The Yamnaya Steppe Herders from Russia

Genetic relationships between the Iron Age nomads and other ancient populations
In the 10th century BCE, during the transition from the Bronze Age to the Iron Age, the Cimmerians appear in the Pontic-Caspian steppe. In the PCA, the chronologically youngest Cimmerian individual (cim357) grouped within the SC including all Sarmatians, one Srubnaya-Alakulskaya individual, and three Scythian individuals. The other Cimmerian individuals were positioned in close proximity to a number of eastern Iron Age individuals from the Altai region (3), as well as Aldy-Bel and Zevakino-Chillikta individuals of the Altai and Western Mongolia regions (Fig. 1C and fig. S9) (12). We tested whether Cimmerians formed a clade with the subsequent Iron Age populations including Scythians and Sarmatians, to the exclusion of Bronze Age populations by calculating f4 statistics in the form of f4(Yoruba, Cimmerians; Srubnaya&Scythians&Sarmatians, BronzeAgePopulation), showing that the Cimmerians shared more drift with the Bronze Age populations of Russia compared to the Srubnaya/-Alakulskaya but not compared to Scythians or Sarmatians (Fig. 3A and tables S11, S12, and S16). The Cimmerians shared more drift with the far eastern Karasuk population compared to the geographically more closely located Srubnaya/-Alakulskaya population (table S16), corroborating the existence of the “Karasuk-Cimmerian cultural-historical community” (22). Pairwise mismatch estimates revealed a slightly higher genetic diversity in Cimmerians compared to that of the Srubnaya-Alakulskaya population (table S10). ADMIXTURE analysis (K = 15) revealed that Cimmerian individuals carried predominantly the WHG and CHG components similar to the Srubnaya individuals, but they also carried other ancestral components including NEN (dark red), Northeast Asian (NEA) (“dark green”), and Southeast Asian (SEA, “light blue”) components. From the oldest to the most recent sample, the amount of NEN component increased, while the NEA and SEA components decreased through time in the Cimmerians (Fig. 3D and fig. S10). The admixture results were further tested with f3 statistics, which were consistent with the observed pattern by means of shared genetic drift between the Cimmerians and the tested populations used as proxies for different genetic components identified in admixture analyses (table S13). These results implicate a more eastern origin of the Cimmerians compared to that of the Srubnaya-Alakulskaya population and an increased amount of NEN-originated admixture in these individuals through time.


Fig. 3
Genetic relationship between Srubnaya-Alakulskaya population and Iron Age nomads.
Visual summary of f4 statistics of a form f4(YRI, TestPop, Pop X, Srubnaya), where TestPop is (A) Cimmerian; (B) Scythian and (C) Sarmatian. (D) Admixture selection: Our ancient individuals and Iron Age individuals from closely related populations (K = 15). K = 15 was chosen to display since it shows SA (lilac) and NEA (dark green) components in addition to the other components. Srubnaya-Alakulskaya population is named as Srubnaya in the panels. IA, Iron Age (fig. S10).

In the seventh century BCE, the Scythians appeared in the North Pontic region. Iron Age western Scythians displayed slightly higher intragroup diversity compared to that of the Bronze Age groups and formed four discrete clusters including NE, SE, SC, and CC clusters (Fig. 1C and table S10). Scythians belonging to the SE cluster were closer to Hungarian Bronze Age and Iron Age individuals including Vatya and Maros. The NE Scythian cluster fell close to the Iron Age individuals from modern-day Montenegro and Sweden (fig. S9). The SC Scythians further grouped with Early Sarmatians (12) and the Iron Age Scythian from modern-day Hungary (23). It has been hypothesized by Terenozhkin that Scythians reached the Pontic-Caspian steppe region from Central Asia (for example, from Andronovo) (7). To formally test this hypothesis, we calculated f4 statistics in the form of f4(Yoruba, Scythian, Srubnaya, BronzeAgeX), where “BronzeAgeX” refers to either Andronovo, Sintashta, or Afanasievo. This analysis revealed that the western Scythians (tested either as a single population or four different clusters) formed a clade together with Andronovo and two other Andronovo-originated populations to the exclusion of Srubnaya-Alakulskaya from the southern Urals (Fig. 3B and table S14), supporting the Central Asian origin of the western Scythians. Furthermore, the western Scythians shared more drift with Andronovo, Afanasievo, Sintashta, and Mezhovskaya to the exclusion of Yamnaya (table S15). While the eastern Scythians from an earlier study (12) formed a clade together with Srubnaya-Alakulskaya to the exclusion of Yamnaya, the western Scythians of the present study did not show this pattern. Only when compared with Karasuk and Okunevo, Yamnaya seemed closer (although scy332 is an exception), which is in line with a shared steppe origin of the Yamanya and the western nomads (table S15). ADMIXTURE analysis at K = 15 revealed that the Scythians belonging to the NE cluster had a more visible West Eurasian component that is highest in the northern populations, while Scythians that belong to the SE cluster had a more visible NEN genetic component, most commonly found in Neolithic Anatolian individuals. The NEN component was also found in individuals falling into the CC, who additionally carried an SA component (“lilac”) shared with the Cimmerians, Sarmatians, and two more Scythian individuals (scy193 and scy006). Scy332 had a SEA (“light blue”) component and was most similar to the Karasuk individuals (Fig. 3 and fig. S10, A and B).

The five Sarmatians grouped close together in the SC (Fig. 1C), but they also had the highest pairwise mismatch estimates compared to other Iron Age nomads, suggesting a larger effective population size (table S10). F4(Yoruba, Sarmatians, PopulationX, Cimmerian), where the PopulationX is Yamnaya, Srubnaya, or Karasuk, revealed that Sarmatians formed a clade together with all these three populations to the exclusion of Cimmerians (table S18). Multiway f4 statistics testing the relationships between Srubnaya/-Alakulskaya, Cimmerians, and Scythians revealed that both Scythians and Cimmerians formed a clade together with Srubnaya/-Alakulskaya to the exclusion of the other population and that Srubnaya/-Alakulskaya was closer to Scythians among the two (Fig. 3C and table S17). The results point to the presence of a deep shared ancestry of all Iron Age nomadic groups associated with Bronze Age populations of the steppe, which, however, is not equivalent with a direct genetic continuity between Srubnaya-Alakulskaya and the western Scythians.



DISCUSSION
The origins of the four steppe populations
The Bronze Age Srubnaya-Alakulskaya individuals from Kazburun 1/Muradym 8 presented genetic similarities to the previously published Srubnaya individuals. However, in f4 statistics, they shared more drift with representatives of the Andronovo and Afanasievo populations compared to the published Srubnaya individuals. Those apparently West Eurasian people lacked significant Siberian components (NEA and SEA) in ADMIXTURE analyses but carried traces of the SA component that could represent an earlier connection to ancient Bactria. The presence of an SA component (as well as finding of metals imported from Tien Shan Mountains in Muradym 8) could therefore reflect a connection to the complex networks of the nomadic transmigration patterns characteristic of seasonal steppe population movements [see (2), figure 6.1, p. 205]. These movements, although dictated by the needs of the nomads and their animals, shaped the economic and social networks linking the outskirts of the steppe and facilitated the flow of goods between settled, semi-nomadic, and nomadic peoples. In contrast, all Cimmerians carried the Siberian genetic component. Both the PCA and f4 statistics supported their closer affinities to the Bronze Age western Siberian populations (including Karasuk) than to Srubnaya. It is noteworthy that the oldest of the Cimmerians studied here (cim357) carried almost equal proportions of Asian and West Eurasian components, resembling the Pazyryks, Aldy-Bel, and Iron Age individuals from Russia and Kazakhstan (12). The second oldest Cimmerian (cim358) was also the only one with both uniparental markers pointing toward East Asia. The Q1* Y chromosome sublineage of Q-M242 is widespread among Asians and Native Americans and is thought to have originated in the Altai Mountains (24). It has previously been identified in numerous ancient samples from Siberia, the Americas, and in representatives of the Siberian Bronze Age and nomadic populations (4, 24). This is the first indication that Cimmerians did not originate in the PCS region but were nomads tracing their origin to the Far East.

The origins of Scythians of the western Pontic-Caspian steppe are difficult to resolve. We identified four different clusters within our geographically continuous sample set, which likely represent a varying gradient of different genetic components: the Northern cluster, SC, CC, and SE cluster. The latter was characterized by the presence of the NEN component representing local semi-nomadic Scythians with clear genetic uptake from the locals and possibly from other settlers such as the Greeks around the Black Sea region. Finally, the Sarmatians fell between all other nomads that form the bulk of the SC, suggesting that southern Urals is where the continuity of western nomads was sustained.

Intragroup genetic diversity of the steppe populations
The diversity of Srubnaya-Alakulskaya individuals was on par with that of Sarmatians and Scythians (table S10) and was also the highest among all published Bronze Age individuals. The Muradym 8/Kazburun 1 site is a unique cultural mixing zone with an unusual number of culturally distinct burials of two different traditions (Srubnaya-Alakulskaya), but the individuals are genetically uniform across the time span of the sites, suggesting that diffusion may have been the main mode of cultural dispersal in the LBA.

Cimmerians resemble individuals within the SC and had higher diversity compared to that of the Srubnaya-Alakulskaya individuals. Despite clustering tightly on the PCA plot, the Cimmerians and Sarmatians had the highest pairwise mismatch estimates among the nomads studied (Fig. 1C and table S10). Although the Scythians showed high variation based on the PCA, their intragroup genetic diversity was comparatively lower than that of the Cimmerians and Sarmatians. This observation is best explained by a smaller ancestral Scythian population base in western Pontic-Caspian steppe than in Sarmatians of the southern Urals. When compared with published Early Sarmatians from the same region (12), the Sarmatians studied here seem to have remained genetically uniform through an approximately 300- to 500-year time span. This might suggest the genetic continuity of Sarmatians in the southern Urals despite a distinct cultural shift and a suspected earlier population replacement between Early and Middle/Late Sarmatians in the region. Thus, the observed high genetic diversity in the Sarmatians could result from a large effective population size rather than gene flow into the region.



Mutual relations and shared ancestry between steppe populations
Our results suggest that the Cimmerians were largely similar to the more eastern Sarmatians (cim357) albeit with an increased amount of a Siberian (NEA) component (cim358 and cim359), thus representing a genetic link between the Iron Age people of the Kazakh steppe region. Similar to the cis-Uralic Srubnaya-Alakulskaya, Cimmerians were not direct ancestors of the Scythians in the Pontic-Caspian steppe; however, all those populations shared a common ancestral gene pool.

Scythians who were thought to have displaced the Cimmerians from the Pontic-Caspian steppe region differed from both Cimmerians and the later Sarmatians. However, it is unclear whether the observed pattern resulted from replacement, since the genetic composition of Cimmerians may have undergone a temporal change, as witnessed by the observed temporal reduction of the NEA and the SEA components in more recent individuals. It has previously been noted that Scythians were not uniform across Eurasia, exhibiting distinct differences between Eastern/Western Eurasian groups (12). In contrast to the eastern steppe Scythians (Pazyryks and Aldy-Bel) that were closely related to Yamnaya, the western North Pontic Scythians were instead more closely related to individuals from Afanasievo and Andronovo groups. Some of the Scythians of the western Pontic-Caspian steppe lacked the SA and the East Eurasian components altogether and instead were more similar to a Montenegro Iron Age individual (3), possibly indicating assimilation of the earlier local groups by the Scythians. Finally, one individual from Nesterivka (scy011), which was the most recent of the Scythians, and possibly representing a transition between different groups, carried a distinct resemblance to the later steppe Sarmatians, corroborating the idea of a more “stable”/”common” steppe signature shared with all Sarmatians or reflecting physical/social connection to the southern Ural steppe zone maintained within the western nomadic world. Toward the end of the Scythian period (fourth century CE), a possible direct influx from the southern Ural steppe zone took place, as indicated by scy332. However, it is possible that this individual might have originated in a different nomadic group despite being found in a Scythian cultural context. This individual instead resembles, genetically, the early eastern Altai Scythians, albeit with even higher contribution of the NEA and the SEA genetic components. This result suggests the presence of a continuous connection between the Western fringes of the Scythian empire and central parts of Eurasia or maybe even the source region in the Altai Mountains. Such a connection could reflect communication associated with population exchange and internal high mobility among the Scythians.

In conclusion, our genomic analyses revealed that both the Bronze Age and Iron Age were highly dynamic periods in the Pontic-Caspian steppe. The time span between 1800 BCE and 400 CE was characterized by mobility, population movements, and replacements, which shaped the complex demography of the region through time. Our results showed that the Western Eurasian steppe nomads were not direct descendants of the Bronze Age Srubnaya-Alakulskaya individuals but shared elements of common ancestry with contribution from different peoples. The early nomads could thus be referred to as a “cultural and chronological horizon” represented by various cultures of the Scythian-Siberian world that was not composed of a genetically homogeneous and/or isolated group. Quite the contrary is observed. We observe little evidence of mobility from the Far East, suggesting that the main source of most Western nomads is likely found in eastern Pontic-Caspian steppe and southern Urals. Thus, we propose that the region, similar to the so-called Mongolian steppe generator of peoples during the Middle Ages, served as the generator of the west nomadic peoples that sustained the western nomadic horizon in the Iron Age.

Science Advances 03 Oct 2018:
Vol. 4, no. 10, eaat4457

Abstract
Hun, Avar and conquering Hungarian nomadic groups arrived to the Carpathian Basin from the Eurasian Steppes and significantly influenced its political and ethnical landscape, however their origin remains largely unknown. In order to shed light on the genetic affinity of above groups we have determined Y chromosomal haplogroups and autosomal loci, suitable to predict biogeographic ancestry, from 49 individuals, supposed to represent the power/military elit. Haplogroups from the Hun-age are consistent with Xiongnu ancestry of European Huns. Most of the Avar-age individuals carry east Eurasian Y haplogroups typical for modern north-eastern Siberian and Buryat populations and their autosomal loci indicate mostly un-admixed Asian characteristics. In contrast the conquering Hungarians seem to be a recently assembled population incorporating un-admixed European, Asian as well as admixed components. Their heterogeneous paternal and maternal lineages indicate similar supposed phylogeographic origin of males and females, derived from Central-Inner Asian and European Pontic Steppe sources.



Population history of the Carpathian Basin was profoundly determined by the invasion of various nomadic groups from the Eurasian Steppes during the Middle Ages. Between 400–453 AD the Huns held possession of the region and brought about a major population reshuffling all over Europe. Recent genetic data connect European Huns to Inner Asian Xiongnus1, but genetic data from Huns of the Carpathian Basin have not been available yet, since Huns left just sporadic lonely graves in the region, as they stayed for short period. We report three Y haplogroups (Hg) from Hun age remains, which possibly belonged to Huns based on their archaeological and anthropological evaluation.

From 568 AD the Avars established an empire in the region lasting nearly for 250 years, until they were defeated by the Franks and Bulgars in 803, then their steppe-empire ended around 822 AD. In its early stage the Avar Khaganate controlled a large territory expanding from the Carpathian Basin to the Pontic-Caspian Steppes and dominated numerous folks including Onogur-Bulgars, which fought their independence in the middle 7th century and established the independent Magna Bulgaria state. Then the Avar Khaganate was shrunken, its range well corresponding to that of the succeeding Hungarian Kingdom. The Avars arrived in multiple waves into the Carpathian Basin and the Avar period left a vast archeological legacy with more than 80 thousand excavated graves in present-day Hungary. The Avar age remains are anthropologically extremely heterogeneous, with considerable proportion of Mongoloid and Europo-Monoloid elements reaching 20–30% on the Great Hungarian Plain2, attesting that the Carpathian Basin witnessed the largest invasion of people from Asia during this period. Most individuals buried with rich grave goods show Mongoloid characters indicating inner Asian origin of the Avar elite, which is also supported by their artifact types, titles (e.g. khagan) and institutions recognized to be derived from Inner Asian Rourans. From the Avar period only a few mitochondrial DNA (mtDNA) data are available from two micro-regions3,4, which showed 15.3% and 6.52% frequency of East Eurasian elements. A recent manuscript described 23 mitogenomes from the 7th-8th century Avar elite group5 and found that 64% of the lineages belong to East Asian haplogroups (C, D, F, M, R, Y and Z) with affinities to ancient and modern Inner Asian populations corroborating their Rouran origin. Though the Avar Khaganate ceased to exist around 822 AD, but its population survived and were incorporated into the succeeding Hungarian state6. It is relevant to note that none of the Hungarian medieval sources know about Avars7, probably because they were not distinguished from the Huns as many foreign medieval sources also identified Avars with Huns, for example the Avars who were Christianized and became tax-payer vassals of the Eastern Frankish Empire were called as Huns in 8718.



Presence of the Hungarians in the Carpathian Basin was documented from 862 AD and between 895–905 they took full command of the region. The Hungarians formed a tribal union but arrived in the frame of a strong centralized steppe-empire under the leadership of prince Álmos and his son Árpád, who were known to be direct descendants of the great Hun leader Attila, and became founders of the Hungarian ruling dynasty and the Hungarian state. The Hungarian Great Principality existed in Central Europe from ca. 862 until 1000, then it was re-organized as a Christian Kingdom by King István I the Saint who was the 5th descendant of Álmos9.

Our recent analysis of conquering Hungarian (hence shortened as Conqueror) mitogenomes revealed that the origin of their maternal lineages can be traced back to distant parts of the Eurasian steppe10. One third of the maternal lineages were derived from Central-Inner Asia and their most probable ultimate sources were the Asian Scythians and Asian Huns, while the majority of the lineages most likely originated from the Bronze Age Potapovka-Poltavka-Srubnaya cultures of the Pontic-Caspian steppe. Population genetic analysis indicated that Conquerors had closest connection to the Onogur-Bulgar ancestors of Volga Tatars.


Figure 1

Although mtDNA data can be informative, since as far as we know none of the above nomadic invasions were pure military expeditions in which raiding males took local women, but entire societies with both men and women migrated together3, however nomadic societies were patrilinealy organized, thus Y-chromosome data are expected to provide more relevant information about their structure and origin than mtDNA. So far 6 Y-chromosome Hg-s have been published from the Conquerors11; which revealed the presence of N1a1- M46 (previously called Tat or N1c), in two out of 4 men, while12 detected two R1b-U106 and two I2a-M170 Hg-s.

In order to generate sufficient data for statistical evaluation and compare paternal and maternal lineages of the same population, we have determined Y-Hg-s from the same cemeteries whose mtDNA Hg-s were described in10. As most Hungarian medieval chronicles describe the conquer as the “second incoming of the Hungarians”7, genetic relations may exist between consecutive nomadic groups, first of all between elite groups.

As the studied Conqueror cemeteries represent mainly the Conqueror elite, we supplemented our Y-Hg studies with samples from the preceding Avar power elite/millitary elite groups and available samples from the Hun period to test possible genetic relations. Avar military leader graves are distinguished by high-value prestige artifacts: belt decorated with gold or silver mounts, decorated horse harness, saddle, sword, bow and quiver with arrowheads, gold decorated plates, silver or gold earrings (Supplementary Information). Conqueror leader graves contain characteristic partial horse burial with horse cranium and leg bones or symbolic horse burial with adorned harness, saddle and stirrup. Elite grave goods often include precious metal jewels, belt with impressed metal belt-buckles, metal-plated sabretache and weaponry; arrowheads, quiver and bow10,12.
ry.