The Yamnaya Steppe Herders from Russia

The vast grasslands making up the Eurasian steppe zones, from Ukraine through Kazakhstan to Mongolia, have served as a crossroad for human population movements during the last 5000 years (1–3), but the dynamics of its human occupation—especially of the earliest period—remain poorly understood. The domestication of the horse at the transition from the Copper Age to the Bronze Age, ~3000 BCE, enhanced human mobility (4, 5) and may have triggered waves of migration. According to the “steppe hypothesis,” this expansion of groups in the western steppe related to the Yamnaya and Afanasievo cultures was associated with the spread of Indo-European (IE) languages into Europe and Asia (1, 2, 4, 6). The peoples who formed the Yamnaya and Afanasievo cultures belonged to the same genetically homogeneous population, with direct ancestry attributed to both Copper Age (CA) western steppe pastoralists, descending primarily from the European Eastern hunter-gatherers (EHG) of the Mesolithic and to Caucasian groups (1, 2) related to Caucasus hunter-gatherers (CHG) (7).

Within Europe, the steppe hypothesis is supported by the reconstruction of Proto-IE (PIE) vocabulary (8), as well as by archaeological and genomic evidence of human mobility and Early Bronze Age (3000 to 2500 BCE) cultural dynamics (9). For Asia, however, several conflicting interpretations have long been debated. These concern the origins and genetic composition of the local Asian populations encountered by the Yamnaya- and Afanasievo-related populations, including the groups associated with Botai, a site that offers the earliest evidence for horse husbandry (10). In contrast, the more western sites that have been supposed by some to reflect the use of horses in the Copper Age (4) lack direct evidence of domesticated horses. Even the later use of horses among Yamnaya pastoralists has been questioned by some (11) despite the key role of horses in the steppe hypothesis. Furthermore, genetic, archaeological, and linguistic hypotheses diverge on the timing and processes by which steppe genetic ancestry and the IE languages spread into South Asia (4, 6, 12). Similarly, in present-day Turkey, the emergence of the Anatolian IE language branch, including the Hittite language, remains enigmatic, with conflicting hypotheses about population migrations leading to its emergence in Anatolia (4, 13).

Ancient genomes inform upon human movements within Asia
We analyzed whole-genome sequence data of 74 ancient humans (14, 15) (tables S1 to S3) ranging from the Mesolithic (~9000 BCE) to Medieval times, spanning ~5000 km across Eastern Europe, Central Asia, and Western Asia (Anatolia) (Fig. 1). Our genome data includes 3 Copper Age individuals (~3500 to 3300 BCE) from Botai in northern Kazakhstan (Botai_CA; 13.6X, 3.7X, and 3X coverage, respectively); 1 Early Bronze Age (~2900 BCE) Yamnaya sample from Karagash, Kazakhstan (16) (YamnayaKaragash_EBA; 25.2X); 1 Mesolithic (~9000 BCE) EHG from Sidelkino, Russia (SidelkinoEHG_ML; 2.9X); 2 Early/Middle Bronze Age (~2200 BCE) central steppe individuals (~4200 BP) (CentralSteppe_EMBA; 4.5X and 9.1X average coverage, respectively) from burials at Sholpan and Gregorievka that display cultural similarities to Yamnaya and Afanasievo (12); 19 individuals of the Bronze Age (~2500 to 2000 BCE) Okunevo culture of the Minusinsk Basin in the Altai region (Okunevo_EMBA; ~1X average coverage; 0.1 to 4.6X); 31 Baikal hunter-gatherer genomes (~1X average coverage; 0.2 to 4.5X) from the cis-Baikal region bordering on Mongolia and ranging in time from the Early Neolithic (~5200 to 4200 BCE; Baikal_EN) to the Early Bronze Age (~2200 to 1800 BCE; Baikal_EBA); 4 Copper Age individuals (~3300 to 3200 BCE; Namazga_CA; ~1X average coverage; 0.1 to 2.2X) from Kara-Depe and Geoksur in the Kopet Dag piedmont strip of Turkmenistan, affiliated with the period III cultural layers at Namazga-Depe (fig. S1), plus 1 Iron Age individual (Turkmenistan_IA; 2.5X) from Takhirbai in the same area dated to ~800 BCE; and 12 individuals from Central Turkey (figs. S2 to S4), spanning from the Early Bronze Age (~2200 BCE; Anatolia_EBA) to the Iron Age (~600 BCE; Anatolia_IA), and including 5 individuals from presumed Hittite-speaking settlements (~1600 BCE; Anatolia_MLBA), and 2 individuals dated to the Ottoman Empire (1500 CE; Anatolia_Ottoman; 0.3 to 0.9X). All the population labels including those referring to previously published ancient samples are listed in table S4 for contextualization. Additionally, we sequenced 41 high-coverage (30X) present-day Central Asian genomes, representing 17 self-declared ethnicities (fig. S5), and collected and genotyped 140 individuals from five IE-speaking populations in northern Pakistan.


Fig. 1 Geographic location and dates of ancient samples.
(A) Location of the 74 samples from the steppe, Lake Baikal region, Turkmenistan, and Anatolia analyzed in the present study. MA1, KK1, and Xiongnu_IA were previously published. Geographical background colors indicate the western steppe (pink), central steppe (orange) and eastern steppe (gray). (B) Timeline in years before present (BP) for each sample. ML, Mesolithic; EHG, Eastern hunter-gatherer; EN, Early Neolithic; LN, Late Neolithic; CA, Copper Age; EBA, Early Bronze Age; EMBA, Early/Middle Bronze Age; MLBA, Middle/Late Bronze Age; IA, Iron Age.

Tests indicated that the contamination proportion of the data was negligible (14) (see table S1), and we removed related individuals from frequency-based statistics (fig. S6 and table S5). Our high-coverage Yamnaya genome from Karagash is consistent with previously published Yamnaya and Afanasievo genomes, and our Sidelkino genome is consistent with previously published EHG genomes, on the basis that there is no statistically significant deviation from 0 of D statistics of the form D(Test, Mbuti; SidelkinoEHG_ML, EHG) (fig. S7) or of the form D(Test, Mbuti; YamnayaKaragash_EBA, Yamnaya) (fig. S8; additional D statistics shown in figs. S9 to S12).

Genetic origins of local Inner Asian populations
In the Early Bronze Age, ~3000 BCE, the Afanasievo culture was formed in the Altai region by people related to the Yamnaya, who migrated 3000 km across the central steppe from the western steppe (1) and are often identified as the ancestors of the IE-speaking Tocharians of first-millennium northwestern China (4, 6). At this time, the region they passed through was populated by horse hunter-herders (4, 10, 17), while further east the Baikal region hosted groups that had remained hunter-gatherers since the Paleolithic (18–22). Subsequently, the Okunevo culture replaced the Afanasievo culture. The genetic origins and relationships of these peoples have been largely unknown (23, 24).

To address these issues, we characterized the genomic ancestry of the local Inner Asian populations around the time of the Yamnaya and Afanasievo expansion. Comparing our ancient samples to a range of present-day and ancient samples with principal components analysis (PCA), we find that the Botai_CA, CentralSteppe_EMBA, Okunevo_EMBA, and Baikal populations (Baikal_EN and Baikal_EBA) are distributed along a previously undescribed genetic cline. This cline extends from the EHG of the western steppe to the Bronze Age (~2000 to 1800 BCE) and Neolithic (~5200 to 4200 BCE) hunter-gatherers of Lake Baikal in Central Asia, which are located on the PCA plot close to modern East Asians and two Early Neolithic (~5700 BCE) Devil’s Gate samples (25) (Fig. 2 and fig. S13). In accordance with their position along the west-to-east gradient in the PCA, increased East Asian ancestry is evident in ADMIXTURE model-based clustering (Fig. 3 and figs. S14 and S15) and by D statistics for Sholpan and Gregorievka (CentralSteppe_EMBA) and Okunevo_EMBA, relative to Botai_CA and the Baikal_EN sample: D(Baikal_EN, Mbuti; Botai_CA, Okunevo_EMBA) = –0.025 Z = –12; D(Baikal_EN, Mbuti; Botai_CA, Sholpan) = –0.028 Z = –8.34; D(Baikal_EN, Mbuti; Botai_CA, Gregorievka) = –0.026 Z = –7.1. The position of this cline suggests that the central steppe Bronze Age populations all form a continuation of the Ancient North Eurasian (ANE) population, previously known from the 24,000-year-old Mal’ta (MA1), the 17,000-year-old AG-2 (26), and the ~14,700-year-old AG-3 (27) individuals from Siberia.


Fig. 2 Principal component analyses using ancient and present-day genetic data.
(A) PCA of ancient and modern Eurasian populations. The ancient steppe ancestry cline from EHG to Baikal_EN is visible at the top outside present-day variation, whereas the YamnayaKaragash_EBA sample has additional CHG ancestry and locates to the left with other Yamnaya and Afanasievo samples. Additionally, a shift in ancestry is observed between the Baikal_EN and Baikal_LNBA, consistent with an increase in ANE-related ancestry in Baikal_LNBA. (B) PCA estimated with a subset of Eurasian ancient individuals from the steppe, Iran, and Anatolia as well as present-day South Asian populations. PC1 and PC2 broadly reflect west-east and north-south geography, respectively. Multiple clines of different ancestry are seen in the South Asians, with a prominent cline even within Dravidians in the direction of the Namazga_CA group, which is positioned above Iranian Neolithic in the direction of EHG. In the later Turkmenistan_IA sample, this shift is more pronounced and toward Steppe EBA and MLBA. The Anatolia_CA, EBA, and MLBA samples are all between Anatolia Neolithic and CHG, not in the direction of steppe samples.