodin, Chemyakina, 1984: 40–62). The Baraba-Suzgun pottery demonstrates features similar to what has been reported from the sites of the transitional Bronze to Iron Age culture in the pre-taiga and taiga zones in the Irtysh basin (Potemkina, Korochkova, Stefanov, 1995; Polevodov, 2003). The major morphological types are slightly and well-profiled pots with a short throat. (…)

chicha-irmen-tagar-baraba-forest-siberian
Map showing the location of Chicha-1.

During the following stage of development of the site, the Chicha population increased with people who practiced cultures others than those noted in earlier collections. The ceramic materials from layer 5 provide data on possible relationships. In addition to migrants from northwestern regions practicing the Suzgun culture, there were people bearing the Krasnoozerka culture. Available data also suggests that people from the northern taiga region with the Atlym culture visited the site.

However, people from the west and southwest represent the greatest migration to the region under study. In all likelihood they moved from the northern forest-steppe zone of modern Kazakhstan and practiced the Berlik culture. The spatial distribution analysis of the Chicha-1 site suggests that the Berlik population was rather large. The Berlik people formed a single settlement with the indigenous Late Irmen people and apparently waged certain common economic activities, but preserved their own ethnic and cultural specificity (Molodin, Parzinger, 2006: 49–55). Judging by the data on the chronological sequence of deposited artifacts, migration took place roughly synchronously, hence Chicha-1 became a real cultural and economic center.

(…) In sum, the noted distribution of ceramics over the culture-bearing horizons suggests that beginning with layer 5, traditions of ceramic manufacture described above were practiced, hence the relevant population inhabited the site. Apparently, there were two predominant traditions: the local Late Irmen cultural tradition and the Berlik tradition, which was brought by the immigrants. The Late Irmen people mostly populated the citadel, while the Berlik immigrants inhabited the areas to the east and the north of the citadel.

The stratigraphic data also suggest that the Early Sargat ceramics emerged at the site likely as a part of the Late Irmen tradition (…) Early Sargat ceramics is apparently linked with the Late Irmen tradition. Artifacts associated with the Sargat culture proper have been found in several areas of Chicha-1 (e.g., in excavation area 16). However, the Sargat people appeared at the site after it had been abandoned by its previous inhabitants, and had eventually become completely desolated. This happened no earlier than the 6th cent. BC, possibly in the 5th cent. BC (in fact, the radiocarbon dates for that horizon are close to the turn of the Christian era).

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