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Post by Admin on May 14, 2023 17:47:47 GMT
Two radiation events from northern coastal China contributed to NA and Japanese gene pools Coalescent age estimations, updated by calibrated radiocarbon dates of ancient DNA samples using tip dating in BEAST (Tables 1 and S6), indicate that the radiations of D4h lineages (aged 32.39 kya, 95% highest probability density [HPD], 24.04–41.45 kya) occurred mainly within two time periods (Figure 3B). The first period fell within the Last Glacial Maximum (LGM; 26.5–19.0 kya),34 during which D4h3 (26.39 kya, 95% HPD, 20.19–33.21 kya), pre-D4h3a (22.29 kya, 95% HPD, 17.24–27.68 kya), pre-D4h3b (21.55 kya, 95% HPD, 16.18–27.94 kya), D4h1 (21.83 kya, 95% HPD, 15.56–29.08 kya), and D4h2 (20.05 kya, 95% HPD, 12.12–29.48 kya) (Tables 1 and S6) differentiated into separate sub-haplogroups (Figure 3B).
Among these sub-haplogroups, D4h3a further dispersed and became one of the pan-American haplogroup of NAs (Figure 4A ). This radiation echoes well with the divergence of basal American branches from ancient eastern Asians 23–20 kya,3 which was likely due to the LGM’s inhospitable climate in the northern regions of Asia.35 During the last deglaciation (19.0–11.5 kya), after the LGM, a second radiation of D4h occurred somewhere near the northern coast of China, as documented by D4h4 (18.11 kya, 95% HPD, 12.67–24.28 kya), D4h1c (16.17 kya, 95% HPD, 10.66–22.36 kya), D4h1a (15.59 kya, 95% HPD, 11.43–20.92 kya), D4h3b (13.22 kya, 95% HPD, 7.55–19.93 kya), D4h1c1 (12.77 kya, 95% HPD, 8.21–17.79 kya), and D4h1e (12.10, 95% HPD, 7.16–17.50 kya) (Figure 4B). Concordant with this phylogenetic radiation, a rapid increase in the effective population size of D4h ∼15 kya was observed in the extended Bayesian skyline plot (EBSP) (Figure 3C), probably due to the post-LGM climate improvement. These results uncover two waves of previously unknown population dispersals along the northern coast of China during the LGM and last deglaciation, which led to the origin and expansion of different D4h lineages (Figure 4). The regions around the Bohai, Huanghai, and East China Seas, which were still connected by land along the northern coast before the Holocene,36 probably allowed these expansions to occur.
Table 1 Coalescent ages of D4h and its sublineages Haplogroups/sub-haplogroups Number of mitogenomesa Age (mean [95% HPD]) (kya)b D4h 237 32.39 (24.04–41.45) >D4h1 112 21.83 (15.56–29.08) >>D4h1a 13 15.59 (11.43–20.92) >>>D4h1a1 12 12.24 (6.72–15.87) >>>>D4h1a1a 5 5.07 (1.83–8.56) >>>>D4h1a1b 7 5.66 (2.87–8.87) >>D4h1b 28 10.63 (6.26–15.53) >>>D4h1b1 25 7.56 (4.41–11.06) >>D4h1c 40 16.17 (10.66–22.36) >>>D4h1c1 35 12.77 (8.21–17.79) >>>>D4h1c1a 34 10.5 (7.01–14.61) >>>D4h1c2 5 7.54 (3.43–12.46) >>D4h1d 18 10.26 (6.47–14.26) >>D4h1e 13 12.10 (7.16–17.50) >D4h2 8 20.05 (12.12–29.48) >>D4h2a 7 10.78 (6.57–15.46) >D4h3 96 26.39 (20.19–33.21) >>Pre-D4h3a 73 22.29 (17.24–27.68) >>>D4h3a 71 19.40 (15.11–24.05) >>Pre-D4h3b 24 21.55 (16.18–27.94) >>>D4h3b 22 13.22 (7.55–19.93) >>>>D4h3b1 3 1.93 (0.29–4.05) >>>>D4h3b2 19 6.18 (3.31–9.56) >D4h4 21 18.11 (12.67–24.28)
a Ancient mitogenome data were included in coalescent age estimations. Incomplete sequences were excluded from age estimations (see Table S4 for details). b The mutation rate was recalibrated using the tip dating method. The best-fitting model was evaluated as previously described.37
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Post by Admin on May 15, 2023 17:32:44 GMT
Figure 4 Two subsequent population radiations in the northern coastal regions of China contributed to NA and Japanese matrilineal ancestry (A) The first radiation occurred during the LGM and involved D4h3, pre-D4h3b, and pre-D4h3a (from which D4h3a, typical of NAs, was derived). (B) A later population expansion in the same general geographic area occurred in the deglaciation period and involved D4h1a1 and D4h2, whose derivatives are found in modern Japanese and ancient Jomons. Intriguingly, two haplogroups, D4h1a1 (12.24 kya, 95% HPD, 6.72–15.87 kya) and D4h2 (20.05 kya, 95% HPD, 12.12–29.48 kya), exhibited prevalent distributions in the Japanese Archipelago (Figures 2, 3A, and S4), suggesting that the expansions from the northern coast of China also exerted an influence in Japan. The discovery of D4h1a in ancient samples dated ∼11 kya from the Nenjiang River valley38 further supports its advent in regions close to Japan at least 11 kya. Similarly, D4h2 has been observed in ancient Jomons,39 who are considered the descendants of Paleolithic settlers in the Japanese Archipelago.40 The median-joining network (Table S5; Figure S4) showed that one branch of D4h2 (namely D4h2a) in China and Southeast Asia, while the other (D4h2b) is distributed in Siberians as well as the Ainu population (indigenous Japanese, 3 of 50 samples) and ancient Jomons. This further supports a genetic contribution possibly from China to different populations including Southeast Asians and ancient Japanese. Therefore, probably both D4h1a1 and D4h2 dispersed from China to Japan after the LGM, possibly via the land bridges that connected China and the Japanese Archipelago until 12 kya.41,42 Potential supports from Y chromosome data The origin of mtDNA D4h in northern coastal China of NAs echoes well also with the differentiation of Y chromosome haplogroup C2a-L1373 (ancestor to NA founder lineages C-MPB373 and C-P39) in low-latitude regions of northern Asia.43 To further evaluate the potential radiation center of C2a-L1373, we assessed the frequencies of C2a-L1373 and its sub-lineages in different provinces of China based on Y chromosome genotyping data from 23Mofang Biotechnology Co., Ltd (totally 458,805 individuals, each with 33,000 Y chromosome SNPs genotyped). We detected the root type (C2a-L1373∗) only in North China (including Beijing [0.020%], Tianjin [0.031%], Henan [0.004%], Heilongjiang [0.030%], Jilin [0.063%], Liaoning [0.071%], Shaanxi [0.035%]) and northwest China (Gansu [0.016%]; Table S8). It is worth underscoring that the highest C2a-L1373∗ frequencies were observed in Liaoning, Jilin, Heilongjiang, Tianjin, and Beijing (Table S8), which are all located close to northern coastal China. Moreover, the majority of other C2a-L1373 sub-lineages, including C-FGC28903, which is a sister branch of C-P39, harbor their highest frequencies in North China (Table S8). Moreover, samples belonging to C2a-L1373 in other places like South Asia, Central Asia, Europe, etc., were sporadically found or mainly occupied the terminal branches.43 This evidence strongly suggests that C2a-L1373 differentiated in northern China, especially in the regions near the coast, similarly to mtDNA D4h. In addition, two ancient samples from Songnen Plain in northern China, dated ∼14,000 years ago, were found to belong to mtDNA D4h3 and Y chromosome C2a-L1373,33 thus revealing the coexistence of both maternal and paternal ancestor lineages of NAs in northern coastal China. Interestingly, C2-M217 (∼39.3 [34.7–44.5] kya)22 and D4h (∼32.39 [24.04–41.45] kya) had similar coalescent ages, and the divergence time of C2a-L1373 (about 21.6 [19.1–24.4] kya)22 is similar to the time of the first D4h radiation estimated in this study, making it likely that an ancestral population from this region contributed to both the maternal and paternal gene pools of NAs. In fact, besides lineages of mtDNA D4h and Y chromosome C2-M217, substantial maternal and paternal lineages have also been observed in this region, e.g., Y chromosome lineages C-F106744 and mtDNA haplogroups A5, D4a, D4b, D4e, N9a, etc.,29 most of which arose around the LGM.44,45 This lends support to the scenario that this region was a differentiation center in East Asia after the LGM, which probably facilitated the expansions of different lineages including mtDNA D4h3 and Y chromosome C2a-L1373. Meanwhile, Y chromosome haplogroup C2-M217 has also been observed at a higher frequency in the Ainu (15%) than in other Japanese (3%).46 Additionally, the coexistence of mtDNA D4h3 and Y chromosome C2 had also been reported in the same archaeological site in South America (∼8 kya).12 These observations collectively suggest that an ancestral population from northern China carrying mtDNA D4h and Y chromosome haplogroup C2 also spread into the Americas and the Japanese Archipelago.
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Post by Admin on Jul 2, 2023 21:57:06 GMT
Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan Summary Although it is widely recognized that the ancestors of Native Americans (NAs) primarily came from Siberia, the link between mitochondrial DNA (mtDNA) lineage D4h3a (typical of NAs) and D4h3b (found so far only in East China and Thailand) raises the possibility that the ancestral sources for early NAs were more variegated than hypothesized. Here, we analyze 216 contemporary (including 106 newly sequenced) D4h mitogenomes and 39 previously reported ancient D4h data. The results reveal two radiation events of D4h in northern coastal China, one during the Last Glacial Maximum and the other within the last deglaciation, which facilitated the dispersals of D4h sub-branches to different areas including the Americas and the Japanese archipelago. The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs. Graphical abstract Introduction As the last continent settled by modern humans, the peopling of the Americas and subsequent dispersals within the continent have been the focus of intense interest by geneticists.1,2,3,4,5,6 Previous studies have shown that the ancestors of Indigenous Americans, also called Native Americans (NAs), originated in Asia, most likely in the eastern part of Asia,3,6,7,8,9 and settled in the Americas by means of multiple dispersals through Siberia/Beringia10 via the coastal route and possibly the inland ice-free corridor,11 followed by later divergence into sub-groups.12 The origin of early NAs, to date, has been attributed to a complex process involving multiple dispersals from different source places. As indicated by substantial investigations, besides the widely recognized Siberian ancestry, ancestries from other places, although limited, have also been identified, including North Asia,6,9 East Asia,6,13 Southeast Asia,14 and even Australo-Melanesia.15 In agreement with these observations, evidence from uniparental markers further indicates that the majority of NAs show closer genetic affinity to Siberians, as manifested by NA founder types, e.g., mitochondrial DNA (mtDNA) haplogroups A2, B2, C1, C4c, D1, etc.,16,17,18,19 and Y chromosome haplogroups Q-L54 (Q-Z780, Q-M848, and Q-M4303) and C-L1373 (C-MBP373),19,20,21,22,23,24 and thus may trace their ancestral sources in Siberia. In contrast, a sister lineage of the NA matrilineal founder D4h3a,25,26 viz., D4h3b, has been so far observed only in China25 and Thailand,27,28 suggesting that the ancestral maternal sources for early NAs were not restricted to Siberia but were from a much wider Asian geographic range. To address this issue, an investigation integrating all available D4h data from a large-scale dataset covering the whole of Eurasia is needed. Given that D4h3 and its ancestor type D4h are relatively rare in contemporary populations (∼0.5%),29 we surveyed a total of 101,319 Eurasian individuals and identified the mtDNAs belonging to D4h3 and its ancestral node D4h. These included 60,979 samples for which partial sequence data, mainly hypervariable segment (HVS) data (Table S1), were available and 40,340 samples with the complete (or almost complete) mitogenome sequence (Table S2; Figure 1). This survey identified 110 mtDNAs that could be assigned unambiguously to haplogroup D4h based on mitogenome information as well as 112 mtDNAs likely belonging to D4h based on their HVS or genotyping data (Table S3), whose complete sequencing revealed 106 additional D4h mitogenomes (Figure S1). Furthermore, to reconstruct the evolutionary history of D4h, we also searched this haplogroup in 15,460 ancient samples compiled by indo-european.eu (https://indo-european.eu/ancient-dna/),30 thus covering virtually all global reported ancient mtDNA data, as well as additional 232 recently reported ancient mtDNA data from East Asia.31,32 This survey yielded 39 ancient D4h samples (30 with the entire mitogenome and nine with HVS data) (Figure 1; Tables S4 and S5), which reflected the rarity of Dh4 in ancient times. Therefore, we integrated these ancient and contemporary data of this rare haplogroup to fully investigate its origin and expansion history. www.cell.com/cell-reports/fulltext/S2211-1247(23)00424-2
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Post by Admin on Jul 14, 2023 1:02:58 GMT
Figure 1 Geographic sources of mtDNA data employed in this study Circles: populations surveyed for HVS variation are in light blue, while those surveyed for the variation of the entire mitogenome are in yellow. Only data from population surveys (99,722 samples from 1,135 populations) are shown. The remaining 1,597 mtDNAs are not shown on the map either because they were sporadic samples or because geographic information was lacking. For more details concerning the 101,319 samples, see Tables S1 and S2. Triangles: D4h samples, including published (hollow triangles) and newly sequenced samples (filled triangles). Ancient Asian samples harboring D4h mtDNAs were indicated by arrows, with the information shown on the right. The ancient samples from the Americas (see Table S4) are not shown. Results Differentiation of D4h3 and D4h in Central and North China To shed light on the origin of the NA founder D4h3a, we explored its ancestor D4h3. Our findings allowed an update of the D4h3 phylogeny and its branches (Figures 2A and S2). Specifically, to avoid any confusion, we kept the names of D4h3a and D4h3b and tentatively named their upstream nodes “pre-D4h3a” and “pre-D4h3b,” respectively. Different from the NA founder D4h3a, the other branches of D4h3 are mainly distributed in China. In detail, D4h3b1 (root type in Hebei Province in North China) is found in North and Central China, while D4h3b2 (root type in Hubei Province) is mainly distributed in Central China. Coincidentally, among the reported ancient mtDNA data from different locations in Eurasia, we found three ancient samples belonging to D4h3 dated as early as 14–15 kilo years ago (kya) in the Amur River Valley (located in northern North China).33 One of these mtDNAs, sample NE-5 (∼14 kya), derives from pre-D4h3a and is phylogenetically the closest (six mutations apart; Figure S2) to the NA founder D4h3a mitogenome. The remaining two, samples NE34 (∼14 kya) and NE-18 (∼7 kya), are both members of pre-D4h3b. Overall these findings indicate that the ancestral homeland of D4h3 is most likely Central and North China and that both branches of D4h3 were there during the Paleolithic period. These branches locate in Central/North China and reflect the closest Asian matrilineal link to D4h3a, one of the founder pan-American mtDNA haplogroups.25,26 Figure 2 Phylogeography of haplogroup D4h and its sub-lineages (A) Phylogenetic tree of D4h, with branch lengths proportional to number of variants. Circles: mitogenomes from this study; diamonds: previously published mitogenomes; black outlines: present-day samples; red outlines: ancient samples. The different colors, consistent with those in (B), refer to the different geographic source regions. (B) Geographic sources of D4h mitogenomes in (A). Numbers on the map refer to the codes of samples and correspond to those in Figure 2A and Table S3.
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Post by Admin on Jul 15, 2023 19:42:04 GMT
Figure 3Geographic distribution and schematic tree of haplogroup D4h (A) Geographic distributions of different branches of D4h. Each circle represents one sample, with geographic origin of samples shown by different colors, consistent with those in Figure 2B. Contour maps display spatial frequency distributions of haplogroups (see Table S7). Circles without outlines represent datasets from phylogenetic rather than population studies and thus were excluded in calculations of spatial frequencies. (B) Bayesian age estimates using complete mitogenomes. Sizes of triangles are proportional to sub-haplogroup sample sizes. Colors represent different geographic regions, consistent with Figure 2B. Ancient samples are indicated in red. Green and yellow diamonds show the divergences within the LGM and the last deglaciation, respectively. (C) Extended Bayesian skyline plot (EBSP) of D4h, showing effective population size changes through time. Given that some of the mitogenome data from literature are from phylogenetic rather than population studies, and given the relative scarcity of mitogenomes from Siberia, which will introduce bias to the phylogeographic analyses, we also collected and analyzed mtDNA HVS data from population studies (Table S1). Only few potential D4h samples were found in North Asian samples (n = 4,176) (for example, two belonging to D4h1d, which is defined by T16172C and C16174T, and one belonging to D4h1e, which is defined by C16174T and A16343G) (Figure S4), lending support to its rarity in North Asia. The median-joining network based on HVS data (Figure S4) revealed instead a much wider distribution range of D4h in Asia. Indeed, the majority of Asian D4h mtDNAs are observed in Central (58/228; 25.43%) and North (44/228; 21.05%) China, followed by Southwest China (35/228; 15.35%), Northwest China (15/228; 6.57%), Japan (29/228; 12.72%), Southeast Asia (11/228; 4.82%), South China (6/228; 2.63%), and North Asia (9/228; 3.94%). Moreover, the root types of the major branches, e.g., D4h1b, D4h1c, D4h1d, D4h1e, and D4h3b, are primarily found in Central and North China, while the terminal branches mainly contain samples from other regions, e.g., Southwest China, Northwest China, Southeast Asia, South Asia, and Central Asia. Finally, D4h1a and D4h2 are restricted to Japan and its surroundings, lending support to the founder events. Taken together, these results indicate that the phylogenetic differentiation of D4h occurred somewhere in Central or North China, most likely in a region geographically close to the northern coast of China. In fact, among the North/Central China samples, more than half (64/92, 69.57%) were found in provinces along (Hebei, Liaoning, Tianjin, Shandong, Jiangsu, Shanghai, and Zhejiang) or near (Heilongjiang, Jilin, Beijing, Anhui, and Jiangxi) the northern coast of China (Table S4). Therefore, we propose that the northern coast of China might have played a critical role in the divergence and spread of D4h and its sub-haplogroups. Two radiation events from northern coastal China contributed to NA and Japanese gene pools Coalescent age estimations, updated by calibrated radiocarbon dates of ancient DNA samples using tip dating in BEAST (Tables 1 and S6), indicate that the radiations of D4h lineages (aged 32.39 kya, 95% highest probability density [HPD], 24.04–41.45 kya) occurred mainly within two time periods (Figure 3B). The first period fell within the Last Glacial Maximum (LGM; 26.5–19.0 kya),34 during which D4h3 (26.39 kya, 95% HPD, 20.19–33.21 kya), pre-D4h3a (22.29 kya, 95% HPD, 17.24–27.68 kya), pre-D4h3b (21.55 kya, 95% HPD, 16.18–27.94 kya), D4h1 (21.83 kya, 95% HPD, 15.56–29.08 kya), and D4h2 (20.05 kya, 95% HPD, 12.12–29.48 kya) (Tables 1 and S6) differentiated into separate sub-haplogroups (Figure 3B). Among these sub-haplogroups, D4h3a further dispersed and became one of the pan-American haplogroup of NAs (Figure 4A ). This radiation echoes well with the divergence of basal American branches from ancient eastern Asians 23–20 kya,3 which was likely due to the LGM’s inhospitable climate in the northern regions of Asia.35 During the last deglaciation (19.0–11.5 kya), after the LGM, a second radiation of D4h occurred somewhere near the northern coast of China, as documented by D4h4 (18.11 kya, 95% HPD, 12.67–24.28 kya), D4h1c (16.17 kya, 95% HPD, 10.66–22.36 kya), D4h1a (15.59 kya, 95% HPD, 11.43–20.92 kya), D4h3b (13.22 kya, 95% HPD, 7.55–19.93 kya), D4h1c1 (12.77 kya, 95% HPD, 8.21–17.79 kya), and D4h1e (12.10, 95% HPD, 7.16–17.50 kya) (Figure 4B). Concordant with this phylogenetic radiation, a rapid increase in the effective population size of D4h ∼15 kya was observed in the extended Bayesian skyline plot (EBSP) (Figure 3C), probably due to the post-LGM climate improvement. These results uncover two waves of previously unknown population dispersals along the northern coast of China during the LGM and last deglaciation, which led to the origin and expansion of different D4h lineages (Figure 4). The regions around the Bohai, Huanghai, and East China Seas, which were still connected by land along the northern coast before the Holocene,36 probably allowed these expansions to occur.
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