The Yamnaya Steppe Herders from Russia

In the figure above, the numbers correspond to the following crops: Munkh Khairkan and Sagsai at the end of the Bronze Age. During this period, the domestication of the horse as well as the use of the tanks, allowing to be more mobile, will participate in the development and the diffusion of these cultures along the Eurasian steppes. She analyzed the DNA of 69 samples from different Bronze Age sites in the Altai region: In the figure above, the numbers correspond to the following crops: Will participate in the development and spread of these crops along the Eurasian steppes.

Afanasievo (3500 to 2600 BC) and Okunevo (2300 to 1800 BC)
Elunino (2300 to 1700 BC)
Bol'shemysskaya (4th millennium BC) and Afanasievo (3500-2600 BC).
Chemurchek (2500 to 2300 BC)
Sagsai (1400 to 1100 BC)
Sagsai (1400 to 900 BC) and Afanasievo (2740 BC).
Chemurchek (2300 to 1800 BC)
Munkh-Khairkhan (1700-1400 BC)
Munkh-Khairkhan (1700-1400 BC)
Chemurchek (24300 to 20800 BC)
Baitag (1200 to 900 BC)



Genetic analyses performed on these samples were sex determination, autosomal STRs, HVR1 mitochondrial region sequencing, mitochondrial coding region SNPs test to discriminate major haplogroups, 17 STRs assay of the chromosome Y, the 27 Y SNPs to discriminate the main haplogroups, and the assay of 28 autosomal SNPs to determine phenotypic characteristics: hair and eye color.

Regarding the oldest populations: Bol'shemysskaya and Afanasievo, the individuals belong to the haplogroup R1b of the Y chromosome, Except for one individual from Mongolia of the haplogroup Q. Among the R1b individuals, two were tested positive for M269. Moreover, analysis of the STR haplotypes indicates that these individuals R1b group with individuals R1b-L23. These results are similar to previous studies which showed that individuals of the Yamnaya population of the Pontic Steppes were also of the haplogroup R1b-L23. The mitochondrial haplogroups of the skeletons of these populations are half western: H and U, half oriental: C. Finally, the results of autosomal STR markers show that the Afanasievo individuals are of western origin, close to the present Europeans.



For the next phase, individuals in the Okunevo culture show an evolution of their haplogroups of the Y chromosome. If an individual inherits the Afanasievo population with a haplogroup R1b-M269, the other individuals are from the haplogroup Q or N thus indicating a north-eastern influence. Their mitochondrial haplogroups are shared between western lineages: H, J, T, U and eastern lineages: C, A, D. Similarly, individuals in the Chemurchek culture have Oriental Y chromosome haplogroups: C and mitochondrial haplogroups Both western and eastern. The results of autosomal STR markers show that Okunevo individuals are of mixed western and eastern origin.

At the end of the Bronze Age, the western haplogroup of the Y chromosome appears: R1a. It is associated with oriental haplogroups: Q, N and C. Mitochondrial haplogroups are also shared between western and eastern lineages. The results of autosomal STR markers show that these individuals are of mixed western and eastern origin. The figure below summarizes the origin of the populations tested for the three phases of the Bronze Age:

Figure 1
Geographic Location and Chronologies for Latvian and Ukrainian Sites

In Europe, the Neolithic transition marked the beginning of a period of innovations that saw communities shift from a mobile lifestyle, dependent on hunting and gathering for survival, to a more sedentary way of life based on food production. This new lifeway, which originated in the Near East ∼11,500 calibrated years before present (cal BP) [5, 6], had arrived in southeast Europe by ∼8,500 cal BP [7], from where it spread quickly across the continental interior of Europe and introduced animal husbandry, cultivated cereals, pottery, and ground stone tools to the region. There is a long-standing debate among archaeologists whether this spread was due to the dispersal of farmers into new lands (i.e., demic diffusion) or horizontal cultural transmission [8]. Genetic evidence suggests that these cultural and technological changes were accompanied by profound genomic transformation, consistent with the migration of people of most likely Anatolian origin [9, 10, 11, 12]. In contrast to central Europe, the adoption of agriculture in northern and eastern parts of this continent, in the areas which encompass modern-day Latvia and Ukraine, was slow and relatively recent [13, 14, 15, 16]. Although some features of the Neolithic package, such as ceramics, appeared as early as 8,500–7,500 cal BP [17, 18], agriculture was not adopted as a primary subsistence economy until the Late Neolithic/Bronze Age [13, 14, 15, 16, 19].

The Neolithic transition in the Baltic and Ukraine thus had a different tempo to that of central Europe, and it is unclear how this may have shaped the genetic composition of these regions. To investigate this, we sampled three Mesolithic and three Neolithic individuals from the archaeological site of Zvejnieki (Latvia), which is one of the richest Stone Age cemeteries in Northern Europe for number of inhumations, as well as duration of use [20, 21] (see the Supplemental Experimental Procedures for site details). We also sampled a Mesolithic and a Neolithic individual from cemeteries found along the Dnieper River in Ukraine (Vasilyevka 3 and Vovnigi 2, respectively). DNA was extracted from the petrous portion of the temporal bone (see the Experimental Procedures), which yielded between 4.30% and 55.99% endogenous DNA for all samples. Samples were shotgun sequenced using Illumina sequencing technology to between 0.22- and 4.37-fold coverage (Figure 1). The authenticity of the data was assessed in silico by examining the data for signatures of post-mortem DNA damage and evaluating the mitochondrial contamination rate in all samples along with the X chromosome contamination rate in males (see the Supplemental Experimental Procedures). All samples had degradation patterns typical of ancient DNA (Figure S1) and low contamination estimates of ∼1% or less (Table 1).


Figure 2
PCA and ADMIXTURE Analysis for Ancient Latvian and Ukrainian Samples

The two earliest samples in our Baltic time series, Latvia_HG1 (8,417–8,199 cal BP), associated with the Kunda culture, and Latvia_HG2 (7,791–7,586 cal BP), associated with the Narva culture, derive from the Late Mesolithic period [17, 21]. A third sample, Latvia_HG3 (7,252–6,802 cal BP), dates to the Late Mesolithic/Early Neolithic period, with the burial showing no major departures from the preceding Mesolithic traditions [21]. Principal component analysis (PCA) with ancient samples projected onto modern Eurasian genetic variation (see the Supplemental Experimental Procedures) shows that these three hunter-gatherer samples group together in a PCA plot (first two components, Figures 2A and S1A). In keeping with their geographical origins, they are in an intermediate position between Western European hunter-gatherer samples (WHG; from Luxembourg, Hungary, Italy, France, and Switzerland) and Eastern European hunter-gatherer samples (EHG; from Russia). They are composed of the same (blue) major component as these other hunter-gatherer groups in an ancestry coefficient decomposition analysis performed using ADMIXTURE [25] (Figure 2B), suggesting a close relationship between these groups. We found that although the Latvian Mesolithic samples share closer affinity to WHG than to EHG, the Latvian Mesolithic samples do not belong entirely to either hunter-gatherer group (tested using D statistics [27], which offer a formal test of admixture; Table 2). This suggests that they may be a previously unsampled component of a hunter-gatherer meta-population that stretched across Northern Europe during the early Holocene.

Next we sampled two Middle Neolithic individuals, Latvia_MN1 (6,201–5,926 cal BP), from an isolated grave located among burials from earlier periods, and Latvia_MN2 (6,179–5,750 cal BP), who was interred in a collective burial with five other individuals. During the Middle Neolithic at Zvejnieki, mortuary practices from the preceding periods were partially maintained, but some new features appeared, including collective burials and votive deposits, which are associated with the Comb Ware culture or its influences in the Baltic [21]. Despite having been roughly contemporaneous, these Middle Neolithic samples cluster in different regions of our PCA plot (Figure 2A) and have distinct profiles in ADMIXTURE analysis (Figure 2B). In both analyses, Latvia_MN1 groups with the Mesolithic Latvian samples, suggesting a degree of continuity across the Mesolithic-Neolithic transition in this region and consistent with suggestions that the eastern Baltic was a genetic refugium for hunter-gatherer populations during the Neolithic period [28]. The persistence of hunter-gatherer ancestry in the Baltic until at least the Middle Neolithic also provides a possible source for the resurgence of hunter-gatherer ancestry that is proposed to have occurred in central Europe from 7,000–5,000 cal BP [1]. In contrast, Latvia_MN2 is placed toward EHG in PCA space and has several components in ADMIXTURE analysis that are found in Native Americans, Siberians, and hunter-gatherer samples from the Caucasus. In keeping with these results, we found that there has been a northern Eurasian influence in the Baltic region since the Mesolithic period, as suggested by significantly positive statistics for the test D(Mbuti, X; Latvia Mesolithic, Latvia_MN2) when X was an EHG, modern and ancient Siberian (including the Upper Palaeolithic Mal’ta genome [29]), or Native American (Table 2). This influence is supported archaeologically by the appearance of copper rings and amber jewelry in Middle Neolithic collective burials that bear similarities to artifacts found in Estonia, Finland, and northwestern Russia [21, 30].



The latest Neolithic sample in our Baltic time series, Latvia_LN1 (5,039–4,626 cal BP), which was found in a crouched burial of the type associated with the Late Neolithic Corded Ware culture [21], falls near other Late Neolithic and Bronze Age European and Steppe samples in PCA analysis (Figure 2A). In ADMIXTURE analysis, it is composed of the blue component (Figure 2B), which is predominant in all of the older Latvian samples, but also a green component, which is maximized in hunter-gatherer samples from the Caucasus. A Caucasus-related influence in this sample is also suggested by positive results (although without formal significance, Z > 2) for tests of the form D(Mbuti, Caucasus hunter-gatherer; Latvian Mesolithic, Latvia_LN1). Ancestry related to hunter-gatherers from the Caucasus has previously been postulated to have arrived in Europe through herders from the Pontic Steppe [1, 31], and these migrations could potentially be the source of this ancestry in our sample. Interestingly, this individual lived around the time of later date estimates (∼4,500–7,000 cal BP) proposed for the split of Proto-Balto-Slavic from other Indo-European languages [3, 4]. There are two major theories to explain the distribution of Indo-European languages that constitute the most widely spoken language family in the world: (1) they have an Anatolian origin and were spread by Neolithic agriculturalists [32, 33] and (2) they developed in the Pontic Steppe and proliferated through Late Neolithic/Bronze Age migrations [1, 3, 34]. The presence of a Steppe-related component in Latvia_LN1 in the absence of an Anatolian farmer-related genetic input supports a Steppe rather than an Anatolian origin for the Balto-Slavic branch of the Indo-European language family.

It is striking that we did not find evidence for early European or Anatolian farmer admixture in any of our Latvian Neolithic samples using both D statistics (Table 2) and ADMIXTURE (Figure 2A). This lack of admixture is also supported by the mitochondrial haplogroup of the Latvian Neolithic samples (all belong to U; Figure 1), which is prevalent in European hunter-gatherers [1, 35], including our Latvian Mesolithic samples, but not in early farmers. It is interesting that among the grave goods found in the burial of Latvia_LN1 was a chisel made from the bone of a domesticated goat or sheep [17, 21]. The presence of this tool made from a domesticate as well as dietary isotope data (δ15N and δ13C), which show greater reliance on terrestrial resources than in previous periods [17], is consistent with either the adoption of farming without early European farmer-related genetic admixture or the existence of trade networks with farming communities that were largely independent of genomic exchange. Although we find no genetic input from Anatolian or early European farmers in our time series, ADMIXTURE analysis of an Estonian Corded Ware sample [26] (Figure 2B) has suggested that this farmer genetic influence, which is present in contemporary Northern European populations (Figure S2), had arrived in the Baltic by at least the Bronze Age.