The Yamnaya Steppe Herders from Russia

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The Yamnaya Steppe Herders from Russia Jan 14, 2017 20:35:37 GMT

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Post by Admin on Jan 14, 2017 20:35:37 GMT

Climate shifts dramatically influenced the occupation of Southwest Asia by anatomically modern humans since their first occupation at the sites of Skhul and Qafzeh in Israel some 80 to 130 ka1. These first archaeologically identified modern humans outside of Africa appear to have left no genetic impact, with the next modern human remains in the Levant dating to around 45–50 ka1. Climate change impacts on population mobility and cultural developments have been hotly debated2. Aridity restricted larger human populations to refugia sited around the Mediterranean3, the Black Sea4, and possibly the southern Arabian Peninsula5, that were distinguished by tool cultures in the archaeological record6,7, during the Last Glacial Period (LGP) ending some 12 ka. Post-glacial warming, and later, agriculture, allowed expansions of these populations within SW Asia8. Archaeological evidence shows post-LGP population expansions shifting from mobile foraging to a more sedentary lifestyle4,9 with permanent settlements, early cultivation of wild plants10,11, stored goods, and emerging trade and exchange networks12,13. The Fertile Crescent based “Neolithic Revolution” replaced most cultures across the region, spreading Indo-European languages from an Anatolian homeland14, both westward to Europe, northward to the steppes, and eastward to the Iranian plateau and beyond.

Autosomal analyses have identified a cryptic population, “Basal Eurasians,” that injected significant genetics into the European population distinct from the Southwest Asian agricultural revolution signature15. Subsequent work16,17 has suggested that Yamnaya aDNA appears to have been a source of the genetics associated with corded ware culture, and provides further evidence for a late Neolithic through early Bronze Age wave introducing Indo-European languages.

Lineages that evolved in relatively isolated refugia populations could carry genetic evidence of that isolation and subsequent expansion. Such signals identified source populations for admixture events marking European settlement15,16,18,19. However, specific associations between Southwest Asian post-LGP expansion genetics and their original refugia, and the identification of the timing and directions of their various dispersal events, are still being determined. Most recently, analyses of complete mitochondrial genomes have identified a possible Arabian refugia in the LGP, within which several mtDNA haplogroups including R0a emerged and from which they dispersed to the Fertile Crescent, the Levant and the Horn of Africa20. Y-chromosome analysis has identified highest frequencies for J1 haplogroup to be most common in the Saudi Peninsula21 marking the Muslim expansion22 with J2 being common in the coastal Levant23, and identified early on as a possible marker of the European expansion of the post-Neolithic expansion8,24, while their origins have been identified roughly within Iran, Armenia, Georgia, and/or Eastern Turkey. However, even though J2 appeared to mark a post-Neolithic expansion, this haplogroup has been identified in ancient DNA analysis of remains archaeologically associated with the late Bronze Era25. Both Haplogroups origins have been identified roughly within Iran, Armenia, Georgia, and/or Eastern Turkey.

Here, we take the approach of identifying and dating population isolation prior to expansion, and tracing routes of dispersal throughout Southwest Asia and into Europe and Africa. We analyzed a comprehensive autosomal and Y-chromosome dataset of Eurasian and African populations identifying genetic signals of regional LGP population isolation, and contrasted expansion time estimates and dispersal routes in the region with archaeological4,9, palaeontological26, palaeobotanical27, and climate4,27 data.

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The Yamnaya Steppe Herders from Russia Jan 15, 2017 20:23:36 GMT

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Figure 1. MDS analyses of RST distances based on STR haplogroup variances (a) across all haplogroups, for (b) J*(xJ2), and (c) J2.

Maximal diversities, indicative of possible origins, are observed for J*(xJ2) in the Caucasus and for J2 in Armenia, decreasing south and east, although high diversities do not entirely correlate with high relative frequencies (frequency contour Supplementary Figure S2 and variance contour Supplementary Figure S3). BATWING TMRCA (Supplementary information) estimates for J*, J1, J1e, J2, and E1b1b are shown in Table 1. These results indicate slightly greater time depth information of J, J1, and J2 in Turkey and populations from the Caucasus, in agreement with their higher diversity in this area. They also show greater differentiation of the E1b1b1 haplogroups between North Africa and the rest of Asia. The great time depth of J2 and E in Iberia are consistent with a longer period of isolated evolution. Haplogroup J* is the least differentiated in time, but shows maximum values in Turkey Iran as well as North Africa, with decreasing values progressively further away from these geographical locations. Due to the phylogenetic relationship between J1 and J2 markers, the TMRCAs for these are identical. The J1 and J2 split shows deepest time in the Caucasus, Syria and Turkey at 8.9 ka and 8.4 ka, respectively.

The population split estimates (Fig. 2) show divergences largely reflecting the trend in TMRCAs with older dates closer to the Caucasus, but with differentiation times roughly 1/3 of the TMRCAs, suggesting that 2/3 of STR diversity evolution occurred prior to the earliest population differentiations that followed the Late Glacial Period expansions. Expansions therefore distributed a broad spectrum of shared STR haplotypes that had already evolved within their isolated populations. This broadly shared diversity explains the weak geographical discrimination observed in the phylogenetic networks (Supplementary Figure S5) and the lack of organization found in the MDS analysis for haplogroup specific J*(xJ2) and J2 Y STR FSTs (Fig. 1b and c).

Figure 2. BATWING population split time estimates for Middle Eastern populations marking expansion histories for haplogroups (a) J1, (b) J2 and (c) E1b1b1.

The J1 haplogroup shows greatest differentiation of the Caucasus at 8.9 ka, then Ethiopia at 7.9 ka, followed by Armenia and Turkey at 6.9 ka. The J2 Haplogroup shows an earliest isolation of the Caucasus at 8.4 ka. For the E1b1b1 haplogroup, Egypt, North Africa, and the rest of the populations differentiated at 11.6 ka nearly polytomously (Fig. 2).

We performed an ADMIXTURE analysis to identify and quantify ancestral components in Southwest Asians across all chromosomes using 188,974 SNPs (Fig. 3). ADMIXTURE’s cross-validation (CV) shows decreasing CV error with decreasing dimensions to K = 1, with a basin from K = 3 to K = 1. In K = 3, Saudi, Georgian, and Palestinian populations show samples marking pure derivations of the K = 3 ancestral populations. Since the cross-validation scores minimized at K = 1, its utility in identifying a best estimate for ancestral population count is weak for these populations. However, the PCA and pairwise FST results give a strong suggestion that more ancestral signals are present. For this reason, ADMIXTURE analyses were presented for higher Ks in order to offer information regarding the structure PCA presents, showing results consistent with PCA and pairwise FST.

The rest show mixtures of these three, with Northern and Palestinian ancestral contributions appearing in Levantine and Fertile Crescent regions including Turkey and Armenia. The split to K = 4 primarily impacted the Palestinian ancestral group, splitting it. That 4th ancestral group is not purely represented in any of the modern populations, but is mostly represented in the Levantine through the Fertile Crescent regions. However, some of the samples clearly shifted character from mixtures to pure ancestral groups, reflecting increasing instability in the computations. PCA analysis (Fig. 4) most clearly identifies the same three evolutionary centers as extremes in the plot, strongly echoing, and largely clarifying, the information contained in the ADMIXTURE analysis.

Figure 3. Genome-wide analysis of populations from Southwest Asia using 188,974 autosomal SNPs. (a) Map showing populations analyzed (Base map constructed from Map data: Google, Digital Globe, (b) Population. structure inferred by ADMIXTURE. Each horizontal line represents ancestry probabilities of an individual in 2 constructed ancestral populations.

Specifically, the K = 5 ADMIXTURE identifies an ancestral population that completely dominates the Palestinian population, which corresponds to the Palestinian group on the PCA. The Saudi Arabian population shows an ancestral population marked in red for K = 5, with admixture into the Levantine populations, but nearly absent in Turkey, Armenia, and totally absent from Georgia. In the PCA, the Saudi population occupies a well-defined area, with a tail that admixes with the Levantine populations. The Georgian population is dominated by a strongly defined ancestral population, which shows admixed presence along the northern Fertile Crescent, and into the Levant. This is consistent with the genetic distances as shown in the PCA. The ADMIXTURE FST’s tended to increase with increasing K. The largest FST in the K = 3 group was 0.075, and the smallest was 0.057. This corresponds to 36.4 ka and 27.4 ka (we assume Ne = 8,060 - the harmonic average of 7,000 and 9,500 as in the supplementary information, which yields 1260 generations, or 36.4 ka for FST = 0.075, and 946 generations or 27.4 ka for FST = 0.057), all well into the LGP.

The unrooted NJ trees show strikingly varying branch lengths, and remarkably differentiated substructure within the major putative northern and southern refugia, as well as some suggestion of a Levantine refugium. For those populations expanding from the north, the trees reveal a similar east/west split as identified for the J1/J2 expansions. We note the pairwise FST date estimates are much younger, at 6.6 ka (assuming initial divergence around 11 ka) than the ancestral differentiation dates suggested by the ADMIXTURE derived FST ancestral date estimates of 37.4 ka and 27.4 ka.

Figure 4: PCA showing Genome-wide analysis of populations from Southwest Asia using 188,974 autosomal SNPs.

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The Yamnaya Steppe Herders from Russia Jan 17, 2017 20:29:04 GMT

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Post by Admin on Jan 17, 2017 20:29:04 GMT

Our Y chromosome and autosomal analysis identified genetic signatures of three likely centers of isolated evolution followed by population expansions. These modern centers correspond to archaeologically known LGP refugia4,9,27 in Southwest Asia4,5,34. The first, identified by Obsidian sourcing35 as an expansion center in Georgia/eastern Turkey12,13. Clear evidence of trade, and tool cultures mark the second refuge in the northern Levant7. The third in the southern Arabian Peninsula5 identified recently by Gandini et al.20. Archaeologically, the time period marking post glacial population expansions through Southwest Asia is associated with the early and middle Pre-Pottery Neolithic B, the increased reliance on domesticated plants and animals, increased evidence of trade and exchange along the earlier established obsidian trade routes, and coastal to inland trade of marine resources36 (Fig. 5).

Figure 5

BATWING characterized three features in the genetic record during the expansion of J1 and J2. The earliest dates, with the oldest differentiations for J2 at 8.4 ka, and J1 at 8.9 ka, show an early divergence between the Caucasus from the rest of the populations. BATWING does not model admixture; population split estimates dates to the time admixture ceases. In practice, very minor admixture can cause split times to be underestimated. The branches, to the east down through Mesopotamia and to the west down through the Levant, maintained mutual isolation. Those earliest dispersions show post-last-glacial-period dates but could have been earlier than BATWING estimated if admixture persisted. Later, a significant number of branches occurred within a very narrow window of time, nearly polytomously, followed by relatively stability, marking the emergence of stronger regional isolation suggesting sedentism. That window marks a period near the end of the Holocene Climatic Optimum (HCO - 9 ka–5 ka). Generally, the expansions show movement from northern regions until the HCO, with subsequent isolation and differentiation in the arable regions (Fertile Crescent, Levant, etc.) during aridification.

Subsequent expansions of J1 show the Mesopotamian branch extending to Arabia and Yemen at about 4 ka. The signal of the original North African J1 expansion is overwhelmed in Egypt by more recent Levantine J1s (Fig. 2a). J2 shows similar but deeper isolation during the HCO, with a similar expansion date into North Africa (5.9 ka) as J1 (4.9 ka, Fig. 2b). Yet, its isolation in Egypt is far older, around 8.1 ka. Further, J2′s Mesopotamian population differentiated earlier from the Levantine populations (7.3 ka), with much more recent admixture among J2′s in Turkey (5.1 ka).

Y-M35 (E1b1b1) dominates North Africa much more than Southwest Asia, with a Neolithic split at 11.6 ka between eastern and western North Africa. BATWING will interpret unique haplotypes among rare E1b1b1 samples as older isolation. Most of the populations show apparent isolation dating to the HCO with some associations showing as recent links between central Asians and the Southern Levant (2.9 ka), and the Caucasus with Mesopotamia (4.6 ka Fig. 2).

The population split estimates (Fig. 2) show divergences largely reflecting the trend in TMRCAs with older dates closer to the Caucasus, but with differentiation times that are roughly 1/3 of the TMRCAs, suggesting that 2/3 of STR diversity evolution occurred prior to the earliest population differentiations that followed the Late Glacial Period expansions. Expansions, therefore, distributed a broad spectrum of STR haplotypes that had already evolved within their refugia. This diversity explains the weak geographical discrimination observed in the phylogenetic networks (Figure S5) and the lack of organization found in the MDS analysis for haplogroup specific J*(xJ2) and J2 Y STR FSTs (Fig. 1b and c).

A recent study15 incorporating aDNA data, along with modern population structure, inferred that most Europeans derive from three primary population groups. One of these, Early European Farmers, was putatively derived from West Eurasian Hunter Gatherers and “Basal Eurasians” which enjoyed isolated evolution distinct from all other out-of-Africa groups prior to genetic expansion into Europe. The Basal Eurasians appear to be the main candidate group associated with the earliest transition from West Eurasian hunter-gathering to agriculture15. Two subsequent studies seeking to identify the origin of these groups identified Yamnaya as a likely genetic origin in addition to contributing to Indo-European languages16,17.

They differed on possible origins of Yamnaya, with one team, Haak et al., suggesting association possibly through the Caucasus16 and the other, Allentoft et al. denying it17. Interestingly, the Haak et al. study’s Y chromosome Yamnaya haplogroups were R1b1a or R1b1a2. Another recent study38 supports this result, though claims affinity with an “Armenian-like Near Eastern source.” Our study has identified the Caucasus refugium as the likely source for the J1 and J2 haplogroups that now dominate Southwest Asia, and previously appeared to mark the Neolithic Revolution’s expansion into Europe39. Yet, haplogroups J1 and J2 are distinctly lacking in the earlier Yamnaya samples. The geographic separation of modern J haplogroups in Southwest Asia, and the prevalence of J2 but not J1 in the expansion into Europe is striking given their close origins39,40.

Platt, D. E. et al. Mapping Post-Glacial expansions: The Peopling of Southwest Asia. Sci. Rep. 7, 40338; doi: 10.1038/srep40338 (2017).

Last Edit: Jan 17, 2017 20:31:50 GMT by Admin

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The Yamnaya Steppe Herders from Russia Jan 26, 2017 20:29:21 GMT

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Post by Admin on Jan 26, 2017 20:29:21 GMT

People of the Yamna culture consisted of three distinct phenotypes corresponding to the relatively recent blend between three populations. The dominant type was tall, dolichocephalic, with broad faces of medium height. The second type was more robust with high and wide Proto-Europoid faces. The third type was more gracile, with narrow and high faces of the East Mediterranean type.

The average height for Yamnayan men was 175.5cm (5 ft 9 in), approximately the same as the modern average for American and French men, and slightly taller than the average Mesolithic EHG men, who stood at 173.2 cm.

Yamnayan DNA tested by Haak (2015), Wilde (2014), Mathieson (2015) showed that Yamna people (or at least the few elite samples concerned) had predominantly brown eyes, dark hair, and had a skin colour that was moderately light, lighter than Mesolithic Europeans, but somewhat darker than that of the modern North Europeans.

Haak et al. (2015) identified Yamnaya haplogroups as R1b1a or R1b1a2. While haplogroup R1b is quite rare among the modern Russian population (5.8%), 34.4% belong to R1b1a2 among the Bashkirs, who are likely to be the descendants of the Yamnaya steppe herders as R1b1a2 is the identical haplogroup that the ancient Yamnaya samples tested by Haak et al. (2015) carried. The Bashkirs also fit the description of the Yamnaya steppe herders described as brown-eyed and brown-haired people (Allentoft et al. 2015), based on a low frequency of rs12913832, a major determinant of blue versus brown eyes in humans, from the Pontic-Caspian steppe populations (2%-3%).

Last Edit: Mar 13, 2019 19:48:04 GMT by Admin

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The Yamnaya Steppe Herders from Russia Jan 28, 2017 20:21:27 GMT

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Post by Admin on Jan 28, 2017 20:21:27 GMT

The archaeological record testifies to major cultural changes in
Europe and Asia after the Neolithic period. By 3000 BC, the
Neolithic farming cultures in temperate Eastern Europe appear to
be largely replaced by the Early Bronze Age Yamnaya culture, which
is associated with a completely new perception of family, property and
personhood13,14, rapidly stretching from Hungary to the Urals15. By
2800 BC a new social and economic formation, variously named
Corded Ware, Single Grave or Battle Axe cultures developed in temperate
Europe, possibly deriving from the Yamnaya background, and
culturally replacing the remaining Neolithic farmers16,17 (Fig. 1). In
western and Central Asia, hunter-gatherers still dominated in Early
Bronze Age, except in the Altai Mountains and Minusinsk Basin
where the Afanasievo culture existed with a close cultural affinity to
Yamnaya15 (Fig. 1). From the beginning of 2000 BC, a new class of
master artisans known as the Sintashta culture emerged in the Urals,
building chariots, breeding and training horses (Fig. 1), and producing
sophisticated new weapons18. These innovations quickly
spread across Europe and into Asia where they appeared to give rise
to the Andronovo culture19,20 (Fig. 1). In the Late Bronze Age around
1500 BC, the Andronovo culture was gradually replaced by the
Mezhovskaya, Karasuk, and Koryakova cultures21. It remains debated
if these major cultural shifts during the Bronze Age in Europe and
Asia resulted from the migration of people or through cultural diffusion
among settled groups15–17, and if the spread of the Indo-
European languages was linked to these events or predates them15.

Figure 1: Distribution maps of ancient samples. Localities, cultural associations, and approximate timeline of 101 sampled ancient individuals from Europe and Central Asia (left). Distribution of Early Bronze Age cultures Yamnaya, Corded Ware, and Afanasievo with arrows showing the Yamnaya expansions (top right). Middle and Late Bronze Age cultures Sintashta, Andronovo, Okunevo, and Karasuk with the eastward migration indicated (bottom right). Black markers represent chariot burials (2000–1800 bc) with similar horse cheek pieces, as evidence of expanding cultures. Tocharian is the second-oldest branch of Indo-European languages, preserved in Western China. CA, Copper Age; MN, Middle Neolithic; LN, Late Neolithic; EBA, Early Bronze Age; MBA, Middle Bronze Age; LBA, Late Bronze Age; IA, Iron Age; BAC, Battle Axe culture; CWC, Corded Ware culture.

By analysing our genomic data in relation to previously published
ancient and modern data (Supplementary Information, section 6),
we find evidence for a genetically structured Europe during the
Bronze Age (Fig. 2; Extended Data Fig. 1; and Supplementary Figs 5
and 6). Populations in northern and central Europe were composed of
a mixture of the earlier hunter-gatherer and Neolithic farmer10
groups, but received ‘Caucasian’ genetic input at the onset of the
Bronze Age (Fig. 2). This coincides with the archaeologically welldefined
expansion of the Yamnaya culture from the Pontic-Caspian
steppe into Europe (Figs 1 and 2). This admixture event resulted in the
formation of peoples of the Corded Ware and related cultures, as
supported by negative ‘admixture’ f3 statistics when using Yamnaya
as a source population (Extended Data Table 2, Supplementary Table
12). Although European Late Neolithic and Bronze Age cultures such
as Corded Ware, Bell Beakers, Unetice, and the Scandinavian cultures
are genetically very similar to each other (Fig. 2), they still display a
cline of genetic affinity with Yamnaya, with highest levels in Corded
Ware, lowest in Hungary, and central European Bell Beakers being
intermediate (Fig. 2b and Extended Data Table 1). Using D-statistics,
we find that Corded Ware and Yamnaya individuals form a clade to
the exclusion of Bronze Age Armenians (Extended Data Table 1)
showing that the genetic ‘Caucasus component’ present in Bronze
Age Europe has a steppe origin rather than a southern Caucasus
origin. Earlier studies have shown that southern Europeans received
substantial gene flow from Neolithic farmers during the Neolithic9.
Despite being slightly later, we find that the Copper Age Remedello
culture in Italy does not have the ‘Caucasian’ genetic component and
is still clustering genetically with Neolithic farmers (Fig. 2; Extended
Data Fig. 1 and Supplementary Fig. 6). Hence this region was either
unaffected by the Yamnaya expansion or the Remedello pre-dates
such an expansion into southern Europe. The ‘Caucasian’ component
is clearly present during Late Bronze Age in Montenegro (Fig. 2b).
The close affinity we observe between peoples of Corded Ware and
Sintashta cultures (Extended Data Fig. 2a) suggests similar genetic
sources of the two, which contrasts with previous hypotheses placing
the origin of Sintastha in Asia or the Middle East28. Although we
cannot formally test whether the Sintashta derives directly from an
eastward migration of Corded Ware peoples or if they share common
ancestry with an earlier steppe population, the presence of European
Neolithic farmer ancestry in both the Corded Ware and the Sintashta,
combined with the absence of Neolithic farmer ancestry in the earlier
Yamnaya, would suggest the former being more probable (Fig. 2b and
Extended Data Table 1).

Figure 2: Genetic structure of ancient Europe and the Pontic-Caspian steppe. a, Principal component analysis (PCA) of ancient individuals (n = 93) from different periods projected onto contemporary individuals from Europe, West Asia, and Caucasus. Grey labels represent population codes showing coordinates for individuals (small) and population median (large). Coloured circles indicate ancient individuals b, ADMIXTURE ancestry components (K = 16) for ancient (n = 93) and selected contemporary individuals. The width of the bars representing ancient individuals is increased to aid visualization. Individuals with less than 20,000 SNPs have lighter colours. Coloured circles indicate corresponding group in the PCA. Probable Yamnaya-related admixture is indicated by the dashed arrow.

We find that the Bronze Age in Asia is equally dynamic and characterized
by large-scale migrations and population replacements. The
Early Bronze Age Afanasievo culture in the Altai-Sayan region is
genetically indistinguishable from Yamnaya, confirming an eastward
expansion across the steppe (Figs 1 and 3b; Extended Data Fig. 2b and
Extended Data Table 1), in addition to the westward expansion into
Europe. Thus, the Yamnaya migrations resulted in gene flow across
vast distances, essentially connecting Altai in Siberia with Scandinavia
in the Early Bronze Age (Fig. 1). The Andronovo culture, which arose
in Central Asia during the later Bronze Age (Fig. 1), is genetically
closely related to the Sintashta peoples (Extended Data Fig. 2c), and
clearly distinct from both Yamnaya and Afanasievo (Fig. 3b and
Extended Data Table 1). Therefore, Andronovo represents a temporal
and geographical extension of the Sintashta gene pool. Towards the
end of the Bronze Age in Asia, Andronovo was replaced by the
Karasuk, Mezhovskaya, and Iron Age cultures which appear multiethnic
and show gradual admixture with East Asians (Fig. 3b and
Extended Data Table 2), corresponding with anthropological and
biological research29. However, Iron Age individuals from Central
Asia still show higher levels of West Eurasian ancestry than contemporary
populations from the same region (Fig. 3b). Intriguingly, individuals
of the Bronze Age Okunevo culture from the Sayano-Altai
region (Fig. 1) are related to present-day Native Americans (Extended
Data Fig. 2d), which confirms previous craniometric studies30. This
finding implies that Okunevo could represent a remnant population
related to the Upper Palaeolithic Mal’ta hunter-gatherer population
from Lake Baikal that contributed genetic material to Native
Americans4.

Last Edit: Mar 13, 2019 19:53:16 GMT by Admin