Post by Admin on Feb 7, 2019 18:03:49 GMT
Characterising the Steppe ancestry profile
Individuals from the North Caucasian steppe associated with the Yamnaya cultural formation (5300–4400 BP, 3300–2400 calBCE) appear genetically almost identical to previously reported Yamnaya individuals from Kalmykia19 immediately to the north, the middle Volga region18,22, Ukraine, and to other BA individuals from the Eurasian steppes who share the characteristic ‘steppe ancestry’ profile as a mixture of EHG and CHG-related ancestry9,13. These individuals form a tight cluster in PCA space (Fig. 2) and can be shown formally to be a mixture by significantly negative admixture f3-statistics of the form f3(EHG, CHG; target) (Supplementary Fig. 2). This cluster also involves individuals of the North Caucasus culture (4800–4500 BP, 2800–2500 calBCE) in the piedmont steppe, who share the steppe ancestry profile, as do individuals from the Catacomb culture in the Kuban, Caspian and piedmont steppes (4600–4200 BP, 2600–2200 calBCE), which succeeded the Yamnaya horizon.
The individuals of the MBA post-Catacomb horizon (4200–3700 BP, 2200–1700 calBCE) such as Late North Caucasus and Lola cultures represent both ancestry profiles common in the North Caucasus: individuals from the mountain site Kabardinka show a typical steppe ancestry profile, whereas individuals from the site Kudachurt 90 km to the west or our most recent individual from the western LBA Dolmen culture (3400–3200 BP, 1400–1200 calBCE) retain the ‘southern’ Caucasus profile. In contrast, one Lola culture individual resembles the ancestry profile of the Steppe Maykop individuals.
Admixture into the steppe zone from the south
Evidence for interaction between the Caucasus and the Steppe clusters is visible in our genetic data from individuals associated with the later Steppe Maykop phase around 5300–5100 years ago. These ‘outlier’ individuals were buried in the same mounds as those with steppe and in particular Steppe Maykop ancestry profiles but share a higher proportion of AF ancestry visible in the ADMIXTURE plot and are also shifted towards the Caucasus cluster in PC space (Fig. 2d). This observation is confirmed by formal D-statistics (Supplementary Fig. 3). By modelling Steppe Maykop outliers successfully as a two-way mixture of Steppe Maykop and representatives of the Caucasus cluster (Supplementary Table 3), we can show that these individuals received additional ‘Anatolian and Iranian Neolithic ancestry’, most likely from contemporaneous sources in the south. We used ALDER32 to estimate an average admixture time for the observed farmer-related ancestry in Steppe Maykop outliers of 20 generations or 560 years ago (Supplementary Note 5).
Anatolian farmer-related ancestry in steppe groups
Eneolithic Samara individuals form a cline in PC space running from EHG to CHG (Fig. 2d), which is continued by the newly reported Eneolithic steppe individuals. However, the trajectory of this cline changes in the subsequent centuries. Here we observe a cline from Eneolithic_steppe towards the Caucasus cluster. We can qualitatively explain this ‘tilting cline’ by developments south of the Caucasus, where Iranian and AF ancestries continue to mix, resulting in a blend that is also observed in the Caucasus cluster, from where it could have spread onto the steppe. The first appearance of ‘combined farmer-related ancestry’ in the steppe zone is evident in Steppe Maykop outliers. However, PCA results suggest that Yamnaya and later groups of the West Eurasian steppe carry also some farmer-related ancestry as they are slightly shifted towards ‘European Neolithic groups’ in PC2 (Fig. 2d) compared to the preceding Eneolithic steppe individuals. The ‘tilting cline’ is also confirmed by admixture f3-statistics, which provide statistically significant negative values for AG3 and any AF group as the two sources (Supplementary Table 11). Using f- and D-statistics we also observe an increase in farmer-related ancestry (both Anatolian and Iranian) in our Steppe cluster, distinguishing the Eneolithic steppe from later groups. In addition, we find the Caucasus cluster or Levant/AF groups to share more alleles with Steppe groups than with EHG or Samara_Eneolithic (Supplementary Figs. 4 and 5). MLBA groups such as Poltavka, Andronovo, Srubnaya, and Sintashta show a further increase of AF ancestry consistent with previous studies9,22, reflecting different processes not directly related to events in the Caucasus (Supplementary Fig. 6).
We then used qpWave and qpAdm to explore the number of ancestry sources for the AF component to evaluate whether geographically proximate groups contributed plausibly to the subtle shift of Eneolithic ancestry in the steppe towards Neolithic groups. Specifically, we tested whether any of the Eurasian steppe ancestry groups can be successfully modelled as a two-way admixture between Eneolithic steppe and a population X derived from Anatolian- or Iranian farmer-related ancestry, respectively. Surprisingly, we found that a minimum of four streams of ancestry is needed to explain all eight steppe ancestry groups tested (Fig. 2; Supplementary Table 12). Importantly, our results show a subtle contribution of both AF ancestry and WHG-related ancestry (Fig. 4; Supplementary Tables 13 and 14), likely brought in through MN/LN farming groups from adjacent regions in the West. A direct source of AF ancestry can be ruled out (Supplementary Table 15). At present, due to the limits of our resolution, we cannot identify a single best source population. However, geographically proximal and contemporaneous groups such as Globular Amphora and Eneolithic groups from the Black Sea area (Ukraine and Bulgaria), representing all four distal sources (CHG, EHG, WHG, and Anatolian_Neolithic), are among the best supported candidates (Fig. 4; Supplementary Table 16). Applying the same method to the subsequent North Caucasian Steppe groups such as Catacomb, (Late) North Caucasus confirms this pattern (Supplementary Table 16).
Using qpAdm with Globular Amphora as a proximate surrogate population, we estimated the contribution of AF ancestry into Yamnaya and other steppe groups. We find that Yamnaya Samara individuals have 13.2 ± 2.7% and Ukraine or Caucasus Yamnaya individuals 16.6 ± 2.9% AF ancestry (Fig. 4; Supplementary Table 17)—statistically indistinguishable proportions. Substituting Globular Amphora with Iberia Chalcolithic does not alter the results profoundly (Supplementary Table 18). This suggests that the source population was a mixture of AF ancestry and a minimum of 20% WHG ancestry, a genetic profile shared by many European MN/LN and Chalcolithic individuals of the 3rd millennium BCE analysed thus far.
To account for potentially un-modelled ancestry from the Caucasus groups, we added ‘Eneolithic Caucasus’ as an additional source to build a three-way model. We found that Yamnaya Caucasus, Yamnaya Ukraine Ozera, North Caucasus and Late North Caucasus had likely received additional ancestry (6–40%) from nearby Caucasus groups (Supplementary Table 19). This suggests a more complex and dynamic picture of steppe ancestry groups through time, including the formation of a local variant of steppe ancestry in the North Caucasian steppe from the local Eneolithic, a contribution of Steppe Maykop groups, and population continuity between the early Yamnaya period and the MBA (5300–3200 BP, 3300–2200 calBCE).
Insights from micro-transects through time
The availability of multiple individuals from one burial mounds allowed us to test genetic continuity on a micro-transect level. By focusing on two kurgans (Marinskaya 5 and Sharakhalsun 6) with four and five individuals, respectively, we observe that the genetic ancestry varied through time, alternating between the Steppe and Caucasus ancestries (Supplementary Fig. 7), suggesting a shifting genetic border between the two genetic clusters. We also detected various degrees of kinship between individuals buried in the same mound, which supports the view that particular mounds reflected genealogical lineages. Overall, we observe a balanced sex ratio within our sites across the individuals tested (Supplementary Note 4).
Individuals from the North Caucasian steppe associated with the Yamnaya cultural formation (5300–4400 BP, 3300–2400 calBCE) appear genetically almost identical to previously reported Yamnaya individuals from Kalmykia19 immediately to the north, the middle Volga region18,22, Ukraine, and to other BA individuals from the Eurasian steppes who share the characteristic ‘steppe ancestry’ profile as a mixture of EHG and CHG-related ancestry9,13. These individuals form a tight cluster in PCA space (Fig. 2) and can be shown formally to be a mixture by significantly negative admixture f3-statistics of the form f3(EHG, CHG; target) (Supplementary Fig. 2). This cluster also involves individuals of the North Caucasus culture (4800–4500 BP, 2800–2500 calBCE) in the piedmont steppe, who share the steppe ancestry profile, as do individuals from the Catacomb culture in the Kuban, Caspian and piedmont steppes (4600–4200 BP, 2600–2200 calBCE), which succeeded the Yamnaya horizon.
The individuals of the MBA post-Catacomb horizon (4200–3700 BP, 2200–1700 calBCE) such as Late North Caucasus and Lola cultures represent both ancestry profiles common in the North Caucasus: individuals from the mountain site Kabardinka show a typical steppe ancestry profile, whereas individuals from the site Kudachurt 90 km to the west or our most recent individual from the western LBA Dolmen culture (3400–3200 BP, 1400–1200 calBCE) retain the ‘southern’ Caucasus profile. In contrast, one Lola culture individual resembles the ancestry profile of the Steppe Maykop individuals.
Admixture into the steppe zone from the south
Evidence for interaction between the Caucasus and the Steppe clusters is visible in our genetic data from individuals associated with the later Steppe Maykop phase around 5300–5100 years ago. These ‘outlier’ individuals were buried in the same mounds as those with steppe and in particular Steppe Maykop ancestry profiles but share a higher proportion of AF ancestry visible in the ADMIXTURE plot and are also shifted towards the Caucasus cluster in PC space (Fig. 2d). This observation is confirmed by formal D-statistics (Supplementary Fig. 3). By modelling Steppe Maykop outliers successfully as a two-way mixture of Steppe Maykop and representatives of the Caucasus cluster (Supplementary Table 3), we can show that these individuals received additional ‘Anatolian and Iranian Neolithic ancestry’, most likely from contemporaneous sources in the south. We used ALDER32 to estimate an average admixture time for the observed farmer-related ancestry in Steppe Maykop outliers of 20 generations or 560 years ago (Supplementary Note 5).
Anatolian farmer-related ancestry in steppe groups
Eneolithic Samara individuals form a cline in PC space running from EHG to CHG (Fig. 2d), which is continued by the newly reported Eneolithic steppe individuals. However, the trajectory of this cline changes in the subsequent centuries. Here we observe a cline from Eneolithic_steppe towards the Caucasus cluster. We can qualitatively explain this ‘tilting cline’ by developments south of the Caucasus, where Iranian and AF ancestries continue to mix, resulting in a blend that is also observed in the Caucasus cluster, from where it could have spread onto the steppe. The first appearance of ‘combined farmer-related ancestry’ in the steppe zone is evident in Steppe Maykop outliers. However, PCA results suggest that Yamnaya and later groups of the West Eurasian steppe carry also some farmer-related ancestry as they are slightly shifted towards ‘European Neolithic groups’ in PC2 (Fig. 2d) compared to the preceding Eneolithic steppe individuals. The ‘tilting cline’ is also confirmed by admixture f3-statistics, which provide statistically significant negative values for AG3 and any AF group as the two sources (Supplementary Table 11). Using f- and D-statistics we also observe an increase in farmer-related ancestry (both Anatolian and Iranian) in our Steppe cluster, distinguishing the Eneolithic steppe from later groups. In addition, we find the Caucasus cluster or Levant/AF groups to share more alleles with Steppe groups than with EHG or Samara_Eneolithic (Supplementary Figs. 4 and 5). MLBA groups such as Poltavka, Andronovo, Srubnaya, and Sintashta show a further increase of AF ancestry consistent with previous studies9,22, reflecting different processes not directly related to events in the Caucasus (Supplementary Fig. 6).
We then used qpWave and qpAdm to explore the number of ancestry sources for the AF component to evaluate whether geographically proximate groups contributed plausibly to the subtle shift of Eneolithic ancestry in the steppe towards Neolithic groups. Specifically, we tested whether any of the Eurasian steppe ancestry groups can be successfully modelled as a two-way admixture between Eneolithic steppe and a population X derived from Anatolian- or Iranian farmer-related ancestry, respectively. Surprisingly, we found that a minimum of four streams of ancestry is needed to explain all eight steppe ancestry groups tested (Fig. 2; Supplementary Table 12). Importantly, our results show a subtle contribution of both AF ancestry and WHG-related ancestry (Fig. 4; Supplementary Tables 13 and 14), likely brought in through MN/LN farming groups from adjacent regions in the West. A direct source of AF ancestry can be ruled out (Supplementary Table 15). At present, due to the limits of our resolution, we cannot identify a single best source population. However, geographically proximal and contemporaneous groups such as Globular Amphora and Eneolithic groups from the Black Sea area (Ukraine and Bulgaria), representing all four distal sources (CHG, EHG, WHG, and Anatolian_Neolithic), are among the best supported candidates (Fig. 4; Supplementary Table 16). Applying the same method to the subsequent North Caucasian Steppe groups such as Catacomb, (Late) North Caucasus confirms this pattern (Supplementary Table 16).
Using qpAdm with Globular Amphora as a proximate surrogate population, we estimated the contribution of AF ancestry into Yamnaya and other steppe groups. We find that Yamnaya Samara individuals have 13.2 ± 2.7% and Ukraine or Caucasus Yamnaya individuals 16.6 ± 2.9% AF ancestry (Fig. 4; Supplementary Table 17)—statistically indistinguishable proportions. Substituting Globular Amphora with Iberia Chalcolithic does not alter the results profoundly (Supplementary Table 18). This suggests that the source population was a mixture of AF ancestry and a minimum of 20% WHG ancestry, a genetic profile shared by many European MN/LN and Chalcolithic individuals of the 3rd millennium BCE analysed thus far.
To account for potentially un-modelled ancestry from the Caucasus groups, we added ‘Eneolithic Caucasus’ as an additional source to build a three-way model. We found that Yamnaya Caucasus, Yamnaya Ukraine Ozera, North Caucasus and Late North Caucasus had likely received additional ancestry (6–40%) from nearby Caucasus groups (Supplementary Table 19). This suggests a more complex and dynamic picture of steppe ancestry groups through time, including the formation of a local variant of steppe ancestry in the North Caucasian steppe from the local Eneolithic, a contribution of Steppe Maykop groups, and population continuity between the early Yamnaya period and the MBA (5300–3200 BP, 3300–2200 calBCE).
Insights from micro-transects through time
The availability of multiple individuals from one burial mounds allowed us to test genetic continuity on a micro-transect level. By focusing on two kurgans (Marinskaya 5 and Sharakhalsun 6) with four and five individuals, respectively, we observe that the genetic ancestry varied through time, alternating between the Steppe and Caucasus ancestries (Supplementary Fig. 7), suggesting a shifting genetic border between the two genetic clusters. We also detected various degrees of kinship between individuals buried in the same mound, which supports the view that particular mounds reflected genealogical lineages. Overall, we observe a balanced sex ratio within our sites across the individuals tested (Supplementary Note 4).