The Yamnaya Steppe Herders from Russia

Figure 1: Location and SNP coverage of samples included in this study.

We used this technology to study population transformations in Europe. We began by preparing 212 DNA libraries from 119 ancient samples in dedicated clean rooms, and testing these by light shotgun sequencing and mitochondrial genome capture (SI1, Online Table 1). We restricted to libraries with molecular signatures of authentic ancient DNA (elevated damage in the terminal nucleotide), negligible evidence of contamination based on mismatches to the mitochondrial consensus13, and, where available, a mitochondrial DNA haplogroup that matched previous results using PCR4,14,15 (SI2). For 123 libraries prepared in the presence of Uracil-DNA-glycosylase16 to reduce errors due to ancient DNA damage17, we performed 390k capture, carried out paired end sequencing, and mapped to the human genome. We restricted analysis to 95 libraries from 69 samples that had at least 0.06-fold average target coverage (average of 3.8-fold), and used majority rule to call an allele at each SNP covered at least once (Online Table 1). After combining our data (SI3) with 25 ancient samples from the literature — three Upper Paleolithic samples from Russia1,7,6, seven people of European hunter gatherer ancestry4,5,8,2, and fifteen European farmers2,8,4,3, — we had data from 94 ancient Europeans. Geographically, these came from Germany (n=41), Spain (n=10), Russia (n=14), Sweden (n=12), Hungary (n=15), Italy (n=1) and Luxembourg (n=1) (Extended Data Table 2). Following the central European chronology, these included 19 hunter-gatherers (>5,500 BCE), 28 Early Neolithic farmers (EN: ~6,000-4,000 BCE), 11 Middle Neolithic farmers (MN: ~4,000-3,000 BCE) including the Tyrolean Iceman3 , 9 Late Copper/Early Bronze Age individuals (Yamnaya: ~3,300-2,700 BCE), 15 Late Neolithic individuals (LN: ~2,500-2,200 BCE), 9 Early Bronze Age individuals (~2,200-1,500 BCE), two Late Bronze Age individuals (~1,200-1,100 BCE) and one Iron Age individual (~900 BCE). Two individuals were excluded from analyses as they were related to others from the same population. The average number of SNPs covered at least once was 212,375 and the minimum was 22,869 (Fig. 1).


Figure 2: Population transformations in Europe.

We determined that 34 of the 69 newly analyzed individuals were male and used 2,258 Y chromosome SNPs targets included in the capture to obtain high resolution Y chromosome haplogroup calls (SI4). Outside Russia, and before the Late Neolithic period, only a single R1b individual was found (early Neolithic Spain) in the combined literature (n=70). By contrast, haplogroups R1a and R1b were found in 60% of Late Neolithic/Bronze Age Europeans outside Russia (n=10), and in 100% of the samples from European Russia from all periods (7,500-2,700 BCE; n=9). R1a and R1b are the most common haplogroups in many European populations today18,19, and our results suggest that they spread into Europe from the East after 3,000 BCE. Two hunter-gatherers from Russia included in our study belonged to R1a (Karelia) and R1b (Samara), the earliest documented ancient samples of either haplogroup discovered to date. These two hunter-gatherers did not belong to the derived lineages M417 within R1a and M269 within R1b that are predominant in Europeans today18,19, but all 7 Yamnaya males did belong to the M269 subclade18 of haplogroup R1b.

Principal components analysis (PCA) of all ancient individuals along with 777 present-day West Eurasians4 (Fig. 2a, SI5) replicates the positioning of present-day Europeans between the Near East and European hunter-gatherers4,20, and the clustering of early farmers from across Europe with present day Sardinians3,4,27 , suggesting that farming expansions across the Mediterranean to Spain and via the Danubian route to Hungary and Germany descended from a common stock. By adding samples from later periods and additional locations, we also observe several new patterns. All samples from Russia have affinity to the ~24,000 year old MA16 , the type specimen for the Ancient North Eurasians (ANE) who contributed to both Europeans4 and Native Americans4,6,8 . The two hunter-gatherers from Russia (Karelia in the northwest of the country and Samara on the steppe near the Urals) form an “eastern European hunter-gatherer” (EHG) cluster at one end of a hunter-gatherer cline across Europe; people of hunter-gatherer ancestry from Luxembourg, Spain, and Hungary sit at the opposite “western European hunter-gatherer4” (WHG) end, while the hunter-gatherers from Sweden4,8 (SHG) are intermediate. Against this background of differentiated European hunter-gatherers and homogeneous early farmers, multiple events transpired in all parts of Europe included in our study. Middle Neolithic Europeans from Germany, Spain, Hungary, and Sweden from the period ~4,000-3,000 BCE are intermediate between the earlier farmers and the WHG, suggesting an increase of WHG ancestry throughout much of Europe. By contrast, in Russia, the later Yamnaya steppe herders of ~3,000 BCE plot between the EHG and the Near East / Caucasus, suggesting a decrease of EHG ancestry during the same time period. The Late Neolithic and Bronze Age samples from Germany and Hungary2 are distinct from the preceding Middle Neolithic and plot between them and the Yamnaya. This pattern is also seen in ADMIXTURE analysis (Fig. 2b, SI6), which implies that the Yamnaya have ancestry from populations related to the Caucasus and South Asia that is largely absent in 38 Early or Middle Neolithic farmers but present in all 25 Late Neolithic or Bronze Age individuals. This ancestry appears in Central Europe for the first time in our series with the Corded Ware around 2,500 BCE (SI6, Fig. 2b, Extended Data Fig. 1). The Corded Ware shared elements of material culture with steppe groups such as the Yamnaya although whether this reflects movements of people has been contentious21 . Our genetic data provide direct evidence of migration and suggest that it was relatively sudden. The Corded Ware are genetically closest to the Yamnaya ~2,600 kilometers away, as inferred both from PCA and ADMIXTURE (Fig. 2) and FST (0.011 ± 0.002) (Extended Data Table 3). If continuous gene flow from the east, rather than migration, had occurred, we would expect successive cultures in Europe to become increasingly differentiated from the Middle Neolithic, but instead, the Corded Ware are both the earliest and most strongly differentiated from the Middle Neolithic population.


Figure 3: Admixture proportions.

To distinguish whether a Yamnaya or an EHG source fits the data better, we added ancient samples as outgroups (SI9). Adding any Early or Middle Neolithic farmer results in EHGrelated genetic input into Late Neolithic populations being a poor fit to the data (SI9); thus, Late Neolithic populations have ancestry that cannot be explained by a mixture of EHG and Middle Neolithic. When using Yamnaya instead of EHG, however, we obtain a good fit (SI9, SI10). These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6). We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG. The estimate of Yamnaya related ancestry in the Corded Ware is consistent when using either present populations or ancient Europeans as outgroups (SI9, SI10), and is 73.1 ± 2.2% when both sets are combined (SI10). The best proxies for ANE ancestry in Europe4 were initially Native Americans12, 22, and then the Siberian MA16 , but both are geographically and temporally too remote for what appears to be a recent migration into Europe4 . We can now add three new pieces to the puzzle of how ANE ancestry was transmitted to Europe: first the EHG, then the Yamnaya formed by mixture between EHG and a Near Eastern related population, and then the Corded Ware who were formed by a mixture of the Yamnaya with Middle Neolithic Europeans. We caution that the sampled Yamnaya individuals from Samara might not be directly ancestral to Corded Ware individuals from Germany. It is possible that a more western Yamnaya population, or an earlier (pre-Yamnaya) steppe population may have migrated into central Europe, and future work may uncover more missing links in the chain of transmission of steppe ancestry.

By extending our model to a three way mixture of WHG, Early Neolithic and Yamnaya, we estimate that the ancestry of the Corded Ware was 79% Yamnaya-like, 4% WHG, and 17% Early Neolithic (Fig. 3). A small contribution of the first farmers is also consistent with uniparentally inherited DNA: e.g. mitochondrial DNA haplogroup N1a and Y chromosome haplogroup G2a, common in early central European farmers14,23, almost disappear during the Late Neolithic and Bronze Age, when they are largely replaced by Y haplogroups R1a and R1b (SI4) and mtDNA haplogroups I, T1, U2, U4, U5a, W, and subtypes of H14,23,24 (SI2).


Extended Data Figure 1: Outgroup f3 statistic f3(Dinka; X, Y), measuring the degree of shared drift among pairs of ancient individuals.

Our results support a view of European pre-history punctuated by two major migrations: first, the arrival of first farmers during the Early Neolithic from the Near East, and second of Yamnaya pastoralists during the Late Neolithic from the steppe (Extended Data Fig. 5). Our data further show that both migrations were followed by resurgences of the previous inhabitants: first, during the Middle Neolithic, when hunter-gatherer ancestry rose again after its Early Neolithic decline, and then between the Late Neolithic and the present, when farmer and hunter-gatherer ancestry rose after its Late Neolithic decline. This second resurgence must have started during the Late Neolithic/Bronze Age period itself, as the Bell Beaker and Unetice groups had reduced Yamnaya ancestry compared to the earlier Corded Ware, and comparable levels to that in some present-day Europeans (Fig. 3). Today, Yamnaya related ancestry is lower in southern Europe and higher in northern Europe. Further data are needed to determine whether the steppe ancestry arrived in southern Europe at the time of the Late Neolithic / Bronze Age, or is due to migrations in historical times from northern Europe25,26.

Our results provide new data relevant to debates on the origin and expansion of Indo-European languages in Europe (SI11). Although ancient DNA is silent on the question of the languages spoken by preliterate populations, it does carry evidence about processes of migration which are invoked by theories on Indo-European language dispersals. Such theories make predictions about movements of people to account for the spread of languages and material culture. The technology of ancient DNA makes it possible to reject or confirm the proposed migratory movements, as well as to identify new movements that were not previously known. The best argument for the “Anatolian hypothesis27” that Indo-European languages arrived in Europe from Anatolia ~8,500 years ago is that major language replacements are thought to require major migrations, and that after the Early Neolithic when farmers established themselves in Europe, the population base was likely to have been so large as to be impervious to subsequent turnover27,28. However, our study shows that a later major turnover did occur, and that steppe migrants replaced ~3/4 of the ancestry of central Europeans. An alternative theory is the “Steppe hypothesis”, which proposes that early Indo-European speakers were pastoralists of the grasslands north of the Black and Caspian Seas, and that their languages spread into Europe after the invention of wheeled vehicles9. Our results make a compelling case for the steppe as a source of at least some of the Indo-European languages in Europe by documenting a massive migration ~4,500 years ago associated with the Yamnaya and Corded Ware cultures, which are identified by proponents of the Steppe hypothesis as vectors for the spread of Indo-European languages into Europe. These results challenge the Anatolian hypothesis by showing that not all Indo-European languages in Europe can plausibly derive from the first farmer migrations thousands of years earlier (SI11). We caution that the location of the Proto-Indo-European9,27,29,30 homeland that also gave rise to the Indo-European languages of Asia, as well as the Indo-European languages of southeastern Europe, cannot be determined from the data reported here (SI11). Studying the mixture in the Yamnaya themselves, and understanding the genetic relationships among a broader set of ancient and present-day Indo-European speakers, may lead to new insight about the shared homeland.

Nature 522, 207–211 (11 June 2015)