The Iron Age expansion of Southern Siberian groups and ancestry with Scythians

iron_age-sarmatians

Maternal genetic features of the Iron Age Tagar population from Southern Siberia (1st millennium BC), by Pilipenko et al. (2018).

Interesting excerpts (emphasis mine):

The positions of non-Tagar Iron Age groups in the MDS plot were correlated with their geographic position within the Eurasian steppe belt and with frequencies of Western and Eastern Eurasian mtDNA lineages in their gene pools. Series from chronological Tagar stages (similar to the overall Tagar series) were located within the genetic variability (in terms of mtDNA) of Scythian World nomadic groups (Figs 5 and 6; S4 and S6 Tables). Specifically, the Early Tagar series was more similar to western nomads (North Pontic Scythians), while the Middle Tagar was more similar to the Southern Siberian populations of the Scythian period. The Late Tagar group (Tes`culture) belonging to the Early Xiongnu period had the “western-most” location on the MDS plot with the maximal genetic difference from Xiongnu and other eastern nomadic groups (but see Discussion concerning the low sample size for the Tes`series).

In a comparison of our Tagar series with modern populations in Eurasia, we detected similarity between the Tagar group and some modern Turkic-speaking populations (with the exception of the Indo-Iranian Tajik population) (Fig 7; S2 Table). Among the modern Turkic-speaking groups, populations from the western part of the Eurasian steppe belt, such as Bashkirs from the Volga-Ural region and Siberian Tatars from the West Siberian forest-steppe zone, were more similar to the Tagar group than modern Turkic-speaking populations of the Altay-Sayan mountain system (including the Khakassians from the Minusinsk basin) (Fig 7).

tagar-archaeology
Location of Tagar archaeological sites from which samples for this study were obtained. Burial grounds: 1—Novaya Chernaya-1; 2—Podgornoe Ozero, Barsuchiha-1, Barsuchiha-6, Barsuchiha-7; 3—Perevozinskiy; 4—Ulug-Kyuzyur, Kichik-Kyuzyur, Sovetskaya Khakassiya; 5—Tepsey-3, Tepsey-8, Tepsey-9; 6—Dolgiy Kurgan. https://doi.org/10.1371/journal.pone.0204062.g001

Mitochondrial DNA diversity and genetic relationships of the Tagar population

Our results are not inconsistent with the assumption of a probable role of gene flow due to the migration from Western Eurasia to the Minusinsk basin in the Bronze Age in the formation of the genetic composition of the Tagar population. Particularly, we detected many mtDNA lineages/clusters with probable West Eurasian origin that were dominant in modern populations of different parts of Europe, Caucasus, and the Near East (such as K and HV6) in our Tagar series based on a phylogeographic analysis.

We detected relatively low genetic distances between our Tagar population and two Bronze Age populations from the Minusinsk basin—the Okunevo culture population (pre-Andronovo Bronze Age) and Andronovo culture population, followed by Afanasievo population from the Minusinsk Basin and Middle Bronze Age population from the Mongolian Altai Mountains (the region adjacent to the Minusinsk basin) (Figs 3 and 6; S3 and S5 Tables). Among West Eurasian part of our Tagar series we also observed haplogroups/sub-haplogroups and haplotypes shared with Early and Middle Bronze Age populations from Minusinsk Basin and western part of Eurasian steppe belt (Fig 4; S5 Table). Thus, our results suggested a potentially significant role of the genetic components, introduced by migrants from Western Eurasia during the Bronze Age, in the formation of the genetic composition of the Tagar population. It is necessary to note the relatively small size of available mtDNA samples from the Bronze Age populations of Minusinsk basin; accordingly, additional mtDNA data for these populations are required to further confirm our inference.

tagar-mtdna-tree
Phylogenetic tree of mtDNA lineages from the Tagar population. Color coding of the Tagar stages: orange—the Early Tagar stage; blue—the Middle Tagar Stage; green—the Late Tagar stage. Color of haplogroup labels: yellow—for Western Eurasian haplogroups; red—for Eastern Eurasian haplogroups. https://doi.org/10.1371/journal.pone.0204062.g002

Another substantial part of the mtDNA pool of the Tagar and other eastern populations of the Scythian World is typical of populations in Southern Siberia and adjacent regions of Central Asia (autochthonous Central Asian mtDNA clusters). Most of these components belong to the East Eurasian cluster of mtDNA haplogroups. Moreover, the role of each of these components in the formation of the genetic composition of subsequent (to the present) populations in South Siberia and Central Asia could be very different. In this regard, cluster C4a2a (and its subcluster C4a2a1), and haplogroup A8 are of particular interest.

Genetic features of successive Tagar groups

We compared successive Tagar groups (Early, Middle, and Late Tagar) with each other and with other Iron Age nomadic populations to evaluate changes in the mtDNA pool structure. Despite the genetic similarity between the Early and Middle Tagar series and Scythian World nomadic groups (Figs 5 and 6; S4 and S6 Tables), there were some peculiarities. For example, the Early Tagar series was more similar to North Pontic Classic Scythians, while the Middle Tagar samples were more similar to the Southern Siberian populations of the Scythian period (i.e., completely synchronous populations of regions neighboring the Minusinsk basin, such as the Pazyryk population from the Altay Mountains and Aldy-Bel population from Tuva).

We observed differences in the mtDNA pool structure between the Early and the Middle chronological stages of the Tagar culture population, as evidenced by the change in the ratio of Western to Eastern Eurasian mtDNA components. The contribution of Eastern Eurasian lineages increased from about one-third (34.8%) in the Early Tagar group to almost one-half (45.8%) in the Middle Tagar group.

tagar-mtdna-fst
Results of multidimensional scaling based on matrix of Slatkin population differentiation (FST) according to frequencies of mtDNA haplogroup in Tagar populations and modern populations of Eurasia. Populations: Tagar (red pentagon) (this study); Mongolian-speaking populations: Khamnigans (Buryat Republic, Russia) [43]; Barghuts (Inner Mongolia, China) [44]; Buryats (Buryat Republic, Southern Siberia, Russia) [43]; Mongols (Mongolia) [45]. Turkic-speaking populations: Tuvinians (Tuva Republic, Russia) [43]; Tofalars (Irkutsk region, Russia) [46]; Altai-Kizhi ((Altai Republic, Russia) [43, 47]; Telenghits (Altai Republic, Russia) [43,47]; Tubalars (Altai Republic) [48]; Shors (Kemerovo region, Russia) [43, 47]; Khakassians (Khakassian Rupublic, Russia) [43, 46]; Altaian Kazakhs (Altai Republic) [49]; Kazakhs (Kazakhstan, Uzbekistan) [50, 51]; Kirghiz (Kyrgyzstan) [50, 51]; Uighurs (Kazakhstan and Xinjiang) [50, 52]; Siberian Tatars (Tyumen and Omsk regions, Russia) [53]; Tatars (Volga-Ural rigion, Russia) [54]; Bashkirs (Volga-Ural region, Russia) [55]; Uzbeks (Uzbekistan) [51, 56]; Turkmens (Turkmenistan) [51, 56]; Nogays [57]; Turkeys [58]; other populations: Evenks [43, 46]; Ulchi [59]; Koreans (South Korea) [43]; Han Chinese [60]; Zhuang (Guangxi, China) [61]; Tadjiks (Tadjikistan) [43, 51]; Iranians [60]; Russians [62]. https://doi.org/10.1371/journal.pone.0204062.g007

At the level of mtDNA haplogroups, we detected a decrease in the diversity of phylogenetic clusters during the transition from the Early Tagar to the Middle Tagar. This decline in diversity equally affected the West Eurasian and East Eurasian components of the Tagar mtDNA pool. It should be noted that this decrease can be partially explained by the smaller number of Middle Tagar than Early Tagar samples. Under a simple binomial approximation the mtDNA clusters, observed at frequencies of 6.3% and 11.7%, could be lost by chance in our Early (N = 46) and Middle (N = 24) Tagar samples, respectively. However, the simultaneous lack of several such clusters, with a total frequency in the gene pool of the Early group of 34.8%, is unlikely.

The observed reduction in the genetic distance between the Middle Tagar population and other Scythian-like populations of Southern Siberia(Fig 5; S4 Table), in our opinion, is primarily associated with an increase in the role of East Eurasian mtDNA lineages in the gene pool (up to nearly half of the gene pool) and a substantial increase in the joint frequency of haplogroups C and D (from 8.7% in the Early Tagar series to 37.5% in the Middle Tagar series). These features are characteristic of many ancient and modern populations of Southern Siberia and adjacent regions of Central Asia, including the Pazyryk population of the Altai Mountains. We did not obtain strong evidence for an intensification of genetic contact between the population of the Minusinsk basin and the Altai Mountains in the Middle Tagar period compared with the Early Tagar period. Although, several archaeologists have found evidence for the intensification of contact at the level of material culture, namely, a cultural influence of the population of the Altai Mountains (represented by the Pazyryk population) on the population of the Minusinsk basin (the Saragash Tagar group) [6, 71, 72].

Another important issue is the change in the genetic structure of the Tagar population during the transition from the Middle (Saragash) to the Late (Tes`) stage. The Late Tagar stage refers to the Xiongnu period. Many archaeologists suggest that the formation of the Tes`stage involved the direct cultural influence of the Xiongnu and/or related groups of nomads from more eastern regions of Central Asia [71, 73]. Some archaeologists have even suggested renaming the Tes`stage in the Tes`culture [71], emphasizing the role of new eastern cultural elements. If this influence also existed at the genetic level, then we would expect to observe new genetic elements in the Tes`gene pool, particularly those of East Eurasian origin.

Siberian ancestry

Just a reminder of the recent session in ISBA 8 on expanding Scythians (and also Mongolians and Turks) spreading Siberian ancestry, usually (wrongly) identified as “Uralic-Yeniseian” based on modern populations (similar to how steppe ancestry is wrongly identified as “Indo-European”), see the following graphic including the Tagar population:

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

And also the poster by Alexander M. Kim et al. Yeniseian hypotheses in light of genome-wide ancient DNA from historical Siberia:

The relevance of ancient DNA data to debates in historical linguistics is an emphatic strand in much recent work on the archaeogenetics of Eurasia, where the discussion has focused heavily on Indo-European (Haak et al. 2015; Narasimhan et al. 2018; de Barros Damgaard et al. 2018a,b). We present new genome-wide ancient DNA data from a historical Siberian individual in relation to Yeniseian, an isolated language “microfamily” (Vajda 2014) that nonetheless sits at the center of numerous controversial proposals in historical linguistics and cultural interaction. Yeniseian’s sole surviving representative is Ket, a critically endangered language fluently spoken by only a few dozen individuals near the Middle Yenisei River of Central Siberia.

In strong contrast to the present-day picture, river names and argued substrate influences and loanwords in languages outside the current range of Yeniseian, as well as direct records from the Russian colonial period, indicate that speakers of extinct Yeniseian languages had a formerly much broader presence in the taiga of Central Siberia as well as further south in the mountainous Altai-Sayan region – and perhaps even further afield in Inner Asia (Vajda 2010; Gorbachov 2017; Blažek 2016). The consilience of these proposals with genetic data is not straightforward (Flegontov et al. 2015, 2017) and faces a major obstacle in the lack of genetic information from verifiable speakers of Yeniseian languages other than the Kets, who have had complex ongoing interactions with speakers of non-Yeniseian languages such as the Samoyedic Selkups. We attempt to remedy this with new historical Siberian aDNA data, orienting our search for common denominators and systematic difference in a broader landscape of concordance, discordance, and uncertainty at the interface of diachronic linguistics and genetics.

Related

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.

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

Y-DNA haplogroups of Tuvinian tribes show little effect of the Mongol expansion

uralic-turkic

Open access Estimating the impact of the Mongol expansion upon the gene pool of Tuvans, by Balanovskaya et al., Vavilov Journal of genetics and breeding (2018), 22(5):611-619.

Abstract (emphasis mine):

With a view to trace the Mongol expansion in Tuvinian gene pool we studied two largest Tuvinian clans – those in which, according to data of humanities, one could expect the highest Central Asian ancestry, connected with the Mongol expansion. Thus, the results of Central Asian ancestry in these two clans component may be used as upper limit of the Mongol influence upon the Tuvinian gene pool in a whole. According to the data of 59 Y-chromosomal SNP markers, the haplogroup spectra in these Tuvinian tribal groups (Mongush, N = 64, and Oorzhak, N = 27) were similar. On average, two-thirds of their gene pools (63 %) are composed by North Eurasian haplogroups (N*, N1a2, N3a, Q) connected with autochtonous populations of modern area of Tuvans. The Central Asian haplogroups (C2, O2) composed less then fifth part (17 %) of gene pools of the clans studied. The opposite ratio was revealed in Mongols: there were 10 % North Eurasian haplogroups and 75 % Central Asian haplogroups in their gene pool. All the results derived – “genetic portraits”, the matrix of genetic distances, the dendrogram and the multidimensional scaling plot, which mirror the genetic connections between Tuvinian clans and populations of South Siberia and East Asia, demonstrated the prominent similarity of the Tuvinian gene pools with populations from and Khakassia and Altai. It could be therefore assumed that Tuvinian clans Mongush and Oorzhak originated from autochtonous people (supposedly, from the local Samoyed and Kets substrata). The minor component of Central Asian haplogroups in the gene pool of these clans allowed to suppose that Mongol expansion did not have a significant influence upon the Tuvinan gene pool at a whole.

tuvan-clans-y-dna

Interesting excerpts:

Haplogroup C2 peaks in Central Asia (Wells et al., 2001; Zerial et al., 2003), though its variants are abundant in other peoples of Siberia and Far East. For instance, in one of Buryat clans, namely Ekhirids, hg C2 frequency is 88 % (Y-base); in Kazakhs from different regions of Kazakhstan, total occurrence of hg C2 variants averages between 17 and 81 % (Abilev et al., 2012; Zhabagin et al., 2013, 2014, 2017), in populations of the Amur River (such as Nanais, Negidals, Nivkhs, Ulchs) – between 40 and 65 %, in Evenks – up to 68 % (Y-base), in Kyrgyz people of Pamir-Alay – up to 22 %, correspondingly; of all Turkic peoples of Altai, relatively high hg C2 frequency (16 %) is detected only in Telengits (Balanovskaya et al., 2014; Balaganskaya et al., 2011a, 2016). In Tuvinian clans under the study, hg C2 frequency is rather low – 19 % in Mongush and 11 % in Oorzhak, while in Mongols it makes up almost two thirds of the entire gene pool an comprises different genetic lines (subhaplogroups).

tuvinian-y-chromosome
Y-chromosomal haplogroup spectra in gene pools of Tuvinian Oorzhak and Mongush clans and of the neighboring populations of South Siberia and Central Asia.

Haplogroup N is abundant all over North Eurasia from Scandinavia to Far East (Rootsi et al., 2007). The study on whole Y-chromosome sequencing conducted with participation of our group (Ilumäe et al., 2016) subdivided this haplogroup into several branches with their regional distribution. In gene pools of the Tuvans involved, hg N was represented by two sub-clades, namely N1a2 and N3a.

Sub-clade N1a2 peaks in populations of West Siberia (in Nganasans, frequency is 92 %) and South Siberia (in Khakas 34 %, in Tofalars 25 %) (Y-base). In Tuvans, N1a2 occurrence is nearly 16 % in Mongush and 15 % in Oorzhak clans, respectively, while in Mongols, the frequency is three times less (5 %). Hg N1a2 is supposed to display the impact of the Samoyedic component to the gene pool of Tuvinian clans (Kharkov et al., 2013).

Sub-clade N3a is major in the Oorzhak clan comprising almost half of the gene pool (45 %); it is represented by two sub-clades, namely N3a* and N3a5. The same sub-branches are specific to the Mongush clan as well, though with lower frequencies: N3a* – 9 % and N3a5 – 14 % (see Table). In Khori-Buryats from the Transbaikal region, a high frequency is observed – 82 % (Kharkov et al., 2014), while in Mongols, N3a5 occurs rather rarely (6 %). Hg N3a* was detected in populations of South Siberia only, and was widely spread in Khakas-Sagays and Shors (up to 40 %) (Ilumäe et al., 2016) (Y-base).

samoyedic
Map of distribution of Samoyedic languages (red) in the XVII century (approximate; hatching) and in the end of XX century (continuous background). Modified from Wikipedia, with the Tuva region labelled.

Within the pan-Eurasian haplogroup R1a1a, two large genetic lines (sub-haplogroups) are identified: “European” (marker M458) and “Asian” (marker Z93) the latter almost never occurring in Europe (Balanovsky, 2015) but abundant in South Siberia and northern Hindustan. In the Altai-Sayan region, high frequencies of the “Asian” branch are spread in many peoples – Shors, Tubalars, Altai-Kizhi people, Telengits, Sagays, Kyzyl Khakas, Koibals, Teleuts (Y-base) (Kharkov et al., 2009). Hg R1a1a comprises perceptible parts of gene pools of Tuvinian clans (19 % in Mongush, and 15 % in Oorzhak), though its occurrence in Mongols is much lower (6 %). Those results also count in favor of the hypothesis of autochtonous component dominance even in the gene pools of clans potentially most influenced by Mongolian ancestry. If we add R1a1a variants to the “North Eurasian” haplogroups, the “not-Central Asian” component will compose average four fifth of the entire gene pools for Tuvinian clans (in Mongush 77 %, and in Oorzhak 81 %), being only 16 % in Mongols. Such data are definitely contrary to the hypothesis of a crucial influence of the Mongol expansion upon the development of Tuvinian gene pool.

I found interesting the high proportion of R1a-Z93 subclades among Sagays in Khakhasia, which stem from a local Samoyed substratum, as described by the paper…

Featured Image: Map of Uralic and Altaic languages, from Wikipedia.

Related

Updated phylogenetic tree of haplogroup Q-M242 points to Palaeolithic expansions

palaeo-siberian-haplogroup-y-dna

New paper (behind paywall) Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences by Wei et al., Eur. J. Hum. Genet. (2018)

Interesting excerpts (for Eurasian migrations):

Differentiation and diffusion in Palaeolithic Siberia

Based on the phylogenetic analyses and the current distributions of relative sub-lineages, we propose that the prehistoric population differentiation in Siberia after the LGM (post-LGM) provided the genetic basis for the emergence of the Paleo-Indian, American aborigine, population. According to the phylogenetic tree of Y-chromosome haplogroup C2-M217 (Fig. 2 and Figure S1), eight sub-lineages emerged in a short period between 15.3 kya and 14.3 kya (Table S5). Within these sub-lineages, haplogroups C2-M48, C2-F1918, and C2- F1756 are predominant paternal lineages in modern Altaic-speaking populations [46, 51, 52]. Samples of haplogroups C2-F8535 and C2-P53.1 were found in two Turkic- and Mongolic-speaking minorities in China (Table S1). Both archeological and genetic data suggest that Altaic-speaking populations are results of population expansion in the past several thousand years in the Altai Mountain, Mongolia Plateau, and Amur River region [51–54].

By contrast, three other sub-lineages, C2-B79, C2-B77, and C2-P39, appear only in Koryaks and Native Americans [16, 35]. The latitude of the Altai Mountain, the Mongolia Plateau, and Amur River region are much lower than that of Beringia, where the ancestors of Native Americans finally separated from their close relatives in Siberia. Therefore, the phylogeographic patterns of sub-lineages of C2-M217 in this study reveal a major splitting event between populations in a lower latitude region of Siberia and ancestors of Koryaks and Native Americans during the post-LGM period.

The sub-lineages of the Y-chromosome Q-M242 haplogroup were found in populations throughout the Eurasia continent. According to available data, the Q1-L804 lineage is exclusively found in Northwest Europe, while Q1-M120 is primarily restricted to East Asia [48]. Additionally, the lineage Q1-L330 is the predominant paternal lineage in Altai, Tuva, and Kets in South Siberia [34–36, 55]. A number of Q1-M242 samples have also been found in ancient remains from South Siberia and adjacent regions [56, 57]. Other sub-lineages of Q-M242 are scattered widely in different geographic regions of Eurasia, including Q1-L275, Q1-M25, and Q1-Y2659 [14, 35, 37, 58]. Additionally, the Y-chromosome of a 6000–5100 BCE sample (I4550) from Zvejnieki, Latvia has been identified as Q1-L56 [59]. These findings suggest that the sub-lineages of Q-M242 started to diffuse throughout Eurasia in a very ancient period.

y-dna-q-siberia
Founding paternal lineages of American aborigines and their most closely related lineages among Eurasia populations

Emergence of Paleo-Indian populations

The revised phylogenetic tree of Y-chromosome haplogroup Q-M242 in this study provides clues regarding the origin of Native American lineages Q1-M3 and Q1-Z780 (Fig. 3). According to our estimates, haplogroup Q1-L54 expanded rapidly between 17.2 kya and 15.0 kya and finally gave rise to two major founding paternal lineages of Native American populations, known as Q1-Z780 and Q1-M3. Ancient DNA studies indicate that the early population in South Siberia, represented by MA1 genomes, had a genetic influence on both modern western European and Native American populations [7]. Therefore, we conclude that the accumulated diversity of sub-lineages of Q-M242 before 15.3 kya resulted from the in situ differentiation of Q-M242 in Central Eurasia and South Siberia since the Paleolithic Age, and the appearance of the Paleo-Indian population is part of the great human diffusion throughout the Eurasia after the Last Glacial Maximum.

The Southern Caucasus PIE homeland

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 origin of Q-M242 in Zvejnieki, like those of Lola (Q1a2-M25) and Steppe Maykop (Q1a2-M25) from Wang et al. (2018) are therefore most likely migrations throughout North Eurasia dated to the Palaeolithic.

As you might remember, the sample of haplogroup Q1a from Khvalynsk was the closest one (in the PCA, see above) to those we now know most likely represent one or more groups of the steppe north of the Caucasus, which were absorbed during the formation and expansion of Khvalynsk.

NOTE. In fact, the position of this early Khvalynsk sample in the PCA is near the Steppe Eneolithic cluster, in turn near ANE (with the Lola sample Q1a2-M25, circle in dark blue/violet above), and Steppe Maykop (which includes the other Q1a2-M25 sample).

It is often assumed that these populations absorbed in the Pontic-Caspian steppe were dominated by haplogroup J, due to the oldest representatives of CHG ancestry (Kotias Klde and Satsurblia).

However, it would not be surprising now to find out that (one or more of) these “CHG/ANE-rich” groups from the steppe (possibly the Kairshak culture in the North Caspian region) were in fact dominated by Q1-M25 subclades.

If this is the case, I don’t know where the proponents of the (south of the) Caucasus homeland will retreat to.

Related

Origins of equine dentistry in Mongolia in the early first millennium BC

New paper (behind paywall) Origins of equine dentistry, by Taylor et al. PNAS (2018).

Interesting excerpts (emphasis mine):

The practice of horse dentistry by contemporary nomadic peoples in Mongolia, coupled with the centrality of horse transport to Mongolian life, both now and in antiquity, raises the possibility that dental care played an important role in the development of nomadic life and domestic horse use in the past. To investigate, we conducted a detailed archaeozoological study of horse remains from tombs and ritual horse inhumations across the Mongolian Steppe, assessing evidence for anthropogenic dental modifications and comparing our findings with broader patterns in horse use and nomadic material culture.

We conducted a detailed study of archaeological horse collections spanning the past 3,200 y, including those from the Late Bronze Age DSK complex (ca. 1200–700 BCE, n = 70), Early Iron Age Slab Burial culture (ca. 700–300 BCE, n = 4), Pazyryk culture (ca. 600–200 BCE, n = 2), Late Iron Age Xiongnu Empire (ca. 200 BCE–200 CE, n = 3), Early Middle Ages post-Xiongnu period (ca. 100–550 CE, n = 3), and Turkic Khaganate (ca. 600–800 CE, n = 3).

horse-riding-mongolia
A (top): Contemporary Mongolian herder engaged in horseback riding, using left-handed rein position causing asymmetric pressures to the horse’s skull. Photo by Orsoo Bayarsaikhan. B(center) contemporary Mongolian horse skulls, showing asymmetric and skewed thinning to the nasal bones caused by bridle pressure. C(bottom) Asymmetric deformation to the cranial bones of a Deer Stone-Khirigsuur horse (left), alongside an early Middle Ages horse with a similar feature (right). Modified from Taylor and Tuvshinjargal (2018).

Discussion

This Late Bronze Age dental modification counts among the earliest documented instances of equine veterinary care, and the oldest known evidence for horse dentistry. At first glance, the detailed historical record of early equine veterinary care in places such as China, Greece, Rome, and Syria, which spans the late second millennium BCE through the early centuries CE (11, 15, 16), might imply that equine dentistry emerged in the sedentary civilizations of the Old World. However, the earliest textual references describe only nonsurgical medicinal treatments and make few mentions of oral health (11). Recent archaeological discoveries suggest that human care of domestic animals was practiced by hunter-gatherers as far back as the Paleolithic (46), and that pastoralists may have occasionally practiced surgical procedures on domestic animals as early as the Neolithic in Europe (47). The evidence presented here indicates that horse dentistry was developed by nomadic pastoralists living on the steppes of Mongolia and northeast Asia during the Late Bronze Age, concurrent with the local adoption of the metal bit and many centuries before the first mention of dental practices in historical accounts from sedentary Old World civilizations.

Our results reveal a fundamental link between equine dentistry and the emergence of horsemanship in the steppes of Eurasia. At the turn of the first millennium BCE, militarized, horse-mounted peoples reshaped the social and economic landscape of many areas of the Eurasian continent. Conflagrations with equestrian peoples, such as those between the Persian Empire and the Pontic “Scythians,” plagued alluvial civilizations from the Near East to India and China, while large-scale movements of people linked East and West in never-before-seen ways (48). The archaeological and historical records indicate that the earliest horseback riding was accomplished without stirrups or saddles, and probably using only bitless or organic-mouthpiece bridles (49, 50). The bronze snaffle bit, and the improved control it provided, was a key technological development that enabled the use of horseback riding for more stressful and difficult activities, such as long-distance transportation and warfare (32). We argue that these technological improvements in horse control were preceded and sustained by innovations in veterinary dentistry by nomadic peoples living in the continental interior. By increasing herd survival and mitigating behavioral and health issues caused by horse equipment, innovations in equine dentistry improved the reliability of horseback riding for ancient nomads, enabling horses to be used for nonpastoral activities like warfare, high-speed riding, and distance travel.

damage-tooth-horse
Damage to the retained wolf tooth in a 4-5 year old mummified horse, dating to the 2-4th centuries CE from the site of Urd Ulaan-Uneet in western Mongolia

Conclusion

Archaeozoological data from Mongolian horses indicate that the nomadic practice of equine dentistry dates back more than 3,000 y to the DSK complex, a Late Bronze Age culture associated with the first mounted horseback riding and mobile pastoralism in eastern Eurasia. Attempted removal of deciduous incisors through sawing of the exterior suggests experimentation with dental extraction, but not the removal of wolf teeth. The appearance of extracted first premolars in the first millennium BCE coincides with the arrival of metal bits in the archaeological record and oral trauma linked with metal bit use, suggesting that innovations in dental practice were an adaptation to the mechanical changes in horse equipment. These bronze and metal bits provided greater control over the horse, facilitating the development of military uses for the horse, but also introduced new dental problems with the first premolar. Our results indicate that, coincident with the earliest evidence for metal bit use, wolf tooth extraction was practiced in Mongolia by ca. 750 BCE and continued through the early Middle Ages. These results push back the earliest dates for equine dentistry by more than a millennium and suggest that nomadic peoples developed key innovations in veterinary care that enabled more sophisticated horse control, ultimately changing the structure of communication, exchange, and military power in ancient Eurasia.

Related

Genetic history of admixture across inner Eurasia; Botai shows R1b-M73

y-haplogroup-r1b-p343

Open access Characterizing the genetic history of admixture across inner Eurasia, by Jeong et al. (2018).

Abstract (emphasis mine):

The indigenous populations of inner Eurasia, a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra, harbor tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine, and Uzbekistan. We furthermore report genome-wide data of two Eneolithic individuals (~5,400 years before present) associated with the Botai culture in northern Kazakhstan. We find that inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries. This genetic separation is well mirrored by geography. The ancient Botai genomes suggest yet another layer of admixture in inner Eurasia that involves Mesolithic hunter-gatherers in Europe, the Upper Paleolithic southern Siberians and East Asians. Admixture modeling of ancient and modern populations suggests an overwriting of this ancient structure in the Altai-Sayan region by migrations of western steppe herders, but partial retaining of this ancient North Eurasian-related cline further to the North. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.

Interesting excerpts:

On North Eurasians

In a PCA of Eurasian individuals, we find that PC1 separates eastern and western Eurasian populations, PC2 splits eastern Eurasians along a north-south cline, and PC3 captures variation in western Eurasians with Caucasus and northeastern European populations at opposite ends (Figure 2A and Figures S1-S2). Inner Eurasians are scattered across PC1 in between, largely reflecting their geographic locations. Strikingly, inner Eurasian populations seem to be structured into three distinct west-east genetic clines running between different western and eastern Eurasian groups, instead of being evenly spaced in PC space. Individuals from northern Eurasia, speaking Uralic or Yeniseian languages, form a cline connecting northeast Europeans and the Uralic (Samoyedic) speaking Nganasans from northern Siberia (“forest-tundra” cline). Individuals from the Eurasian steppe, mostly speaking Turkic and Mongolic languages, are scattered along two clines below the forest-tundra cline. Both clines run into Turkic- and Mongolic-speaking populations in southern Siberia and Mongolia, and further into Tungusic-speaking populations in Manchuria and the Russian Far East in the East; however, they diverge in the west, oneheading to the Caucasus and the other heading to populations of the Volga-308 Ural area (the “southern steppe” and “steppe-forest” clines, respectively; Figure 2 and Figure S2).
(…)
The forest-tundra cline populations derive most of their eastern Eurasian ancestry from a component most enriched in Nganasans, while those on the steppe-forest and southern steppe clines have this component together with another component most enriched in populations from the Russian Far East, such as Ulchi and Nivkh. The southern steppe cline groups are distinct from the others in their western Eurasian ancestry profile, in the sense that they have a high proportion of a component most enriched in Mesolithic Caucasus hunter-gatherers (“CHG”) and Neolithic Iranians (“Iran_N”) and frequently harbor another component enriched in South Asians (Figure S4).

north-eurasian-uralic
qpAdm-based admixture models for the forest-tundra cline populations. For populations to the east of the Urals (Enets, Selkups, Kets, and Mansi), EHG+Yamnaya+Nganasan provides a good fit, except for Mansi, for which adding WHG significantly increases the model fit. For the rest of the groups, WHG+LBK_EN+Yamnaya+Nganasan in general provides a good fit. 5 cM jackknifing standard errors are marked by the horizontal bar.

For the forest-tundra cline populations, for which currently no relevant Holocene ancient genomes are available, we took a more generalized approach of using proxies for contemporary Europeans: WHG, WSH (represented by “Yamnaya_Samara”), and early Neolithic European farmers (EEF; represented by “LBK_EN”; Table S2). Adding Nganasans as the fourth reference, we find that most Uralic-speaking populations in Europe (i.e. west of the Urals) and Russians are well modeled by this four-way admixture model (χ 2 p ≥ 0.05 for all but three groups; Figure 5 and Table S8). Nganasan-related ancestry substantially contributes to their gene pools and cannot be removed from the model without a significant decrease in model fit (4.7% to 29.1% contribution; χ 2 p ≤ 1.12×10-8; Table S8). The ratio of contributions from three European references varies from group to group, probably reflecting genetic exchange with neighboring non-Uralic groups. For example, Saami from northern Fennoscandia contain a higher WHG and lower WSH contribution (16.1% and 41.3%, respectively) than Udmurts or Besermyans from the Volga river region do (4.9-6.6% and 50.7-53.2%, respectively), while the three groups have similar amounts of Nganasan-related ancestry (25.5-29.1%).

The Caucasus Mountains form a barrier to gene flow

By applying EEMS to the Caucasus region, we identify a strong barrier to gene flow separating North and South Caucasus populations. This genetic barrier coincides with the Greater Caucasus mountain ridge even to small scale: a weaker barrier in the middle, overlapping with Ossetia, matches well with the region where the ridge also becomes narrow. We also observe weak barriers running in the north-south direction that separate northeastern populations from northwestern ones. Together with PCA, EEMS results suggest that the Caucasus Mountains have posed a strong barrier to human migration.

caucasus-genetic-barrier
The Greater Caucasus mountain ridge as a barrier to 856 genetic exchange. Barriers (brown) and conduits (green) of gene flow around the Caucasus region are estimated by the EEMS program. Red diamonds show the location of vertices to which groups are assigned. A strong barrier to gene flow overlaps with the Greater Caucasus mountain ridge reflecting the genetic differentiation between populations of the north and south of the Caucasus. The barrier becomes considerably weaker in the middle where present-day Ossetians live.

On the Botai individuals

The Y-chromosome of the male Botai individual (TU45) belongs to the haplogroup R1b (Table 411 S6). However, it falls into neither a predominant European branch R1b-L5165 nor into a R1b-GG400 branch found in Yamnaya individuals. Thus, phylogenetically this Botai individual should belong to the R1b-M73 branch which is frequent in the Eurasian steppe (Figure S9). This branch was also found in Mesolithic samples from Latvia as well as in numerous modern southern Siberian and Central Asian groups.

The Botai genomes provide a critical snapshot of the genetic profile of pre-Bronze Age steppe populations. Our admixture modeling positions Botai primarily on an ancient genetic cline of the pre-Neolithic western Eurasian hunter-gatherers: stretching from the post-Ice Age western European hunter-gatherers (e.g. WHG) to EHG in Karelia and Samara to the Upper Paleolithic southern Siberians (e.g. AG3). Botai’s position on this cline, between EHG and AG3, fits well with their geographic location and suggests that ANE-related ancestry in the East did have a lingering genetic impact on Holocene Siberian and Central Asian populations at least till the time of Botai.
(…)
The most recent clear connection with the Botai ancestry can be found in the Middle Bronze Age Okunevo individuals (Figure S6C). In contrast, additional EHG-related ancestry is required to explain the forest-tundra populations to the east of the Urals (Figure 5 and Table S8). Their multi-way mixture model may in fact portrait a prehistoric two-way mixture of a WSH population and a hypothetical eastern Eurasian one that has an ANE-related contribution higher than that in Nganasans. Botai and Okunevo individuals prove the existence of such ANE ancestry-rich populations. Pre-Bronze Age genomes from Siberia will be critical for testing this hypothesis.

botai-pca
The first two PCs summarizing the genetic structure within 2,077 Eurasian individuals. The two PCs generally mirror geography. PC1 separates western and eastern Eurasian populations, with many inner Eurasians in the middle. PC2 separates eastern Eurasians along the north-south cline and also separates Europeans from West Asians. Ancient individuals (color-filled shapes), including two Botai individuals, are projected onto PCs calculated from present-day individuals.

So, to sum up:

  • Northern Eurasia forms a Uralic – Yeniseian cline from east to west, with contribution from Steppe, WHG, and Siberian ancestry. Siberian ancestry is represented by Palaeo-Siberian Nganasans, who adopted Samoyedic quite late. It was already known that the different waves of Siberian ancestry are too late and do not represent the spread of Uralic languages, so that leaves us with Steppe and WHG.
  • The Caucasus Mountains were a long-lasting prehistoric barrier to gene flow (as recently shown in Y-DNA, too).
  • The Botai sample (ca. 3632-3100 BC) represents thus the furthest east that R1b-P297 subclades had expanded (we did know that, and that they didn’t have close genetic links with Khvalynsk, so the haplogroup spread there probably much earlier). It expanded R1b-M269’s sister clade R1b-M73 (also found in the Baltic region), and the Botai are on the ‘eastern’ end of an ancient genetic cline stretching from WHG to EHG to Afontova Gora.

EDIT (23 MAY 2018) Both samples share mtDNA, and the male one shares Y-DNA, with those reported in Damgaard et al. (Nature 2018); although dates are slightly different (3371-3354 calBC for BOT 14), it is within the range given for this one; for the female, the dates are similar (3521-3377 calBC for BOT2016, 3517-3367 cal. BCE for this one). The lack of data on their origin may point to the fact that we only have different bone samples from the same two Botai individuals. So probably still 50% R1b-M73 (with the other 50% being N2* from BOT15)…

It seems therefore not only that R1b-M269 is bound to split from the parent haplogroup in or around the steppe or forest-steppe: the Mesolithic spread of haplogroup R1b in North Eurasia is wider and its relevance thus greater than previously thought.

We may need to rethink the role of haplogroup R1a in spreading EHG and Indo-Uralic from east to west…

Featured image, from the supplementary materials: Frequency distribution map of the Y-chromosomal haplogroup R1b-P343(xM269) identified in the Eneolithic Botai individual. All modern Eurasian samples with this haplogroup tested to date for the downstream markers fall into R1b-M73 branch, suggesting Botai sample be one of its earliest representatives.

Related:

Eurasian steppe dominated by Iranian peoples, Indo-Iranian expanded from East Yamna

yamna-indo-iranian-expansion

The expected study of Eurasian samples is out (behind paywall): 137 ancient human genomes from across the Eurasian steppes, by de Barros Damgaard et al. Nature (2018).

Dicussion (emphasis mine):

Our findings fit well with current insights from the historical linguistics of this region (Supplementary Information section 2). The steppes were probably largely Iranian-speaking in the first and second millennia bc. This is supported by the split of the Indo-Iranian linguistic branch into Iranian and Indian33, the distribution of the Iranian languages, and the preservation of Old Iranian loanwords in Tocharian34. The wide distribution of the Turkic languages from Northwest China, Mongolia and Siberia in the east to Turkey and Bulgaria in the west implies large-scale migrations out of the homeland in Mongolia since about 2,000 years ago35. The diversification within the Turkic languages suggests that several waves of migration occurred36 and, on the basis of the effect of local languages, gradual assimilation to local populations had previously been assumed37. The East Asian migration starting with the Xiongnu accords well with the hypothesis that early Turkic was the major language of Xiongnu groups38. Further migrations of East Asians westwards find a good linguistic correlate in the influence of Mongolian on Turkic and Iranian in the last millennium39. As such, the genomic history of the Eurasian steppes is the story of a gradual transition from Bronze Age pastoralists of West Eurasian ancestry towards mounted warriors of increased East Asian ancestry—a process that continued well into historical times.

This paper will need a careful reading – better in combination with Narasimhan et al. (2018), when their tables are corrected – , to assess the actual ‘Iranian’ nature of the peoples studied. Their wide and long-term dominion over the steppe could also potentially explain some early samples from Hajji Firuz with steppe ancestry.
fku

eurasian-steppe-samples
Principal component analyses. The principal components 1 and 2 were plotted for the ancient data analysed with the present-day data (no projection bias) using 502 individuals at 242,406 autosomal SNP positions. Dimension 1 explains 3% of the variance and represents a gradient stretching from Europe to East Asia. Dimension 2 explains 0.6% of the variance, and is a gradient mainly represented by ancient DNA starting from a ‘basal-rich’ cluster of Natufian hunter-gatherers and ending with EHGs. BA, Bronze Age; EMBA, Early-to-Middle Bronze Age; SHG, Scandinavian hunter-gatherers.

For the moment, at first sight, it seems that, in terms of Y-DNA lineages:

  • R1b-Z93 (especially Z2124 subclades) dominate the steppes in the studied periods.
  • R1b-P312 is found in Hallstatt ca. 810 BC, which is compatible with its role in the Celtic expansion.
  • R1b-U106 is found in a West Germanic chieftain in Poprad (Slovakia) ca. 400 AD, during the Migration Period, hence supporting once again the expansion of Germanic tribes especially with R1b-U106 lineages.
  • A new sample of N1c-L392 (L1025) lineage dated ca. 400 AD, now from Lithuania, points again to a quite late expansion of this lineage to the region, believed to have hosted Uralic speakers for more than 2,000 years before this.
  • A sample of haplogroup R1a-Z282 (Z92) dated ca. 1300 AD in the Golden Horde is probably not quite revealing, not even for the East Slavic expansion.
  • Also, interestingly, some R1b(xM269) lineages seem to be associated with Turkic expansions from the eastern steppe dated around 500 AD, which probably points to a wide Eurasian distribution of early R1b subclades in the Mesolithic.

NOTE. I have referenced not just the reported subclades from the paper, but also (and mainly) further Y-SNP calls studied by Open Genomes. See the spreadsheet here.

Interesting also to read in the supplementary materials the following, by Michaël Peyrot (emphasis mine):

1. Early Indo-Europeans on the steppe: Tocharians and Indo-Iranians

The Indo-European language family is spread over Eurasia and comprises such branches and languages as Greek, Latin, Germanic, Celtic, Sanskrit etc. The branches relevant for the Eurasian steppe are Indo-Aryan (= Indian) and Iranian, which together form the Indo-Iranian branch, and the extinct Tocharian branch. All Indo-European languages derive from a postulated protolanguage termed Proto-Indo-European. This language must have been spoken ca 4500–3500 BCE in the steppe of Eastern Europe21. The Tocharian languages were spoken in the Tarim Basin in present-day Northwest China, as shown by manuscripts from ca 500–1000 CE. The Indo-Aryan branch consists of Sanskrit and several languages of the Indian subcontinent, including Hindi. The Iranian branch is spread today from Kurdish in the west, through a.o. Persian and Pashto, to minority languages in western China, but was in the 2nd and 1st millennia BCE widespread also on the Eurasian steppe. Since despite their location Tocharian and Indo-Iranian show no closer relationship within Indo-European, the early Tocharians may have moved east before the Indo-Iranians. They are probably to be identified with the Afanasievo Culture of South Siberia (ca 2900 – 2500 BCE) and have possibly entered the Tarim Basin ca 2000 BCE103.

The Indo-Iranian branch is an extension of the Indo-European Yamnaya Culture (ca 3000–2400 BCE) towards the east. The rise of the Indo-Iranian language, of which no direct records exist, must be connected with the Abashevo / Sintashta Culture (ca 2100 – 1800 BCE) in the southern Urals and the subsequent rise and spread of Andronovo-related Culture (1700 – 1500 BCE). The most important linguistic evidence of the Indo-Iranian phase is formed by borrowings into Finno-Ugric languages104–106. Kuz’mina (2001) identifies the Finno-Ugrians with the Andronoid cultures in the pre-taiga zone east of the Urals107. Since some of the oldest words borrowed into Finno-Ugric are only found in Indo-Aryan, Indo-Aryan and Iranian apparently had already begun to diverge by the time of these contacts, and when both groups moved east, the Iranians followed the Indo-Aryans108. Being pushed by the expanding Iranians, the Indo-Aryans then moved south, one group surfacing in equestrian terminology of the Anatolian Mitanni kingdom, and the main group entering the Indian subcontinent from the northwest.

steppe-migrations-pastoralists
Summary map. Depictions of the five main migratory events associated with the genomic history of the steppe pastoralists from 3000 bc to the present. a, Depiction of Early Bronze Age migrations related to the expansion of Yamnaya and Afanasievo culture. b, Depiction of Late Bronze Age migrations related to the Sintashta and Andronovo horizons. c, Depiction of Iron Age migrations and sources of admixture. d, Depiction of Hun-period migrations and sources of admixture. e, Depiction of Medieval migrations across the steppes.

2. Andronovo Culture: Early Steppe Iranian

Initially, the Andronovo Culture may have encompassed speakers of Iranian as well as Indo-Aryan, but its large expansion over the Eurasian steppe is most probably to be interpreted as the spread of Iranians. Unfortunately, there is no direct linguistic evidence to prove to what extent the steppe was indeed Iranian speaking in the 2nd millennium BCE. An important piece of indirect evidence is formed by an archaic stratum of Iranian loanwords in Tocharian34,109. Since Tocharian was spoken beyond the eastern end of the steppe, this suggests that speakers of Iranian spread at least that far. In the west of the Tarim Basin the Iranian languages Khotanese and Tumshuqese were spoken. However, the Tocharian B word etswe ‘mule’, borrowed from Iranian *atswa- ‘horse’, cannot derive from these languages, since Khotanese has aśśa- ‘horse’ with śś instead of tsw. The archaic Iranian stratum in Tocharian is therefore rather to be connected with the presence of Andronovo people to the north and possibly to the east of the Tarim Basin from the middle of the 2nd millennium BCE onwards110.

Since Kristiansen and Allentoft sign the paper (and Peyrot is a colleague of Kroonen), it seems that they needed to expressly respond to the growing criticism about their recent Indo-European – Corded Ware Theory. That’s nice.

They are obviously trying to reject the Corded Ware – Uralic links that are on the rise lately among Uralicists, now that Comb Ware is not a suitable candidate for the expansion of the language family.

IECWT-proponents are apparently not prepared to let it go quietly, and instead of challenging the traditional Neolithic Uralic homeland in Eastern Europe with a recent paper on the subject, they selected an older one which partially fit, from Kuz’mina (2001), now shifting the Uralic homeland to the east of the Urals (when Kuz’mina asserts it was south of the Urals).

Different authors comment later in this same paper about East Uralic languages spreading quite late, so even their text is not consistent among collaborating authors.

Also interesting is the need to resort to the questionable argument of early Indo-Aryan loans – which may have evidently been Indo-Iranian instead, since there is no way to prove a difference between both stages in early Uralic borrowings from ca. 4,500-3,500 years ago…

EDIT (10/5/2018) The linguistic supplement of the Science paper deals with different Proto-Indo-Iranian stages in Uralic loans, so on the linguistic side at least this influence is clear to all involved.

A rejection of such proposals of a late, eastern homeland can be found in many recent writings of Finnic scholars; see e.g. my references to Parpola (2017), Kallio (2017), or Nordqvist (2018).

NOTE. I don’t mind repeating it again: Uralic is one possibility (the most likely one) for the substrate language that Corded Ware migrants spread, but it could have been e.g. another Middle PIE dialect, similar to Proto-Anatolian (after the expansion of Suvorovo-Novodanilovka chiefs). I expressly stated this in the Corded Ware substrate hypothesis, since the first edition. What was clear since 2015, and should be clear to anyone now, is that Corded Ware did not spread Late PIE languages to Europe, and that some east CWC groups only spread languages to Asia after admixing with East Yamna. If they did not spread Uralic, then it was a language or group of languages phonetically similar, which has not survived to this day.

Their description of Yamna migrations is already outdated after Olalde et al. & Mathieson et al. (2018), and Narasimhan et al. (2018), so they will need to update their model (yet again) for future papers. As I said before, Anthony seems to be one step behind the current genetic data, and the IECWT seems to be one step behind Anthony in their interpretations.

At least we won’t have the Yamna -> Corded Ware -> BBC nonsense anymore, and they expressly stated that LPIE is to be associated with Yamna, and in particular the “Indo-Iranian branch is an extension of the Indo-European Yamnaya Culture (ca 3000–2400 BCE) to the East” (which will evidently show an East Yamna / Poltavka society of R1b-L23 subclades), so that earlier Eneolithic cultures have to be excluded, and Balto-Slavic identification with East Europe is also out of the way.

Related:

Ancient nomadic tribes of the Mongolian steppe dominated by a single paternal lineage

The genome of an ancient Rouran individual reveals an important paternal lineage in the Donghu population, by Li et al. Am J Phys Anthropol (2018), 1–11.

Abstract (emphasis mine):

Objectives
Following the Xiongnu and Xianbei, the Rouran Khaganate (Rouran) was the third great nomadic tribe on the Mongolian Steppe. However, few human remains from this tribe are available for archaeologists and geneticists to study, as traces of the tombs of these nomadic people have rarely been found. In 2014, the IA‐M1 remains (TL1) at the Khermen Tal site from the Rouran period were found by a Sino‐Mongolian joint archaeological team in Mongolia, providing precious material for research into the genetic imprint of the Rouran.

Materials and methods
The mtDNA hypervariable sequence I (HVS‐I) and Y‐chromosome SNPs were analyzed, and capture of the paternal non‐recombining region of the Y chromosome (NRY) and whole‐genome shotgun sequencing of TL1 were performed. The materials from three sites representing the three ancient nationalities (Donghu, Xianbei, and Shiwei) were selected for comparison with the TL1 individual.

Results
The mitochondrial haplotype of the TL1 individual was D4b1a2a1. The Y‐chromosome haplotype was C2b1a1b/F3830 (ISOGG 2015), which was the same as that of the other two ancient male nomadic samples (ZHS5 and GG3) related to the Xianbei and Shiwei, which were also detected as F3889; this haplotype was reported to be downstream of F3830 by Wei et al. (2017).

Discussion
We conclude that F3889 downstream of F3830 is an important paternal lineage of the ancient Donghu nomads. The Donghu‐Xianbei branch is expected to have made an important paternal genetic contribution to Rouran. This component of gene flow ultimately entered the gene pool of modern Mongolic‐ and Manchu‐speaking populations.

mongol-f3830-tree
The ancient males (TL1, ZHS5, and GG3) was grouped under C2b1a1b1/F3880 on the Y-DNA haplogroup C lineage using BEAST

Excerpt:

These results suggested that TL1 likely presents a close paternal relationship to the Donghu people and may have even descended from a branch of the ancient Donghu-Xianbei people, based on the conclusion that haplogroup C2b1a/F3918 can be considered the paternal branch of the ancient Donghu people (Zhang et al., 2018). The Y-chromosome phylogenetic tree showed that TL1 shared a branch with modern Mongolian-Buryats, Hezhen, Xibo, Yugur, and Kazakh, suggesting that the TL1 individual from the Rouran period should also generally present close paternal genetic relationships with modern Mongolic- and Manchu-speaking peoples.

In general, the Rouran Khaganate originated from an alliance of the ancient Eurasian steppe nomads, which disintegrated and disappeared with the progress of history. This group was complex, and its origin cannot be explained based only on one individual. However, we can trace the genetic imprint of the Rouran people through genome analysis of the TL1 individual. On the basis of the comparison with other ancient nomadic people (Donghu, Xianbei, and Shiwei) and data on modern individuals from published articles (Lippold et al., 2014; Wei et al., 2017) (Supporting Information S5), we found that they all share the same haplotype implying shared paternal ancestry between the Donghu, Xianbei and Rouran populations. Furthermore, this gene flow (mainly haplogroup C2b1a/F3918) did not stop with the disappearance of the Rouran, and a portion was instead passed on in other groups, such as the ancient Shiwei people (later than Rouran), eventually reaching the gene pool of modern Mongolic- and Manchu-speaking populations (Mongolian-Buryats, Hezhen, Xibo, et al).

Interesting to see now confirmed with ancient DNA the proposal of a C3*-DYS448del cluster as the paternal lineage defining ancient Mongolian tribes, a theory based on ancient and modern samples – since it is found in low frequency in almost all Mongolic- and Turkic-speaking populations.

This is yet another proof of how prehistoric ethnolinguistic expansions are usually accompanied by haplogroup expansion and reduction in variability.

I wonder what other ancient chiefdom-type steppe-based nomadic groups were also dominated by a single paternal lineage

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