Post by Admin on Jan 8, 2021 1:28:43 GMT
Fig. 2 PCA and ADMIXTURE analysis.
(A) PCA calculated using a set of world populations. Ancient individuals were projected onto the inferred PC space (see table S2 for information about individuals). Arrows indicate the direction of population changes in time. Asterisk denotes being published in (16). (B) A subset of ADMIXTURE result for K = 14 clusters showing the ancestral composition of investigated ancient individuals.
Population dynamics during and after the LGM in northeast Asia
The Khaiyrgas Cave on the middle Lena is one of the earliest locations of post-LGM human occupation in northeast Asia (8, 19, 20). However, origin and legacy of people who settled this part of northeast Asia remain unknown. We sequenced ancient DNA from a deciduous tooth of a c.16,900-year-old subadult female (Khaiyrgas-1) excavated from the upper layer of the Paleolithic horizon of the Khaiyrgas Cave to investigate the post-LGM population dynamics in northeast Asia. This individual is one the first known post-LGM representatives of the settlers of the Central Siberian Plateau. Human groups geographically represented by this individual retracted from the area during the Bølling-Allerød warming period dated to c.15,000 to 13,000 cal BP (8).
Khaiyrgas-1 exhibited genetic affinity toward present-day Selkups, a north Siberian Uralic-speaking population, on the PCA (Fig. 2A). This individual shared more alleles with indigenous populations of Native America, i.e., Chane, Guarani, and Karitiana, but to a lesser degree with Selkups compared with other world populations as measured by outgroup f3-statistics (fig. S2 and table S3). We estimated ancestral clusters in the genome of Khaiyrgas-1 using ADMIXTURE (21) (Fig. 2B and fig. S3). On the basis of K = 14 ancestral components, a genetic component that is maximized in the present-day Nganasan population from northeast Asia (yellow) and another component that is maximized in the present-day Native America populations (purple) were present at high levels in the genome of Khaiyrgas-1 compared to other Upper Paleolithic individuals from Eurasia and Asia (Fig. 2, figs. S3 and S4, and table S4).
According to the PCA, Khaiyrgas-1 marked the first major genetic shift throughout the region upon the end of the LGM. This individual representing a distinct line of ancestry in a maximum likelihood tree fitted using TreeMix (22) (fig. S5) was positioned on the PCA between two distinct lineages from Siberia encompassing Ancient North Siberians (ANS), the first inhabitants of northeast Siberia, represented by a ~38,000-year-old Upper Paleolithic individual from the Yana RHS (Rhinoceros Horn Site) (Yana_UP), and Ancient Paleo-Siberians (AP), the Siberian ancestors of Native Americans, represented by a ~9800-year-old individual from the Kolyma region (Kolyma_M) (5). To test whether there was a local continuity during and after the LGM, i.e., genetic continuity between the ~38,000-year-old Yana_UP (5), the ~16,900-year-old Khaiyrgas-1, and the ~9800-year-old Kolyma_M (5), or whether there was a possible gene flow from distant sources into the region, we performed formal tests of shared genetic drift through f4-statistics for different tree-like topologies. F4-statistics in the form of f4(Yoruba, Popx; Yana_UP, Khaiyrghas-1) where Popx is either the ~24,000-year-old MA1 (23) or the ~16,000-year-old AfontovaGora3 (24) [Ancient North Eurasians (ANEs)] revealed that Khaiyrgas-1 shares more genetic drift with ANE lineage than Yana_UP (ANS), thus implying a possible gene flow from west Eurasia into the region during the LGM (table S5). F4-statistics in the form of f4(Yoruba, Khaiyrghas-1; Popx, Kolyma_M) and f4(Yoruba, Kolyma_M; Popx, Khaiyrghas-1) (figs. S6 and S7 and table S6) revealed that Khaiyrgas-1 and Kolyma_M share more drift with each other compared to Yana_UP and other Upper Paleolithic individuals from Eurasia and Asia including MA1 (23) and AfontovaGora3 (24), the ~45,000-year-old Ust’ Ishim (25), the ~37,000-year-old Kostenki14 (26) and the ~34,000-year-old Sunghir from Russia (27), and the ~40,000-year-old Tianyuan from China (28). The only exceptions were the ~12,000-year-old Anzick-1 from North America (29) and the ~4000-year-old Saqqaq from Greenland (30), both of which shared more drift with Kolyma_M (5) (fig. S8). Recently, a 14,500-year-old Upper Paleolithic individual from the south of Lake Baikal (UKY) (17) was found to be closely related with Kolyma_M (5). These two individuals (UKY and Kolyma_M) have genetic affinity toward Native American populations. In addition, f4(Yoruba, Anzick-1; Khaiyrghas-1, UKY) revealed that Anzick-1 shared more alleles with the UKY compared to the Khaiyrgas-1 (Z = 2.1). To further assess the complex relationship between Khaiyrgas-1, UKY, and Kolyma_M, we calculated f4-statistics in the form of f4(Yoruba, UKY; Khaiyrghas-1, Kolyma_M); unexpectedly, Khaiyrgas-1 and Kolyma_M appeared symmetrically related to the UKY individual (Z = 0.2). Furthermore, f4(Yoruba, Khaiyrghas-1; Kolyma_M, UKY) also suggested that UKY and Kolyma_M were symmetrically related to Khaiyrgas-1 (Z = 0.01). These results, likely due to a lack of power since these tests are based on a relatively low number of single-nucleotide polymorphisms (SNPs) (9366), leave multiple scenarios consistent with the data. Last, we modeled the Kolyma_M as a two-way mixture of Khaiyrgas-1 (80 ± 19%) and Devils_Cave_N (19 ± 19%) using qpAdm (P = 0.28). Our results show the presence of a new post-LGM lineage in northeast Asia, represented by Khaiyrgas-1, which is distinct from the older ANS who settled the region around 38,000 years ago. This lineage contributed directly to the later groups in the region, the AP who settled the area around 9800 years ago.