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Post by Admin on Jan 15, 2023 17:46:12 GMT
Figure 1 Geographic location and genetic profiles of newly studied individuals Results Genome-wide ancient DNA data In this study, we generate genome wide data from ten newly reported individuals from Inner Asia and northeastern Siberia, dated to as early as 7,500 BP. Genomic data from Inner Asia includes six ancient hunter-gatherer individuals from four archaeological sites in the Altai region, spanning from 7,500 to 5,500 BP (Table 1; Data S1A). Among them, one individual from the Nizhnetytkesken Cave-I was dated to ∼6,500 BP and was found in a site containing rich burial goods with a religious costume and objects interpreted as possible representation of shamanism (see STAR Methods). The genomic data from Northeast Asia encompass a 7,000-year-old hunter-gatherer from the Letuchaya Mysh Cave in the Russian Far East and three ∼500 uncalibrated BP individuals from the Kamchatka Peninsula (Figure 1). We examined contamination levels in mitochondrial DNA (mtDNA) for all individuals and on the X chromosomes for nine males. The Letuchaya Mysh individual was found to carry 14% ± 1% and 40% ± 4% contamination on the mtDNA and X chromosome, respectively, and was therefore filtered to only retain DNA fragments with the typical signature of ancient DNA.8 For all other data, contamination levels were found to be negligible (Table 1). We assigned mtDNA haplogroups for the newly reported individuals to various haplogroups known to be prevalent in Eurasia and in the Americas, such as mtDNA haplogroups C and G1b, which are dominant in Arctic Siberia and Kamchatka, respectively (Table 1). The Y chromosome haplogroups are instead assigned either to Q1a1 or C2b (Table 1), which are highly common in present-day northeastern Eurasians. Table 1 Summary information of the ancient individuals with newly reported genome-wide data
Genetic label Individual Date (95% CI) direct date Sex 1240k SNPs Y chr haplogroup mtDNA haplogroup mtDNA contam. (%) X chr contam. (%) Altai_7500BP FRS001 5,478–5,390 cal BCE M 73,258 CT U2e1b 1 ± 1 2.8 ± 6.1 FRS002 5,479–5,390 cal BCE M 653,871 Q1a1 C 2 ± 1 1.1 ± 0.3 Altai_6500BP NVR001 4,325–4,180 cal BCE M 428,365 Q1a1 D4j 2 ± 1 2.8 ± 0.8 Altai_5500BP TZB001 3,487–3,359 cal BCE M 659,140 C2b1 C4+152 2 ± 1 1.9 ± 0.4 TZB002 3,973–3,818 cal BCE M 281,236 C2b R1b 3 ± 1 5.8 ± 1.5 Nizhnetytkesken_6500BP NIZ001 4,445–4,337 cal BCE M 732,200 C2b1a1 A 1 ± 1 0.4 ± 0.1 LetuchayaMysh_7000BP Letuchaya Mysh.pmd 4,935–4,729 cal BCE M 242,242 C2b D4b1a2a – 4.7 ± 1.8 Kamchatka_500uncalBP KMT001 1,646 ± 68 14C years F 258,456 – G1b 1 ± 1 – KMT002 1,578 ± 52 14C years M 372,840 Q1a1 G1b 1 ± 1 1.1 ± 0.4 KMT003 1,118 ± 31 14C years M 320,342 Q1a1 G1b 1 ± 1 1.1 ± 0.7 See also Data S1A.
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Post by Admin on May 10, 2023 17:26:12 GMT
As the last continents to be settled by humans, the question of how and when people first came to the Americas has long intrigued scientists. A new genetics study published Tuesday in Cell Reports finds that some of the first arrivals came from China during two distinct migrations: the first during the last ice age, and the second shortly after. "Our findings indicate that besides the previously indicated ancestral sources of Native Americans in Siberia, the northern coastal China also served as a genetic reservoir contributing to the gene pool," Yu-Chun Li, one of the report authors, told AFP. Li added that during the second migration, the same lineage of people settled in Japan, which could help explain similarities in prehistoric arrowheads and spears found in the Americas, China and Japan. It was once believed that ancient Siberians, who crossed over a land bridge that existed in the Bering Strait linking modern Russia and Alaska, were the sole ancestors of Native Americans. More recent research, from the late 2000s onwards, has signaled more diverse sources from Asia could be connected to an ancient lineage responsible for founding populations across the Americas, including Bolivia, Brazil, Chile, Ecuador, Mexico and California. Known as D4h, this lineage is found in mitochondrial DNA, which is inherited only from mothers and is used to trace maternal ancestry. The team from the Kunming Institute of Zoology embarked on a ten-year hunt for D4h, combing through 100,000 modern and 15,000 ancient DNA samples across Eurasia. They eventually landed on 216 contemporary and 39 ancient individuals who came from the ancient lineage. By analyzing the mutations that had accrued over time, looking at the samples' geographic locations and using carbon dating, they were able to reconstruct the D4h lineage's origins and expansion history. The results revealed two migration events. The first was between 19,500 and 26,000 years ago during the Last Glacial Maximum, when ice sheet coverage was at its greatest and climate conditions in northern China were likely inhospitable. The second occurred during the melting period, between 19,000 and 11,500 years ago. Increasing human populations during this period might have triggered migrations. - Coastal migration - In both cases, the scientists think the travelers were seafarers who docked in America and traveled along the Pacific coast by boats. This is because a grassy passageway between two ice sheets in modern Canada, known as the "inland ice-free corridor," was not yet opened. In the second migration, a subgroup branched out from northern coastal China to Japan, contributing to the Japanese people, especially the indigenous Ainu, the study said, a finding that chimes with archeological similarities between ancient people in the Americas, China and Japan. Li said a strength of the study was the number of samples they discovered, and complementary evidence from Y chromosomal DNA showing male ancestors of Native Americans lived in northern China at the same time as the female ancestors, made them confident of their findings. "However, we don't know in which specific place in northern coastal China this expansion occurred and what specific events promoted these migrations," he said. "More evidence, especially ancient genomes, are needed to answer these questions." www.cell.com/cell-reports/fulltext/S2211-1247(23)00424-2
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Post by Admin on May 11, 2023 18:32:38 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.
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Post by Admin on May 12, 2023 18:01:43 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
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Post by Admin on May 13, 2023 18:11:47 GMT
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. We then shifted our attention to haplogroup D4h, the most recent common ancestor of D4h3. Except for the NA D4h3a, the other D4h mtDNAs were predominantly found in China, mainly in North (48 out of 150 contemporary samples, discarding four with unknown geographic information) and Central China (44 out of 150) (Table S4; Figure S3). A relatively small number of D4h mtDNAs were also identified in Northwest China (n = 14), Southwest China (n = 16), South China (n = 5), Japan (n = 13), Southeast Asia (n = 7), and North Asia (n = 2) (Table S4; Figure S3). Interestingly, the majority of the ancient D4h samples were detected in the northern regions of China (Figure 1), supporting a similar D4h distribution in the past. Further phylogeographic analyses revealed that the ancient and current samples from the same geographic region tend to cluster together in the same sub-branch, e.g., D4h1a, D4h1c, D4h1d, and D4h3. Meanwhile, most sub-haplogroups of D4h are predominant in North/Central China (i.e., D4h1b, D4h1d, D4h1e, and pre-D4h3b) or showed connections between North/Central China and other regions, including western China (D4h1c and D4h4), Japan (D4h1a), North Asia and Japan (D4h2), and even the Americas (D4h3a) (Figures 2, 3A , and S4). Moreover, samples from South China, Southwest China, Northwest China, Southeast Asia, and North Asia were sporadically distributed across the whole D4h haplogroup and primarily located on the terminal branches (Figures 2A and S2), most likely as a result of gene flow. Finally, the peculiar distributions of certain lineages, for instance D4h1a in Japan and D4h1c in Southwest China (Figures 2A, 3A, and S2), likely indicate founder events. Figure 3 Geographic 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.
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