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Post by Admin on Jul 17, 2023 17:33:07 GMT
Table 1Coalescent 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
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
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Post by Admin on Jul 19, 2023 19:37:26 GMT
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 21, 2023 1:28:24 GMT
Discussion In this study, by integrating ancient and contemporary mitogenomes of D4h from large-scale dataset covering virtually the whole of Eurasia, we traced the ancestry of one rare NA founder lineage (D4h3a) to a lower latitude region in northern coastal China around the Bohai and Huanghai Seas. This region is different from the geographical sources in Siberia hypothesized so far by the common maternal components, including mtDNA haplogroups A2, B2, C1, D4b1a2a1a, etc.7,17,19 Our study thus uncovered an additional ancestral source for the ancestors of NAs beyond Siberia from the matrilineal perspective. This ancestry, although only contributed to a small proportion of the mtDNA gene pool of NAs (D4h3a),25 would be important in complementing the whole picture of origination histories of early NAs. Further support comes from the Y chromosome C2-M217, which harbors an age (∼40 kya) that is similar to the one of mtDNA D4h and also probably radiated in northern coastal China during the LGM (as indicated by C2a-L1373), when the first radiation of D4h occurred. Interestingly, these uniparental ancestries echo well with the ancient ancestry in eastern Asia (∼35 kya) that gave rise to East Asians, Siberians, and NAs at ∼26 kya.3 Meanwhile, it had also been inferred that about 40–23 kya, the ancestors of Jomons split from the ancient ancestry in eastern Asia.47 This evidence strongly supports the existence of an old ancestry source, arising between 40 and 23 kya, that contributed to populations including East Asians, Jomons, Eastern Siberians, and NAs (Figure S5). We propose that mtDNA D4h was one of the matrilineal lineages that witnessed these population splits and expansions. However, different from this East Asian ancestry contributing substantially to eastern Siberia,47 D4h has been rarely found in this area. One explanation would be the loss of D4h during the expansions by genetic drift or matrilineal replacement.48 More mtDNA data from Siberia will be of help to further assess this expansion process. In addition, this genetic connection among China, the Americas, and Japan during the Pleistocene period parallels archaeological similarities, as early as Pleistocene period, among these regions. For instance, in the terminal Pleistocene period, Japanese microblades (18–17 kya), which exhibit similarities to those in Northeast Asia (including North China), display commonalities with contemporaneous stemmed points from incipient Jomon sites (∼15.5 kya).49 Importantly, stemmed points were well distributed around the Pacific rim from Japan to South America with close affinities with each other.50 Recent findings on stemmed projectile points in North America (Cooper’s Ferry site, ∼15–16 kya) show closer affinity to the nonfluted projectile points in Japan than to those in North Asia.51 We attribute this similarity in Paleolithic technology, as well as the phylogenetic relationships of D4h sub-lineages in China, the Americas, and Japan, to a probable Pleistocene connection among these regions (Figure 4B). Our results also shed important light on the dispersal route of early NAs into the Americas. Given that mtDNA D4h radiated from northern coastal China, which is geographically close to Pacific coastal rim, we speculate that D4h would have documented LGM and post-LGM dispersals along the eastern Pacific coast. This echoes well with the dispersal D4h3a along the Pacific coastal path25 when the ice-free corridor was closed.11,52 Similarly, Y chromosome C-L1373, which probably radiated in parallel with mtDNA D4h, has also been reported in South Koreans (http://koreangenome.org/) and the Nivkh,53 thus lending support to a coastal population expansion scenario initiated from northern coastal China. This, together with the Paleolithic cultural affinities along the Pacific, e.g., stemmed points,51 and the palaeoecological feasibility of maritime dispersals (e.g., kelp highway hypothesis)54 lends further support to the coastal route hypothesis of early NAs.50,51,55 Limitations of the study By dissecting the origin of a rare NA founder lineage, our study revealed an ancestral root of both NAs and the Japanese in northern coastal China. However, some detailed expansions from this region into the Americas need to be further dissected. First, more data concerning mtDNA D4h from both ancient and contemporary samples are needed to elucidate the detailed expansion history of this lineage, especially from Siberia, where a relatively low number of mitogenomes have been assessed. Second, high-resolution Y chromosome data of C-L1373 from large-scale population dataset will help to verify this radiation from paternal perspective. Third, investigations integrating mitogenomes, the Y chromosome, and autosomal genomes are also essential to explore whether there are differences between maternal, paternal, and autosomal markers and thus complement the whole picture of origination history of NAs.
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Post by Admin on Aug 1, 2023 23:53:34 GMT
Ancient Brazilian skeleton discovered to be descendant of First Americans An article to be published on July 31 in Nature Ecology & Evolution reveals that Luzio, the oldest human skeleton found in São Paulo state (Brazil), was a descendant of the ancestral population that settled the Americas at least 16,000 years ago and gave rise to all present-day Indigenous peoples, such as the Tupi. Based on the largest set of Brazilian archeological genomic data, the study reported in the article also offers an explanation for the disappearance of the oldest coastal communities, who built the icons of Brazilian archeology known as sambaquis, huge mounds of shells and fishbones used as dwellings, cemeteries and territorial boundaries. Archeologists often refer to these monuments as shell mounds or kitchen middens. After the Andean civilizations, the Atlantic coast sambaqui builders were the human phenomenon with the highest demographic density in pre-colonial South America. They were the 'kings of the coast' for thousands and thousands of years. They vanished suddenly about 2,000 years ago." André Menezes Strauss, an archeologist at the University of São Paulo's Museum of Archeology and Ethnology (MAE-USP) and principal investigator for the study The first author of the article is Tiago Ferraz.The study was supported by FAPESP (projects 17/16451-2 and 20/06527-4) and conducted in partnership with researchers at the University of Tübingen's Senckenberg Center for Human Evolution and Paleoenvironment (Germany). The authors analyzed the genomes of 34 samples from four different areas of Brazil's coast. The fossils were at least 10,000 years old. They came from sambaquis and other parts of eight sites (Cabeçuda, Capelinha, Cubatão, Limão, Jabuticabeira II, Palmeiras Xingu, Pedra do Alexandre and Vau Una). This material included Luzio, São Paulo's oldest skeleton, found in the Capelinha river midden in the Ribeira de Iguape valley by a group led by Levy Figuti, a professor at MAE-USP. The morphology of its skull is similar to that of Luzia, the oldest human fossil found to date in South America, dating from about 13,000 years ago. The researchers thought it might have belonged to a biologically different population from present-day Amerindians, who settled in what is now Brazil some 14,000 years ago, but it turns out they were mistaken. "Genetic analysis showed Luzio to be an Amerindian, like the Tupi, Quechua or Cherokee. That doesn't mean they're all the same, but from a global perspective, they all derive from a single migratory wave that arrived in the Americas not more than 16,000 years ago. If there was another population here 30,000 years ago, it didn't leave descendants among these groups," Strauss said. Luzio's DNA also answered another question. River middens are different from coastal ones, so the find cannot be considered a direct ancestor of the huge classical sambaquis that appeared later. This discovery suggests there were two distinct migrations – into the hinterland and along the coast. What happened to the sambaqui builders? Analysis of the genetic material revealed heterogeneous communities with cultural similarities but significant biological differences, especially between coastal communities in the southeast and south. "Studies of cranial morphology conducted in the 2000s had already pointed to a subtle difference between these communities, and our genetic analysis confirmed it," Strauss said. "We discovered that one of the reasons was that these coastal populations weren't isolated but 'swapped genes' with inland communities. Over thousands of years, this process must have contributed to the regional differences between sambaquis." Regarding the mysterious disappearance of this coastal civilization, comprising the first hunter-gatherers of the Holocene, analysis of the DNA samples clearly showed that, in contrast with the European Neolithic substitution of entire populations, what happened in this part of the world was a change of practices, with a decline in construction of shell middens and the introduction of pottery by sambaqui builders. For example, the genetic material found at Galheta IV ( Catarina state), the most emblematic site for the period, has remains not of shells but of ceramics and is similar to the classic sambaquis in this respect. "This information is compatible with a 2014 study that analyzed pottery shards from sambaquis and found that the pots in question were used to cook not domesticated vegetables but fish. They appropriated technology from the hinterland to process food that was already traditional there," Strauss said. Source: São Paulo Research Foundation (FAPESP) Journal reference: Ferraz, T., et al. (2023). Genomic history of coastal societies from eastern South America. Nature Ecology & Evolution. doi.org/10.1038/s41559-023-02114-9. www.nature.com/articles/s41559-023-02114-9
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