The Yamnaya Steppe Herders from Russia

Genetic relationships between Srubnaya-Alakulskaya and other ancient populations
The Bronze Age in Eurasia was a dynamic period with several human groups participating in different migratory processes. As a result, there were extensive interactions between European Bronze Age populations (3). The Srubnaya-Alakulskaya individuals, originating from a site of cultural dualism in the forest steppe of the Trans-Volga region, were genetically similar to the previously published Srubnaya and Andronovo individuals from the Pontic-Kazakh steppe (3, 9) and to the European Bronze Age groups, including individuals of the Corded Ware, Unetice, and Bell Beaker complexes (Fig. 1C and fig. S5). Consistent with other Bronze Age populations, the Srubnaya-Alakulskaya individuals were positioned between the genetic variation of the European Mesolithic and the Near East Neolithic populations, being closer to the former and especially to the east European hunter-gatherers (Fig. 1C and figs. S6 and S8). These individuals had higher genetic affinity to Scythians compared to other Iron Age groups (fig. S9). To test whether our Bronze Age sample from a cultural mixing zone between the Srubnaya and the Alakulskaya complexes shared more genetic drift with previously published representatives of Srubnaya, we calculated f4 statistics of f4(Yoruba, SrubnayaX, SrubnayaY, BronzeX), where “BronzeX” refers to a Bronze Age Russian population. The test revealed that the Srubnaya-Alakulskaya population formed a clade together with Andronovo, Afanasievo, and Sintashta to the exclusion of the previously published data of other Srubnaya individuals (tables S7 and S8). Furthermore, to trace the plausible origin the Caucasus genetic component identified in Srubnaya-Alakulskaya individuals, we adopt the f4 statistics in the form of f4(Yoruba, Srubnaya-Alakulskaya, PopulationX, Yamnaya), where PopulationX was one of the Eurasian Bronze Age populations. The results showed that Srubnaya-Alakulskaya formed a clade together with Yamnaya to the exclusion of other Bronze Age populations from Russia, Armenia, Jordan, and Hungary. This finding indicates that the Caucasus genetic contribution to the Srubnaya-Alakulskaya individuals was mediated by steppe ancestry instead of originating from the Levant (table S9). Both mean f3 statistics within populations and conditional nucleotide diversity (21) revealed that the genetic diversity was highest in the LBA Srubnaya-Alakulskaya population from the southern Ural region compared to all other Eurasian Bronze Age populations (Fig. 2, A and B, and table S10).



Fig. 2 Genetic diversity and ancestral components of Srubnaya-Alakulskaya population. Diversity and ancestral components of Srubnaya-Alakulskaya population (here called “Srubnaya”): (A) Mean f3 statistics for Srubnaya and other Bronze Age populations. Srubnaya group was color-coded the same as with PCA. (B) Pairwise mismatch estimates for Bronze Age populations. (C) ADMIXTURE results for K = 15. K = 15 was chosen to display since it shows SA component (lilac) and Northeast Asian (NEA, “dark green”) components in addition to the other components. BA, Bronze Age; EBA, Early Bronze Age; MBA, Middle Bronze Age; CA, Chalcolithic; N, Neolithic; EN, Early Neolithic; LN, Late Neolithic; HG, hunter-gatherers; SHG, Scandinavian hunter-gatherers (fig. S10).

To evaluate the ancestral components of Srubnaya-Alakulskaya, we conducted ADMIXTURE analysis for K = 2 to K = 15 ancestral clusters (fig. S10A). K = 15 clusters revealed that Srubnaya-Alakulskaya individuals consisted of two major ancestral components; first, an “orange” component predominantly found in west and NE hunter-gatherers (WHG) and in present-day NE populations, and second, a “light green” component typical of Caucasus hunter-gatherers (CHG) found in south Asian (SA) modern populations. The component associated with Neolithic groups and present-day Near Eastern populations (NEN, “dark red”) contributed less to our Srubnaya-Alakulskaya individuals compared to the European Bronze Age populations (Fig. 2C and fig. S10B).

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.

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.

Resources

www.science.org/doi/suppl/10.1126/sciadv.aat4457/suppl_file/aat4457_sm.pdf

www.science.org/doi/suppl/10.1126/sciadv.aat4457/suppl_file/aat4457_tabless1_to_s18.zip