Post by Admin on Oct 13, 2021 20:59:47 GMT
Complex Transition between the Early Neolithic and Bronze Age in the Lake Baikal Region
A previous study described the transition between Early Neolithic and Bronze Age populations from the Lake Baikal region as the result of a discrete admixture event of ANE ancestry into the local gene pool (Damgaard et al., 2018a). In this study, we combined the newly sequenced Baikal_EN and Baikal_LNBA individuals with published data from the same time period (Figure 1C) and analyze these two combined datasets, Baikal_EN_all (n = 19) and Baikal_LNBA_all (n = 34), to better elucidate the genetic transition that occurred in this region. Prior to analyzing the combined groups, we confirmed the similarity between the new individuals and published groups using outgroup f3 statistics. Both Baikal_EN and Baikal_LNBA groups showed the highest genetic affinity with published Early Neolithic and LNBA Baikal populations, respectively (Table S4).
From outgroup f3 statistics of the combined groups, we found both of the Baikal Early Neolithic and LNBA groups to be sharing high genetic affinity with ancient and modern northeast Asian and Siberian populations (Figure S3). The LNBA Baikal population also showed a high genetic affinity with the Paleo-Eskimo Saqqaq individual. Compared to their NEA proxy, they both carried extra genetic affinity with ANE-related populations while the LNBA population more so than the Early Neolithic population, as shown by f4 statistics (Figure S3). These results revealed the existence of ANE-related ancestry in the Early Neolithic population and, at the same time, validated the previous finding that an extra ANE ancestry gene flow is responsible for the genetic shift between Early Neolithic and Bronze Age Baikal populations.
Figure S3. Genetic Affinity of Combined Baikal Populations with Worldwide Population, Related to Figure 3
The outgroup f3-statistics in the form of (A) f3(Mbuti, X; Baikal_EN_all) and (B) f3(Mbuti, X; Baikal_LNBA_all) are applied to measure the genetic affinity of Early Neolithic and LNBA Baikal individuals with worldwide population. The ten population with highest f3 are shown in diamonds. Then (C) f4(Mbuti, X; Devil’s Gate, Baikal_EN_all) and (D) f4(Mbuti, X; Baikal_EN_all, Baikal_LNBA_all) are used to show the genetic difference between NEA ancestry, Early Neolithic Baikal population and LNBA Baikal population.
We further applied qpAdm modeling to quantify the proportion of ANE-related ancestry in Early Neolithic and LNBA Baikal populations, Saqqaq and Nganasan. Using Devil’s Gate as the NEA proxy, the Upper Paleolithic UKY was found to be a better fit than Kolyma as the ANE-related proxy for both Baikal populations, while AG3 provided a good fit for the Early Neolithic population (Table S5). Using Devil’s Gate and AG3 as the two proxies of NEA and ANE ancestries, respectively, we estimated the ANE-related ancestry increasing from 14.3% in the Early Neolithic Baikal population to 22.7% in the LNBA population (Figure 3A; Table S3). Of note, the northeastern Siberian Kolyma individual could work as a sufficient ANE proxy for Saqqaq, as described in the study where this genome was first reported (Sikora et al., 2019) but did not provide a good fit for the Baikal populations and Nganasan. This suggests that the Baikal hunter-gatherer and Nganasan populations are more likely to have formed in central or southern Siberia while Paleo-Eskimo ancestry could have emerged in either central or northeastern Siberia.
Figure 3. Genetic Modeling of Early Neolithic to Bronze Age Baikal Individuals and Admixture Dating
(A) qpAdm modeling of Early Neolithic and LNBA Baikal populations, together with Nganasan and Saqqaq, as admixture between NEA ancestry represented by Devil’s Gate and different ANE ancestries. The error bars show the standard errors of estimated ancestry proportions. Details for the modeling are provided in Table S3.
(B) Estimated dates of admixture events between ANE and NEA ancestries in Early Neolithic and LNBA Baikal population. The individual ages are the averages and standard deviations of median radiocarbon dates without correcting for freshwater reservoir effect, to be consistent with previously published individuals. The estimated admixture dates are calculated with generation time of 29 years, and the error bars show the sum of standard errors of DATES estimations and individual ages.
See also Figures S3 and S4 and Tables S3, S4, and S5.
Furthermore, the program DATES was used to date the admixture events between ANE and NEA ancestries in the Baikal population based on the decay of ancestry covariance (Moorjani and Patterson, 2018). We detected a recent admixture signal in the Early Neolithic population, estimated to around 21 generations ago, while the admixture signal in LNBA population was dated to 71 generations ago, although this group harbored significantly more ANE-related ancestry (Table S5). When considering the average radiocarbon date of each population and the standard errors of their admixture dates, we identified contiguous intervals for the admixture events that spanned ∼8,500–6,000 BP, considering a generation time of 29 years (Figure 3B; Figure S4; Table S1; Table S5). Assuming a dating offset of 400–500 years due to freshwater reservoir effect estimated for the newly reported individuals, the admixture timings ranged between ∼8,000 and 5,500 BP. This suggests that both Baikal populations could have been formed through an extended admixture process between local groups and northeast Asian-related populations. The Early Neolithic groups were thus found to have experienced a prolonged admixture process, in contrast to the discrete and rather abrupt event suggested earlier (Damgaard et al., 2018a). This admixture, however, did not continue substantially in the Late Neolithic and Bronze Age, as suggested by the older admixture date for the LNBA population (Figure 3B) and the relatively larger genetic variation among Early Neolithic individuals compared to the homogeneous LNBA cluster, as shown in the PCA plot (Figure 1C).
Figure S4. Dating of the Admixture Events in Baikal, Okunevo Population, and the BZK002 Individual, Related to Figures 3 and 5 and Table S5
This figure shows the DATES estimation of (A) time of admixture events in Early Neolithic and LNBA Baikal population and (B) time of admixture events in Okunevo population and BZK002 with different ancestor pairs. The red cross dots show the weighted ancestry covariance in different genetic distances, and the green curves show the exponential fitting starting at 0.5 cM. Details of the results are listed in Table S5.
A previous study described the transition between Early Neolithic and Bronze Age populations from the Lake Baikal region as the result of a discrete admixture event of ANE ancestry into the local gene pool (Damgaard et al., 2018a). In this study, we combined the newly sequenced Baikal_EN and Baikal_LNBA individuals with published data from the same time period (Figure 1C) and analyze these two combined datasets, Baikal_EN_all (n = 19) and Baikal_LNBA_all (n = 34), to better elucidate the genetic transition that occurred in this region. Prior to analyzing the combined groups, we confirmed the similarity between the new individuals and published groups using outgroup f3 statistics. Both Baikal_EN and Baikal_LNBA groups showed the highest genetic affinity with published Early Neolithic and LNBA Baikal populations, respectively (Table S4).
From outgroup f3 statistics of the combined groups, we found both of the Baikal Early Neolithic and LNBA groups to be sharing high genetic affinity with ancient and modern northeast Asian and Siberian populations (Figure S3). The LNBA Baikal population also showed a high genetic affinity with the Paleo-Eskimo Saqqaq individual. Compared to their NEA proxy, they both carried extra genetic affinity with ANE-related populations while the LNBA population more so than the Early Neolithic population, as shown by f4 statistics (Figure S3). These results revealed the existence of ANE-related ancestry in the Early Neolithic population and, at the same time, validated the previous finding that an extra ANE ancestry gene flow is responsible for the genetic shift between Early Neolithic and Bronze Age Baikal populations.
Figure S3. Genetic Affinity of Combined Baikal Populations with Worldwide Population, Related to Figure 3
The outgroup f3-statistics in the form of (A) f3(Mbuti, X; Baikal_EN_all) and (B) f3(Mbuti, X; Baikal_LNBA_all) are applied to measure the genetic affinity of Early Neolithic and LNBA Baikal individuals with worldwide population. The ten population with highest f3 are shown in diamonds. Then (C) f4(Mbuti, X; Devil’s Gate, Baikal_EN_all) and (D) f4(Mbuti, X; Baikal_EN_all, Baikal_LNBA_all) are used to show the genetic difference between NEA ancestry, Early Neolithic Baikal population and LNBA Baikal population.
We further applied qpAdm modeling to quantify the proportion of ANE-related ancestry in Early Neolithic and LNBA Baikal populations, Saqqaq and Nganasan. Using Devil’s Gate as the NEA proxy, the Upper Paleolithic UKY was found to be a better fit than Kolyma as the ANE-related proxy for both Baikal populations, while AG3 provided a good fit for the Early Neolithic population (Table S5). Using Devil’s Gate and AG3 as the two proxies of NEA and ANE ancestries, respectively, we estimated the ANE-related ancestry increasing from 14.3% in the Early Neolithic Baikal population to 22.7% in the LNBA population (Figure 3A; Table S3). Of note, the northeastern Siberian Kolyma individual could work as a sufficient ANE proxy for Saqqaq, as described in the study where this genome was first reported (Sikora et al., 2019) but did not provide a good fit for the Baikal populations and Nganasan. This suggests that the Baikal hunter-gatherer and Nganasan populations are more likely to have formed in central or southern Siberia while Paleo-Eskimo ancestry could have emerged in either central or northeastern Siberia.
Figure 3. Genetic Modeling of Early Neolithic to Bronze Age Baikal Individuals and Admixture Dating
(A) qpAdm modeling of Early Neolithic and LNBA Baikal populations, together with Nganasan and Saqqaq, as admixture between NEA ancestry represented by Devil’s Gate and different ANE ancestries. The error bars show the standard errors of estimated ancestry proportions. Details for the modeling are provided in Table S3.
(B) Estimated dates of admixture events between ANE and NEA ancestries in Early Neolithic and LNBA Baikal population. The individual ages are the averages and standard deviations of median radiocarbon dates without correcting for freshwater reservoir effect, to be consistent with previously published individuals. The estimated admixture dates are calculated with generation time of 29 years, and the error bars show the sum of standard errors of DATES estimations and individual ages.
See also Figures S3 and S4 and Tables S3, S4, and S5.
Furthermore, the program DATES was used to date the admixture events between ANE and NEA ancestries in the Baikal population based on the decay of ancestry covariance (Moorjani and Patterson, 2018). We detected a recent admixture signal in the Early Neolithic population, estimated to around 21 generations ago, while the admixture signal in LNBA population was dated to 71 generations ago, although this group harbored significantly more ANE-related ancestry (Table S5). When considering the average radiocarbon date of each population and the standard errors of their admixture dates, we identified contiguous intervals for the admixture events that spanned ∼8,500–6,000 BP, considering a generation time of 29 years (Figure 3B; Figure S4; Table S1; Table S5). Assuming a dating offset of 400–500 years due to freshwater reservoir effect estimated for the newly reported individuals, the admixture timings ranged between ∼8,000 and 5,500 BP. This suggests that both Baikal populations could have been formed through an extended admixture process between local groups and northeast Asian-related populations. The Early Neolithic groups were thus found to have experienced a prolonged admixture process, in contrast to the discrete and rather abrupt event suggested earlier (Damgaard et al., 2018a). This admixture, however, did not continue substantially in the Late Neolithic and Bronze Age, as suggested by the older admixture date for the LNBA population (Figure 3B) and the relatively larger genetic variation among Early Neolithic individuals compared to the homogeneous LNBA cluster, as shown in the PCA plot (Figure 1C).
Figure S4. Dating of the Admixture Events in Baikal, Okunevo Population, and the BZK002 Individual, Related to Figures 3 and 5 and Table S5
This figure shows the DATES estimation of (A) time of admixture events in Early Neolithic and LNBA Baikal population and (B) time of admixture events in Okunevo population and BZK002 with different ancestor pairs. The red cross dots show the weighted ancestry covariance in different genetic distances, and the green curves show the exponential fitting starting at 0.5 cM. Details of the results are listed in Table S5.