Post by Admin on Nov 12, 2021 21:14:37 GMT
Genetics
We report genomic analyses of 19 authenticated ancient individuals from the Amur, Korea, Kyushu and the Ryukyus and combined them with published genomes that cover the eastern steppe, West Liao, Amur and Yellow River regions, Liaodong, Shandong, the Primorye and Japan between 9500 and 300 BP (Fig. 3a, Extended Data Fig. 4, Supplementary Data 11, 13, 17). We projected them onto a principal component analysis (PCA) of 149 present-day Eurasian populations and 45 East Asian populations (Extended Data Figs. 5–8). Figure 3b models our key ancient populations as an admixture of five genetic components, whereby Jalainur represents Amur, Yangshao the Yellow River and Rokutsu the Jomon genome, whereas Hongshan and Upper Xiajiadian in the West Liao River are composed of Yellow River and Amur genomes (qpAdm admixture of various East Asian genetic components in Supplementary Data 16).
Fig. 3: Spatiotemporal distribution and admixture of ancient genomes.
a, Ancient genomes located in time and space. For detailed legend, see Extended Data Fig. 4. b, QpAdm proximal admixture modelling of 20 key ancient populations from this study. The x axis shows ancestry proportion estimates for the target populations in the y axis; the error bars represent ± 1 s.e.m. range, estimated by 5-cM block jackknifing.
Contemporary Tungusic as well as Nivkh speakers in the Amur form a tight cluster13 (Extended Data Fig. 5). Neolithic hunter-gatherers from Baikal, Primorye and the southeastern steppe, as well as farmers from the West Liao and Amur, all project within this cluster (Extended Data Figs. 8–10).
Late Neolithic Angangxi (Supplementary Data 12) show a high proportion of Amur-like ancestry, whereas West Liao Neolithic millet farmers show a considerable proportion of Amur-like ancestry with a gradual shift towards the Yellow River genome over time12 (Extended Data Figs. 8–10, Fig. 3b). Although we lack Early Neolithic genomes in the West Liao River, Amur-like ancestry thus is likely to represent the original genetic profile of indigenous pre-Neolithic (or late Palaeolithic) hunter-gatherers covering Baikal, Amur, Primorye, the southeastern steppe and West Liao, continuing in the early farmers from this region. This contradicts a recent genetic study13, which concludes that the absence of Yellow River influence in ancient genomes from Mongolia and the Amur does not support the West Liao genetic correlate of the Transeurasian language family.
The PCA (Extended Data Figs. 8–10) shows a general trend for Neolithic individuals from Mongolia to contain high Amur-like ancestry with extensive gene flow from western Eurasia increasing from the Bronze to Middle Ages37. Whereas the Turkic-speaking Xiongnu38, Old Uyghur and Türk are extremely scattered, the Mongolic-speaking39 Iron Age Xianbei fall closer to the Amur cluster than the Shiwei, Rouran, Khitan and Middle Mongolian Khanate from Antiquity and the Middle Ages.
As Amur-related ancestry can be traced down to speakers of Japanese and Korean13, it appears to be the original genetic component common to all speakers of Transeurasian languages. By analysing ancient genomes from Korea (Supplementary Data 12), we find that Jomon ancestry was present on the Peninsula by 6000 BP (Fig. 3b, Supplementary Data 13).
The proximal qpAdm modelling (Supplementary Data 13) suggests that Neolithic Ando can be entirely derived from an ancestry related to Hongshan, whereas Yŏndaedo and Changhang can be modelled as an admixture of Jomon with a high proportion of Hongshan ancestry, although Yŏndaedo has only limited resolution (Supplementary Data 16, Fig. 3b). Yokchido, on the southern coast of Korea, contains nearly 95% Jomon ancestry. Although our genetic analysis cannot itself distinguish between possible East Asian ancestries for Bronze Age Taejungni, given the Bronze Age date it can be best modelled as Upper Xiajiadian; a possible minor Jomon admixture is not statistically significant (P = 0.228; Supplementary Data 16). We therefore observe a heterogeneous presence of Jomon ancestry in Neolithic Koreans (0–95%) and its eventual disappearance over time, as shown by a negligible Jomon contribution to present-day Koreans. The lack of a significant Jomon component in Taejungni indicates that early populations, without detectable Jomon ancestry linked to present-day Koreans, migrated to the Korean peninsula in association with rice farming, and replaced Neolithic populations with some Jomon admixture—although our genetic data currently do not have resolution to test this hypothesis, owing to limited sample size and coverage. We therefore associate the spread of farming to Korea with different waves of Amur and Yellow River gene flow, modelled by Hongshan for the Neolithic introduction of millet farming and by Upper Xiajiadian for the Bronze Age addition of rice agriculture.
Analysing the genomes from Yayoi farmers (Supplementary Data 12), we found that, like Taejungni, they can be modelled as indigenous Jomon ancestry admixed with Bronze Age Upper Xiajiadian ancestry. Our results support massive migration from Korea into Japan in the Bronze Age.
The Nagabaka genomes from Miyako Island (Supplementary Data 12) represent the first—to our knowledge—ancient genome-wide data from the Ryukyus. Contrary to previous findings that Holocene populations reached the southern Ryukyus from Taiwan40, our results suggest that the prehistoric Nagabaka population originated in Jomon cultures to the north (Extended Data Fig. 7). The genetic turn-over from Jomon- to Yayoi-like ancestry before the early modern period mirrors the late arrival of agriculture and Ryukyan languages in this region.
We report genomic analyses of 19 authenticated ancient individuals from the Amur, Korea, Kyushu and the Ryukyus and combined them with published genomes that cover the eastern steppe, West Liao, Amur and Yellow River regions, Liaodong, Shandong, the Primorye and Japan between 9500 and 300 BP (Fig. 3a, Extended Data Fig. 4, Supplementary Data 11, 13, 17). We projected them onto a principal component analysis (PCA) of 149 present-day Eurasian populations and 45 East Asian populations (Extended Data Figs. 5–8). Figure 3b models our key ancient populations as an admixture of five genetic components, whereby Jalainur represents Amur, Yangshao the Yellow River and Rokutsu the Jomon genome, whereas Hongshan and Upper Xiajiadian in the West Liao River are composed of Yellow River and Amur genomes (qpAdm admixture of various East Asian genetic components in Supplementary Data 16).
Fig. 3: Spatiotemporal distribution and admixture of ancient genomes.
a, Ancient genomes located in time and space. For detailed legend, see Extended Data Fig. 4. b, QpAdm proximal admixture modelling of 20 key ancient populations from this study. The x axis shows ancestry proportion estimates for the target populations in the y axis; the error bars represent ± 1 s.e.m. range, estimated by 5-cM block jackknifing.
Contemporary Tungusic as well as Nivkh speakers in the Amur form a tight cluster13 (Extended Data Fig. 5). Neolithic hunter-gatherers from Baikal, Primorye and the southeastern steppe, as well as farmers from the West Liao and Amur, all project within this cluster (Extended Data Figs. 8–10).
Late Neolithic Angangxi (Supplementary Data 12) show a high proportion of Amur-like ancestry, whereas West Liao Neolithic millet farmers show a considerable proportion of Amur-like ancestry with a gradual shift towards the Yellow River genome over time12 (Extended Data Figs. 8–10, Fig. 3b). Although we lack Early Neolithic genomes in the West Liao River, Amur-like ancestry thus is likely to represent the original genetic profile of indigenous pre-Neolithic (or late Palaeolithic) hunter-gatherers covering Baikal, Amur, Primorye, the southeastern steppe and West Liao, continuing in the early farmers from this region. This contradicts a recent genetic study13, which concludes that the absence of Yellow River influence in ancient genomes from Mongolia and the Amur does not support the West Liao genetic correlate of the Transeurasian language family.
The PCA (Extended Data Figs. 8–10) shows a general trend for Neolithic individuals from Mongolia to contain high Amur-like ancestry with extensive gene flow from western Eurasia increasing from the Bronze to Middle Ages37. Whereas the Turkic-speaking Xiongnu38, Old Uyghur and Türk are extremely scattered, the Mongolic-speaking39 Iron Age Xianbei fall closer to the Amur cluster than the Shiwei, Rouran, Khitan and Middle Mongolian Khanate from Antiquity and the Middle Ages.
As Amur-related ancestry can be traced down to speakers of Japanese and Korean13, it appears to be the original genetic component common to all speakers of Transeurasian languages. By analysing ancient genomes from Korea (Supplementary Data 12), we find that Jomon ancestry was present on the Peninsula by 6000 BP (Fig. 3b, Supplementary Data 13).
The proximal qpAdm modelling (Supplementary Data 13) suggests that Neolithic Ando can be entirely derived from an ancestry related to Hongshan, whereas Yŏndaedo and Changhang can be modelled as an admixture of Jomon with a high proportion of Hongshan ancestry, although Yŏndaedo has only limited resolution (Supplementary Data 16, Fig. 3b). Yokchido, on the southern coast of Korea, contains nearly 95% Jomon ancestry. Although our genetic analysis cannot itself distinguish between possible East Asian ancestries for Bronze Age Taejungni, given the Bronze Age date it can be best modelled as Upper Xiajiadian; a possible minor Jomon admixture is not statistically significant (P = 0.228; Supplementary Data 16). We therefore observe a heterogeneous presence of Jomon ancestry in Neolithic Koreans (0–95%) and its eventual disappearance over time, as shown by a negligible Jomon contribution to present-day Koreans. The lack of a significant Jomon component in Taejungni indicates that early populations, without detectable Jomon ancestry linked to present-day Koreans, migrated to the Korean peninsula in association with rice farming, and replaced Neolithic populations with some Jomon admixture—although our genetic data currently do not have resolution to test this hypothesis, owing to limited sample size and coverage. We therefore associate the spread of farming to Korea with different waves of Amur and Yellow River gene flow, modelled by Hongshan for the Neolithic introduction of millet farming and by Upper Xiajiadian for the Bronze Age addition of rice agriculture.
Analysing the genomes from Yayoi farmers (Supplementary Data 12), we found that, like Taejungni, they can be modelled as indigenous Jomon ancestry admixed with Bronze Age Upper Xiajiadian ancestry. Our results support massive migration from Korea into Japan in the Bronze Age.
The Nagabaka genomes from Miyako Island (Supplementary Data 12) represent the first—to our knowledge—ancient genome-wide data from the Ryukyus. Contrary to previous findings that Holocene populations reached the southern Ryukyus from Taiwan40, our results suggest that the prehistoric Nagabaka population originated in Jomon cultures to the north (Extended Data Fig. 7). The genetic turn-over from Jomon- to Yayoi-like ancestry before the early modern period mirrors the late arrival of agriculture and Ryukyan languages in this region.