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Lin M, Trejaut JA. Diversity and distribution of mitochondrial DNA in non-Austronesian-speaking Taiwanese individuals. Hum Genome Var 2023; 10:2. [PMID: 36653363 PMCID: PMC9849472 DOI: 10.1038/s41439-022-00228-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 11/12/2022] [Accepted: 11/22/2022] [Indexed: 01/19/2023] Open
Abstract
Many studies have described the diversity of Austronesian-speaking Taiwanese people to shed more light on their origin and their connection with the "Out of Taiwan" migrations. However, the genetic relationship between the non-Austronesian-speaking groups of Taiwan and the populations of continental Asia is still unclear. Here, we studied the diversity of mtDNA in 767 non-Austronesian speakers from 16 locations in Taiwan using partial sequencing obtained from the hypervariable segment I (HVS-I) and coding regions 8,001-9,000 and 9.801-10,900 and 85 complete mtDNA genome sequences. Bayesian analysis of population structure was used to examine their relationship with over 3662 individuals representing indigenous groups of Taiwan, continental East Asia, Japan, and Island Southeast Asia. The whole analysis identified 278 haplotypes. Complete genomes revealed 62 novel subhaplogroups, of which 31 were exclusive to Taiwan. Estimates of coalescence times of all subhaplogroups showed peaks of diversification greater than 5.0 kya, likely characterizing gene flow from continental East Asian groups but not excluding in situ Taiwanese ancestry. Furthermore, a significant number of clades exclusive to non-Austronesian speakers of Taiwan (NAN_Tw) showed coalescence peaks between 1.0 and 2.6 kya, suggesting possible late Neolithic to early metal age settlements of NAN_Tw and local expansion in Taiwan.
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Affiliation(s)
- Marie Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
| | - Jean A Trejaut
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
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2
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Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop—Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan. PLoS One 2022; 17:e0272680. [PMID: 36178903 PMCID: PMC9524695 DOI: 10.1371/journal.pone.0272680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/10/2022] [Indexed: 11/23/2022] Open
Abstract
‘Breadfruit’ is a common tree species in Taiwan. In the indigenous Austronesian Amis culture of eastern Taiwan, ‘breadfruit’ is known as Pacilo, and its fruits are consumed as food. On Lanyu (Botel Tobago) where the indigenous Yami people live, ‘breadfruit’ is called Cipoho and used for constructing houses and plank-boats. Elsewhere in Taiwan, ‘breadfruit’ is also a common ornamental tree. As an essential component of traditional Yami culture, Cipoho has long been assumed to have been transported from the Batanes Island of the Philippines to Lanyu. As such, it represents a commensal species that potentially can be used to test the hypothesis of the northward Austronesian migration ‘into’ Taiwan. However, recent phylogenomic studies using target enrichment show that Taiwanese ‘breadfruit’ might not be the same as the Pacific breadfruit (Artocarpus altilis), which was domesticated in Oceania and widely cultivated throughout the tropics. To resolve persistent misidentification of this culturally and economically important tree species of Taiwan, we sampled 36 trees of Taiwanese Artocarpus and used the Moraceae probe set to enrich 529 nuclear genes. Along with 28 archived Artocarpus sequence datasets (representing a dozen taxa from all subgenera), phylogenomic analyses showed that all Taiwanese ‘breadfruit’ samples, together with a cultivated ornamental tree from Hawaii, form a fully supported clade within the A. treculianus complex, which is composed only of endemic Philippine species. Morphologically, the Taiwanese ‘breadfruit’ matches the characters of A. treculianus. Within the Taiwanese samples of A. treculianus, Amis samples form a fully supported clade derived from within the paraphyletic grade composed of Yami samples, suggesting a Lanyu origin. Results of our target enrichment phylogenomics are consistent with the scenario that Cipoho was transported northward from the Philippines to Lanyu by Yami ancestors, though the possibility that A. treculianus is native to Lanyu cannot be ruled out completely.
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Wu DL, Shih HC, Wang JK, Teng HJ, Kuo CC. Commensal Rodent Habitat Expansion Enhances Arthropod Disease Vectors on a Tropical Volcanic Island. Front Vet Sci 2021; 8:736216. [PMID: 34692809 PMCID: PMC8531417 DOI: 10.3389/fvets.2021.736216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022] Open
Abstract
On volcanic islands, the release of animals from predators and competitors can lead to increased body size and population density as well as the expanded habitat use of introduced animals relative to their mainland counterparts. Such alterations might facilitate the spread of diseases on islands when these exotic animals also carry pathogenic agents; however, this has rarely been investigated. The commensal Asian house rat (Rattus tanezumi) is confined to human residential surroundings in mainland Taiwan but can be observed in the forests of nearby Orchid Island, which is a tropical volcanic island. Orchid Island is also a hot spot for scrub typhus, a lethal febrile disease transmitted by larval trombiculid mites (chiggers) that are infected primarily with the rickettsia Orientia tsutsugamushi (OT). We predicted an increase in chigger abundance when rodents (the primary host of chiggers) invade forests from human settlements since soils are largely absent in the latter habitat but necessary for the survival of nymphal and adult mites. A trimonthly rodent survey at 10 sites in three habitats (human residential, grassland, and forest) found only R. tanezumi and showed more R. tanezumi and chiggers in forests than in human residential sites. There was a positive association between rodent and chigger abundance, as well as between rodent body weight and chigger load. Lastly, >95% of chiggers were Leptotrombidium deliense and their OT infection rates were similar among all habitats. Our study demonstrated potentially elevated risks of scrub typhus when this commensal rat species is allowed to invade natural habitats on islands. Additionally, while the success of invasive species can be ascribed to their parasites being left behind, island invaders might instead obtain more parasites if the parasite requires only a single host (e.g., trombiculid mite), is a host generalist (e.g., L. deliense), and is transferred from unsuitable to suitable habitats (i.e., human settlements on the mainland to forests on an island).
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Affiliation(s)
- De-Lun Wu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Han-Chun Shih
- Epidemic Intelligence Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Jen-Kai Wang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Hwa-Jen Teng
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Chi-Chien Kuo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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4
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Tätte K, Metspalu E, Post H, Palencia-Madrid L, Luis JR, Reidla M, Rea A, Tamm E, Moding EJ, de Pancorbo MM, Garcia-Bertrand R, Metspalu M, Herrera RJ. The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations. Eur J Hum Genet 2021; 29:1092-1102. [PMID: 33753914 PMCID: PMC8298601 DOI: 10.1038/s41431-021-00837-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/20/2021] [Accepted: 02/18/2021] [Indexed: 11/09/2022] Open
Abstract
This article reports on the genetic characteristics of the Ami and Yami, two aboriginal populations of Taiwan. Y-SNP and mtDNA markers as well as autosomal SNPs were utilized to investigate the phylogenetic relationships to groups from MSEA (mainland Southeast Asia), ISEA (island Southeast Asia), and Oceania. Both the Ami and Yami have limited genetic diversity, with the Yami having even less diversity than the Ami. The partitioning of populations within the PCA plots based on autosomal SNPs, the profile constitution observed in the structure analyses demonstrating similar composition among specific populations, the average IBD (identical by descent) tract length gradients, the average total length of genome share among the populations, and the outgroup f3 results all indicate genetic affinities among populations that trace a geographical arc from Taiwan south into the Philippine Archipelago, Borneo, Indonesia, and Melanesia. Conversely, a more distant kinship between the Ami/Yami and MSEA based on all the markers examined, the total mtDNA sequences as well as the admixture f3 and f4 analyses argue against strong genetic contribution from MSEA to the Austronesian dispersal. The sharing of long IBD tracts, total genome length, and the large number of segments in common between the Ami/Yami and the Society Archipelago populations East Polynesia standout considering they are located about 10,700 km apart.
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Affiliation(s)
- Kai Tätte
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helen Post
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Javier Rodríguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anneliis Rea
- Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu, Estonia
| | - Erika Tamm
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA, USA
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | | | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, USA.
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Sun J, Li YX, Ma PC, Yan S, Cheng HZ, Fan ZQ, Deng XH, Ru K, Wang CC, Chen G, Wei LH. Shared paternal ancestry of Han, Tai-Kadai-speaking, and Austronesian-speaking populations as revealed by the high resolution phylogeny of O1a-M119 and distribution of its sub-lineages within China. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:686-700. [PMID: 33555039 DOI: 10.1002/ajpa.24240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The aim of this research was to explore the origin, diversification, and demographic history of O1a-M119 over the past 10,000 years, as well as its role during the formation of East Asian and Southeast Asian populations, particularly the Han, Tai-Kadai-speaking, and Austronesian-speaking populations. MATERIALS AND METHODS Y-chromosome sequences (n = 141) of the O1a-M119 lineage, including 17 newly generated in this study, were used to reconstruct a revised phylogenetic tree with age estimates, and identify sub-lineages. The geographic distribution of 12 O1a-M119 sub-lineages was summarized, based on 7325 O1a-M119 individuals identified among 60,009 Chinese males. RESULTS A revised phylogenetic tree, age estimation, and distribution maps indicated continuous expansion of haplogroup O1a-M119 over the past 10,000 years, and differences in demographic history across geographic regions. We propose several sub-lineages of O1a-M119 as founding paternal lineages of Han, Tai-Kadai-speaking, and Austronesian-speaking populations. The sharing of several young O1a-M119 sub-lineages with expansion times less than 6000 years between these three population groups supports a partial common ancestry for them in the Neolithic Age; however, the paternal genetic divergence pattern is much more complex than previous hypotheses based on ethnology, archeology, and linguistics. DISCUSSION Our analyses contribute to a better understanding of the demographic history of O1a-M119 sub-lineages over the past 10,000 years during the emergence of Han, Austronesians, Tai-Kadai-speaking populations. The data described in this study will assist in understanding of the history of Han, Tai-Kadai-speaking, and Austronesian-speaking populations from ethnology, archeology, and linguistic perspectives in the future.
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Affiliation(s)
- Jin Sun
- Xingyi Normal University for Nationalities, Xingyi, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Ying-Xiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Kai Ru
- Enlighten Co., Ltd., Shanghai, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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Sun J, Wei LH, Wang LX, Huang YZ, Yan S, Cheng HZ, Ong RTH, Saw WY, Fan ZQ, Deng XH, Lu Y, Zhang C, Xu SH, Jin L, Teo YY, Li H. Paternal gene pool of Malays in Southeast Asia and its applications for the early expansion of Austronesians. Am J Hum Biol 2020; 33:e23486. [PMID: 32851723 DOI: 10.1002/ajhb.23486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/16/2020] [Accepted: 07/10/2020] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES The origin and differentiation of Austronesian populations and their languages have long fascinated linguists, archeologists, and geneticists. However, the founding process of Austronesians and when they separated from their close relatives, such as the Daic and Austro-Asiatic populations in the mainland of Asia, remain unclear. In this study, we explored the paternal origin of Malays in Southeast Asia and the early differentiation of Austronesians. MATERIALS AND METHODS We generated whole Y-chromosome sequences of 50 Malays and co-analyzed 200 sequences from other Austronesians and related populations. We generated a revised phylogenetic tree with time estimation. RESULTS We identified six founding paternal lineages among the studied Malays samples. These founding lineages showed a surprisingly coincident expansion age at 5000 to 6000 years ago. We also found numerous mostly close related samples of the founding lineages of Malays among populations from Mainland of Asia. CONCLUSION Our analyses provided a refined phylogenetic resolution for the dominant paternal lineages of Austronesians found by previous studies. We suggested that the co-expansion of numerous founding paternal lineages corresponds to the initial differentiation of the most recent common ancestor of modern Austronesians. The splitting time and divergence pattern in perspective of paternal Y-chromosome evidence are highly consistent with the previous theories of ethnologists, linguists, and archeologists.
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Affiliation(s)
- Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | | | - Yun-Zhi Huang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Yan Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China
| | - Chao Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Shu-Hua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Hui Li
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China.,MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
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Abstract
Despite the efforts made to reconstruct the history of modern humans, there are still poorly explored regions that are key for understanding the phylogeography of our species. One of them is the Philippines, which is crucial to unravel the colonization of Southeast Asia and Oceania but where little is known about when and how the first humans arrived. In order to shed light into this settlement, we collected samples from 157 individuals of the Philippines with the four grandparents belonging to the same region and mitochondrial variants older than 20,000 years. Next, we analyzed the hypervariable I mtDNA region by approximate Bayesian computation based on extensive spatially explicit computer simulations to select among several migration routes towards the Philippines and to estimate population genetic parameters of this colonization. We found that the colonization of the Philippines occurred more than 60,000 years ago, with long-distance dispersal and from both north and south migration routes. Our results also suggest an environmental scenario especially optimal for humans, with large carrying capacity and population growth, in comparison to other regions of Asia. In all, our study suggests a rapid expansion of modern humans towards the Philippines that could be associated with the establisment of maritime technologies and favorable environmental conditions.
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Altafi D, Sadeghi S, Hojatian H, Torabi Afra M, Pakizeh Kar S, Gorji M, Houshmand M. Mitochondrial Polymorphisms, in The D-Loop Area, Are Associated with Brain Tumors. CELL JOURNAL 2019; 21:350-356. [PMID: 31210442 PMCID: PMC6582428 DOI: 10.22074/cellj.2019.5947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 10/29/2018] [Indexed: 11/18/2022]
Abstract
Objective This study was carried out to evaluate the relationship between mtDNA D-loop variations and the
pathogenesis of a brain tumor.
Materials and Methods In this experimental study, 25 specimens of brain tumor tissue with their adjacent tissues
from patients and 454 blood samples from different ethnic groups of the Iranian population, as the control group, were
analysed by the polymerase chain reaction (PCR)-sequencing method.
Results Thirty-six variations of the D-loop area were observed in brain tumor tissues as well as the adjacent normal
tissues. A significant difference of A750G (P=0.046), T15936C (P=0.013), C15884G (P=0.013), C16069T (P=0.049),
T16126C (P=0.006), C16186T (P=0.022), T16189C (P=0.041), C16193T (P=0.045), C16223T (P=0.001), T16224C
(P=0.013), C16234T (P=0.013), G16274A (P=0.009), T16311C (P=0.038), C16327T (P=0.045), C16355T (P=0.003),
T16362C (P=0.006), G16384A (P=0.042), G16392A (P=0.013), G16394A (P=0.013), and G16477A (P=0.013) variants
was found between the patients and the controls.
Conclusion The results indicated individuals with C16069T [odds ratio (OR): 2.048], T16126C (OR: 2.226), C16186T
(OR: 3.586), G16274A (OR: 4.831), C16355T (OR: 7.322), and T16362C (OR: 6.682) variants with an OR more than
one are probably associated with a brain tumor. However, given the multifactorial nature of cancer, more investigation
needs to be done to confirm this association.
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Affiliation(s)
- Donya Altafi
- Molecular Biology Department, NourDanesh Institute of Higher Education, Esfahan, Iran. Electronic Address:
| | - Soha Sadeghi
- Molecular Biology Department, NourDanesh Institute of Higher Education, Esfahan, Iran
| | - Hamed Hojatian
- Molecular Biology Department, NourDanesh Institute of Higher Education, Esfahan, Iran
| | - Maryam Torabi Afra
- Molecular Biology Department, NourDanesh Institute of Higher Education, Esfahan, Iran
| | | | - Mojtaba Gorji
- Department of Hematology and Oncology, Lorestan Medical University, Lorestan, Iran
| | - Massoud Houshmand
- Department of Medical Genetics, National Institutes for Genetic Engineering and Biotechnology, Tehran, Iran.,Research Center, Knowledge University, Erbil, Kurdistan Region, Iraq.Electronic Address:
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Trejaut JA, Muyard F, Lai YH, Chen LR, Chen ZS, Loo JH, Huang JY, Lin M. Genetic diversity of the Thao people of Taiwan using Y-chromosome, mitochondrial DNA and HLA gene systems. BMC Evol Biol 2019; 19:64. [PMID: 30813905 PMCID: PMC6391829 DOI: 10.1186/s12862-019-1389-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 02/13/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite attempts in retracing the history of the Thao people in Taiwan using folktales, linguistics, physical anthropology, and ethnic studies, their history remains incomplete. The heritage of Thao has been associated with the Pazeh Western plains peoples and several other mountain peoples of Taiwan. In the last 400 years, their culture and genetic profile have been reshaped by East Asian migrants. They were displaced by the Japanese and the construction of a dam and almost faced extinction. In this paper, genetic information from mitochondrial DNA (mtDNA), Histoleucocyte antigens (HLA), and the non-recombining Y chromosome of 30 Thao individuals are compared to 836 other Taiwan Mountain and Plains Aborigines (TwrIP & TwPp), 384 Non-Aboriginal Taiwanese (non-TwA) and 149 Continental East Asians. RESULTS The phylogeographic analyses of mtDNA haplogroups F4b and B4b1a2 indicated gene flow between Thao, Bunun, and Tsou, and suggested a common ancestry from 10,000 to 3000 years ago. A claim of close contact with the heavily Sinicized Pazeh of the plains was not rejected and suggests that the plains and mountain peoples most likely shared the same Austronesian agriculturist gene pool in the Neolithic. CONCLUSIONS Having been moving repeatedly since their arrival in Taiwan between 6000 and 4500 years ago, the Thao finally settled in the central mountain range. They represent the last plains people whose strong bonds with their original culture allowed them to preserve their genetic heritage, despite significant gene flow from the mainland of Asia. Representing a considerable contribution to the genealogical history of the Thao people, the findings of this study bear on ongoing anthropological and linguistic debates on their origin.
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Affiliation(s)
- Jean A Trejaut
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
| | - Frank Muyard
- Department of French Studies, National Central University, Taoyuan Taiwan & French School of Asian Studies (EFEO), Taoyuan, Taiwan
| | - Ying-Hui Lai
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Lan-Rong Chen
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Zong-Sian Chen
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Jun-Hun Loo
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Jin-Yuan Huang
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Marie Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
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10
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Li L, Xu Y, Luis JR, Alfonso-Sanchez MA, Zeng Z, Garcia-Bertrand R, Herrera RJ. Cebú, Thailand and Taiwanese aboriginal populations according to Y-STR loci. Gene 2019; 721S:100001. [PMID: 34530985 PMCID: PMC7286082 DOI: 10.1016/j.gene.2018.100001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 11/20/2022]
Abstract
Here we report for the first time the Y27-STR Yfiler plus profiles of the insular population of Cebú in the central region of the Philippine Archipelago and the general continental population of Thailand, two strategic locations of interest in connection with the Austronesian expansion. Traditionally, the peopling of Taiwan has been envisioned as a single wave of agriculturists migrating from mainland Southeast Asia. Yet, more recent data support a scenario in which a number of migrations from the continent populated the island. Genetic affinity parameters from this study indicate that certain Formosan tribes are genetically closer to geographical distant populations in the Solomon Island than to other nearby Taiwanese tribes. Furthermore, Taiwanese aboriginal populations in this study partition into three clusters, one associated with populations from the Philippines and Thailand, a second one segregating with populations of the Solomon Islands and a third grouping made up exclusively of Taiwanese aboriginal tribes. The populations within each of these three clusters exhibit different degrees of differentiation among them suggesting unique population histories. All together, these differential genetic affinities of specific Taiwanese tribes to groups from different geographical regions and to each other are compatible with multiple origins of the Austronesian expansion from Formosa as well as from mainland Southeast Asia. Partitioning of Taiwanese aboriginal populations into three clusters. The middle cluster includes the populations from Cebú and Thailand. A second cluster segregates with populations of the Solomon Islands. A third cluster is made up exclusively of Taiwanese aboriginal tribes. Some Formosan tribes are genetically closer to geographical distant Solomon Island populations.
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Affiliation(s)
- Li Li
- Department of Obstetrics & Gynecology, Zhengzhou Central Hospital, Zhengzhou University, Henan, China
| | - Yanli Xu
- Department of Criminal Police, Chifeng City, China
| | - Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Miguel A Alfonso-Sanchez
- Departamento de Genetica y Antropologia Fisica, Facultad de Ciencia y Tecnologia, Universidad del Pais Vasco (UPV/EHU), Bilbao, Spain
| | - Zhaoshu Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, China
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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11
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Kuo SM, Chen YR, Yin SY, Ba QX, Tsai YC, Kuo WHJ, Lin YR. Waxy allele diversification in foxtail millet (Setaria italica) landraces of Taiwan. PLoS One 2018; 13:e0210025. [PMID: 30596758 PMCID: PMC6312202 DOI: 10.1371/journal.pone.0210025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/14/2018] [Indexed: 12/19/2022] Open
Abstract
Foxtail millet (Setaria italica (L.) P. Beauv.), the second most cultivated millet species, is well adapted to diverse environments and remains an important cereal food and forage crop in arid and semiarid regions worldwide. A symbolic crop for indigenous Austronesian peoples, foxtail millet has been cultivated in Taiwan for more than 5,000 years, and landraces reflect diversifying selection for various food applications. A total of 124 accessions collected within Taiwan were assessed for Wx genotypes. Four identified Wx alleles, I, III, IV, and IX were caused by insertion of various transposable elements (TEs) and resulted in endosperm with non-waxy, low amylose content (AC), and waxy, respectively. A total of 16.9%, 4.0%, 49.2%, and 29.8% of accessions were classified as type I, III, IV, and IX, respectively; approximately half of the accessions belonged to the waxy type, indicating that glutinous grains were favored for making traditional food and wine. The TE insertion affected splicing efficiency rather than accuracy, leading to significantly reduced expression of wx in types III, IV, and IX, although their transcripts were the same as wild-type, type I. Consequently, the granule-bound starch synthase I (GBSSI) contents of the three mutated genotypes were relatively low, leading to waxy or low AC endosperm, and the Wx genotypes could explain 78% of variance in AC. The geographic distribution of Wx genotypes are associated with culinary preferences and migration routes of Taiwanese indigenous peoples-in particular, the genotype of landraces collected from Orchid Island was distinct from those from Taiwan Island. This information on the major gene regulating starch biosynthesis in foxtail millet endosperm can be applied to breeding programs for grain quality, and contributes to knowledge of Austronesian cultures.
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Affiliation(s)
- Shu-meng Kuo
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yu-ru Chen
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Song-yu Yin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Qing-xiong Ba
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yuan-ching Tsai
- Department of Agronomy, National Chiayi University, Chiayi, Taiwan
| | - Warren H. J. Kuo
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yann-rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
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12
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Improved phylogenetic resolution for Y-chromosome Haplogroup O2a1c-002611. Sci Rep 2017; 7:1146. [PMID: 28442769 PMCID: PMC5430735 DOI: 10.1038/s41598-017-01340-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/28/2017] [Indexed: 11/25/2022] Open
Abstract
Y-chromosome Haplogroup O2a1c-002611 is one of the dominant lineages of East Asians and Southeast Asians. However, its internal phylogeny remains insufficiently investigated. In this study, we genotyped 89 new highly informative single nucleotide polymorphisms (SNPs) in 305 individuals with Haplogroup O2a1c-002611 identified from 2139 Han Chinese males. Two major branches were identified, O2a1c1-F18 and O2a1c2-L133.2 and the first was further divided into two main subclades, O2a1c1a-F11 and O2a1c1b-F449, accounting for 11.13% and 2.20% of Han Chinese, respectively. In Haplogroup O2a1c1a-F11, we also determined seven sublineages with quite different frequency distributions in Han Chinese ranging from 0.187% to 3.553%, implying they might have different demographic history. The reconstructed haplogroup tree for all the major clades within Haplogroup O2a1c-002611 permits better resolution of male lineages in population studies of East Asia and Southeast Asia. The dataset generated in the present study are also valuable for forensic identification and paternity tests in China.
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13
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Wei LH, Yan S, Teo YY, Huang YZ, Wang LX, Yu G, Saw WY, Ong RTH, Lu Y, Zhang C, Xu SH, Jin L, Li H. Phylogeography of Y-chromosome haplogroup O3a2b2-N6 reveals patrilineal traces of Austronesian populations on the eastern coastal regions of Asia. PLoS One 2017; 12:e0175080. [PMID: 28380021 PMCID: PMC5381892 DOI: 10.1371/journal.pone.0175080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/20/2017] [Indexed: 12/31/2022] Open
Abstract
Austronesian diffusion is considered one of the greatest dispersals in human history; it led to the peopling of an extremely vast region, ranging from Madagascar in the Indian Ocean to Easter Island in Remote Oceania. The Y-chromosome haplogroup O3a2b*-P164(xM134), a predominant paternal lineage of Austronesian populations, is found at high frequencies in Polynesian populations. However, the internal phylogeny of this haplogroup remains poorly investigated. In this study, we analyzed -seventeen Y-chromosome sequences of haplogroup O3a2b*-P164(xM134) and generated a revised phylogenetic tree of this lineage based on 310 non-private Y-chromosome polymorphisms. We discovered that all available O3a2b*-P164(xM134) samples belong to the newly defined haplogroup O3a2b2-N6 and samples from Austronesian populations belong to the sublineage O3a2b2a2-F706. Additionally, we genotyped a series of Y-chromosome polymorphisms in a large collection of samples from China. We confirmed that the sublineage O3a2b2a2b-B451 is unique to Austronesian populations. We found that O3a2b2-N6 samples are widely distributed on the eastern coastal regions of Asia, from Korea to Vietnam. Furthermore, we propose- that the O3a2b2a2b-B451 lineage represents a genetic connection between ancestors of Austronesian populations and ancient populations in North China, where foxtail millet was domesticated about 11,000 years ago. The large number of newly defined Y-chromosome polymorphisms and the revised phylogenetic tree of O3a2b2-N6 will be helpful to explore the origin of proto-Austronesians and the early diffusion process of Austronesian populations.
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Affiliation(s)
- Lan-Hai Wei
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Institut National des Langues et Civilisations Orientales, Paris, France
| | - Shi Yan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yun-Zhi Huang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ling-Xiang Wang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ge Yu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yan Lu
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chao Zhang
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shu-Hua Xu
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail:
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14
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Niedzwiecka K, Kabala AM, Lasserre JP, Tribouillard-Tanvier D, Golik P, Dautant A, di Rago JP, Kucharczyk R. Yeast models of mutations in the mitochondrial ATP6 gene found in human cancer cells. Mitochondrion 2016; 29:7-17. [PMID: 27083309 DOI: 10.1016/j.mito.2016.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 01/09/2023]
Abstract
Since the discovery of somatic mtDNA mutations in tumor cells, multiple studies have focused on establishing a causal relationship between those changes and alterations in energy metabolism, a hallmark of cancer cells. Yet the consequences of these mutations on mitochondrial function remain largely unknown. In this study, Saccharomyces cerevisiae has been used as a model to investigate the functional consequences of four cancer-associated missense mutations (8914C>A, 8932C>T, 8953A>G, 9131T>C) found in the mitochondrial MT-ATP6 gene. This gene encodes the a-subunit of F1FO-ATP synthase, which catalyzes the last steps of ATP production in mitochondria. Although the four studied mutations affected well-conserved residues of the a-subunit, only one of them (8932C>T) had a significant impact on mitochondrial function, due to a less efficient incorporation of the a-subunit into ATP synthase. Our findings indicate that these ATP6 genetic variants found in human tumors are neutral mitochondrial genome substitutions with a limited, if any, impact on the energetic function of mitochondria.
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Affiliation(s)
- Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Magdalena Kabala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Jean-Paul Lasserre
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Pawel Golik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
| | - Alain Dautant
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, Pala M, Mormina M, Hudson B, White J, Ko TM, Saidin M, Zafarina Z, Oppenheimer S, Richards MB, Pereira L, Soares P. Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia. Hum Genet 2016; 135:363-376. [PMID: 26875094 PMCID: PMC4796337 DOI: 10.1007/s00439-016-1640-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/21/2016] [Indexed: 12/30/2022]
Abstract
There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20% of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.
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Affiliation(s)
- Andreia Brandão
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK
- ICBAS (Instituto Ciências Biomédicas Abel Salazar), Universidade do Porto, Rua de Jorge Viterbo Ferreira n.º 228, 4050-313, Porto, Portugal
| | - Ken Khong Eng
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Centre for Global Archaeological Research, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Teresa Rito
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Bruno Cavadas
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
| | - David Bulbeck
- Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Acton ACT, Canberra, 2601, Australia
| | - Francesca Gandini
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK
| | - Maru Mormina
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Department of Applied Social Studies, University of Winchester, Sparkford Road, Winchester, SO22 4NR, UK
| | - Bob Hudson
- Archaeology Department, University of Sydney, New South Wales, 2006, Australia
| | - Joyce White
- Department of Anthropology, University of Pennsylvania Museum, 3260 South St., Philadelphia, USA
| | - Tsang-Ming Ko
- Department of Obstetrics and Gynecology, National Taiwan University, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Mokhtar Saidin
- Centre for Global Archaeological Research, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Zainuddin Zafarina
- Malaysian Institute of Pharmaceuticals and Nutraceuticals Malaysia, National Institutes of Biotechnology Malaysia, Penang, Malaysia
- Human Identification Unit, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Stephen Oppenheimer
- School of Anthropology, Institute of Human Sciences, The Pauling Centre, University of Oxford, 58a Banbury Road, Oxford, OX2 6QS, UK
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK.
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Luísa Pereira
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
- Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Pedro Soares
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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16
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The prevalence of ocular diseases in primary and junior high school students on Orchid Island. Tzu Chi Med J 2014. [DOI: 10.1016/j.tcmj.2014.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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17
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Trejaut JA, Poloni ES, Yen JC, Lai YH, Loo JH, Lee CL, He CL, Lin M. Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia. BMC Genet 2014; 15:77. [PMID: 24965575 PMCID: PMC4083334 DOI: 10.1186/1471-2156-15-77] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 06/10/2014] [Indexed: 01/12/2023] Open
Abstract
Background Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned. Results We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South. Conclusion The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15,000 years ago. The branches of the pincer contributed separately to the paternal gene pool of the Philippines and conjointly to the gene pools of Madagascar and the Solomon Islands. The North to South increase in diversity found for Taiwanese Austronesian speaking groups contrasts with observations based on mitochondrial DNA, thus hinting to a differentiated demographic history of men and women in these populations.
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Affiliation(s)
- Jean A Trejaut
- Mackay Memorial Hospital, Taipei, Molecular Anthropology Laboratory, 45 Min-Sheng Road,225115 Tamsui, New Taipei city, Taiwan.
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18
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Zeng Z, Garcia-Bertrand R, Calderon S, Li L, Zhong M, Herrera RJ. Extreme genetic heterogeneity among the nine major tribal Taiwanese island populations detected with a new generation Y23 STR system. Forensic Sci Int Genet 2014; 12:100-6. [PMID: 24911980 DOI: 10.1016/j.fsigen.2014.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 04/30/2014] [Accepted: 05/03/2014] [Indexed: 11/18/2022]
Abstract
The Taiwanese aborigines have been regarded as the source populations for the Austronesian expansion that populated Oceania to the east and Madagascar off Africa to the West. Although a number of genetic studies have been performed on some of these important tribes, the scope of the investigations has been limited, varying in the specific populations examined as well as the maker systems employed. This has made direct comparison among studies difficult. In an attempt to alleviate this lacuna, we investigate, for the first time, the genetic diversity of all nine major Taiwanese aboriginal tribes (Ami, Atayal, Bunun, Rukai, Paiwan, Saisat, Puyuma, Tsou and Yami) utilizing a new generation multiplex Y-STR system that allows for the genotyping of 23 loci from a single amplification reaction. This comprehensive approach examining 293 individuals from all nine main tribes with the same battery of forensic markers provides for the much-needed equivalent data essential for comparative analyses. Our results have uncovered that these nine major aboriginal populations exhibit limited intrapopulation genetic diversity and are highly heterogeneous from each other, possibly the result of endogamy, isolation, drift and/or unique ancestral populations. Specifically, genetic diversity, discrimination capacity, fraction of unique haplotypes and the most frequent haplotypes differ among the nine tribes, with the Tsou possessing the lowest values for the first three of these parameters. The phylogenetic analyses performed indicate that the genetic diversity among all nine tribes is greater than the diversity observed among the worldwide reference populations examined, indicating an extreme case of genetic heterogeneity among these tribes that have lived as close neighbors for thousands of years confined to the limited geographical area of an island.
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Affiliation(s)
- Zhaoshu Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, China
| | - Ralph Garcia-Bertrand
- Department of Biological Sciences, Colorado College, Colorado Springs, CO, United States.
| | - Silvia Calderon
- Department of Dentistry, New York University, New York, NY, United States
| | - Li Li
- Department of Obstetrics & Gynecology, Zhengzhou Central Hospital, Zhengzhou University, China
| | - Mingxia Zhong
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, China
| | - Rene J Herrera
- Department of Biological Sciences, Colorado College, Colorado Springs, CO, United States
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Loo JH, Trejaut JA, Yen JC, Chen ZS, Ng WM, Huang CY, Hsu KN, Hung KH, Hsiao Y, Wei YH, Lin M. Mitochondrial DNA association study of type 2 diabetes with or without ischemic stroke in Taiwan. BMC Res Notes 2014; 7:223. [PMID: 24713204 PMCID: PMC4108081 DOI: 10.1186/1756-0500-7-223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/01/2014] [Indexed: 11/10/2022] Open
Abstract
Background The importance of mitochondrial DNA (mtDNA) polymorphism in the prediction of type 2 diabetes (T2D) in men and women is not well understood. We questioned whether mtDNA polymorphism, mitochondrial functions, age and gender influenced the occurrence of T2D with or without ischemic stroke (IS). Methods We first designed a matched case–control study of 373 T2D patients and 327 healthy unrelated individuals without history of IS. MtDNA haplogroups were determined on all participants using sequencing of the control region and relevant SNPs from the coding region. Mitochondria functional tests, systemic biochemical measurements and complete genomic mtDNA sequencing were further determined on 239 participants (73 healthy controls, 33 T2D with IS, 70 T2D only and 63 IS patients without T2D). Results MtDNA haplogroups B4a1a, and E2b1 showed significant association with T2D (P <0.05), and haplogroup D4 indicated resistance (P <0.05). Mitochondrial and systemic functional tests showed significantly less variance within groups bearing the same mtDNA haplotypes. There was a pronounced male excess among all T2D patients and prevalence of IS was seen only in the older population. Finally, nucleotide variant np 15746, a determinant of haplogroup G3 seen in Japanese and of B4a1a prevalent in Taiwanese was associated with T2D in both populations. Conclusions Men appeared more susceptible to T2D than women. Although the significant association of B4a1a and E2b1 with T2D ceased when corrected for multiple testings, these haplogroups are seen only among Taiwan Aborigines, Southeast Asian and the Pacific Ocean islanders where T2D is predominant. The data further suggested that physiological and biochemical measurements were influenced by the mtDNA genetic profile of the individual. More understanding of the function of the mitochondrion in the development of T2D might indicate ways of influencing the early course of the disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Marie Lin
- Mackay Memorial Hospital, No, 45, Mínshēng Rd, Danshui District, New Taipei City, Taiwan.
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20
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Zeng Z, Rowold DJ, Garcia-Bertrand R, Calderon S, Regueiro M, Li L, Zhong M, Herrera RJ. Taiwanese aborigines: genetic heterogeneity and paternal contribution to Oceania. Gene 2014; 542:240-7. [PMID: 24613753 DOI: 10.1016/j.gene.2014.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
In the present study, for the first time, 293 Taiwanese aboriginal males from all nine major tribes (Ami, Atayal, Bunun, Rukai, Paiwan, Saisat, Puyuma, Tsou, Yami) were genotyped with 17 YSTR loci in a attend to reveal migrational patterns connected with the Austronesian expansion. We investigate the paternal genetic relationships of these Taiwanese aborigines to 42 Asia-Pacific reference populations, geographically selected to reflect various locations within the Austronesian domain. The Tsou and Puyuma tribes exhibit the lowest (0.1851) and the highest (0.5453) average total genetic diversity, respectively. Further, the fraction of unique haplotypes is also relatively high in the Puyuma (86.7%) and low in Tsou (33.3%) suggesting different demographic histories. Multidimensional scaling (MDS) and analysis of molecular variance (AMOVA) revealed several notable findings: 1) the Taiwan indigenous populations are highly diverse. In fact, the level of inter-population heterogeneity displayed by the Taiwanese aboriginal populations is close to that exhibited among all 51 Asia-Pacific populations examined; 2) the asymmetrical contribution of the Taiwanese aborigines to the Oceanic groups. Ami, Bunun and Saisiyat tribes exhibit the strongest paternal links to the Solomon and Polynesian island communities, whereas most of the remaining Taiwanese aboriginal groups are more genetically distant to these Oceanic inhabitants; 3) the present YSTR analyses does not reveal a strong paternal affinity of the nine Taiwanese tribes to their continental Asian neighbors. Overall, our current findings suggest that, perhaps, only a few of the tribes were involved in the migration out of Taiwan.
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Affiliation(s)
- Zhaoshu Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, China
| | - Diane J Rowold
- Foundation for Applied Molecular Science (FfAME), Gainesville, FL 32601, USA
| | | | - Silvia Calderon
- Department of Dentistry, New York University, New York, NY, USA
| | | | - Li Li
- Department of Obstetrics & Gynecology, Zhengzhou Central Hospital, Zhengzhou University, China
| | - Mingxia Zhong
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, China
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21
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Heyer E, Georges M, Pachner M, Endicott P. Genetic diversity of four Filipino negrito populations from Luzon: comparison of male and female effective population sizes and differential integration of immigrants into Aeta and Agta communities. Hum Biol 2013; 85:189-208. [PMID: 24297226 DOI: 10.3378/027.085.0310] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
Genetic data corresponding to four negrito populations (two Aeta and two Agta; n = 120) from the Luzon region of the Philippines have been analyzed. These data comprise mitochondrial DNA (mtDNA) hypervariable segment 1 haplotypes and haplogroups, Y-chromosome haplogroups and short tandem repeats (STRs), autosomal STRs, and X-chromosome STRs. The genetic diversity and structure of the populations were investigated at a local, regional, and interregional level. We found a high level of autosomal differentiation, combined with no significant reduction in diversity, consistent with long-term settlement of the Luzon region by the ancestors of the Agta and Aeta followed by reduced gene flow between these two ethnolinguistic groups. Collectively, the Aeta have a much higher ratio of female:male effective population size than do the Agta, a finding that supports phylogenetic analysis of their mtDNA and Y-chromosome haplogroups, which suggests different genetic sex-biased contributions from putative Austronesian source populations. We propose that factors of social organization that led to the reduction in Agta female effective population size may also be linked to the limited incorporation of female lineages associated with the settlement of the Philippines by Austronesian speakers; conversely, the reduction in Aeta male effective population size, relative to females, could be indicative of a limited incorporation of male lineages associated with this demographic process.
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Affiliation(s)
- E Heyer
- UMR7206, EcoAnthropologie et Ethnobiologie, MNHN, CNRS, Université Paris Diderot, Paris, France
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Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MGI, Beiko RG. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS One 2013; 8:e69885. [PMID: 23922841 PMCID: PMC3726740 DOI: 10.1371/journal.pone.0069885] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/14/2013] [Indexed: 12/21/2022] Open
Abstract
GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis.
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Affiliation(s)
- Donovan H. Parks
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Timothy Mankowski
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Somayyeh Zangooei
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Michael S. Porter
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David G. Armanini
- Prothea srl, Milan, Italy
- Environment Canada @ Canadian Rivers Institute, University of New Brunswick, Fredericton, Canada
| | - Donald J. Baird
- Environment Canada @ Canadian Rivers Institute, University of New Brunswick, Fredericton, Canada
| | | | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
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Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population. PLoS One 2013; 8:e60793. [PMID: 23577161 PMCID: PMC3618337 DOI: 10.1371/journal.pone.0060793] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 03/03/2013] [Indexed: 01/11/2023] Open
Abstract
The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.
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Mirabal S, Cadenas AM, Garcia-Bertrand R, Herrera RJ. Ascertaining the role of Taiwan as a source for the Austronesian expansion. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:551-64. [PMID: 23440864 DOI: 10.1002/ajpa.22226] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/14/2012] [Indexed: 01/15/2023]
Abstract
Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two-thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the "Out of Taiwan" hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift.
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Affiliation(s)
- Sheyla Mirabal
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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Derenko M, Malyarchuk B, Denisova G, Perkova M, Rogalla U, Grzybowski T, Khusnutdinova E, Dambueva I, Zakharov I. Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PLoS One 2012; 7:e32179. [PMID: 22363811 PMCID: PMC3283723 DOI: 10.1371/journal.pone.0032179] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 01/22/2012] [Indexed: 12/21/2022] Open
Abstract
With the aim of uncovering all of the most basal variation in the northern Asian mitochondrial DNA (mtDNA) haplogroups, we have analyzed mtDNA control region and coding region sequence variation in 98 Altaian Kazakhs from southern Siberia and 149 Barghuts from Inner Mongolia, China. Both populations exhibit the prevalence of eastern Eurasian lineages accounting for 91.9% in Barghuts and 60.2% in Altaian Kazakhs. The strong affinity of Altaian Kazakhs and populations of northern and central Asia has been revealed, reflecting both influences of central Asian inhabitants and essential genetic interaction with the Altai region indigenous populations. Statistical analyses data demonstrate a close positioning of all Mongolic-speaking populations (Mongolians, Buryats, Khamnigans, Kalmyks as well as Barghuts studied here) and Turkic-speaking Sojots, thus suggesting their origin from a common maternal ancestral gene pool. In order to achieve a thorough coverage of DNA lineages revealed in the northern Asian matrilineal gene pool, we have completely sequenced the mtDNA of 55 samples representing haplogroups R11b, B4, B5, F2, M9, M10, M11, M13, N9a and R9c1, which were pinpointed from a massive collection (over 5000 individuals) of northern and eastern Asian, as well as European control region mtDNA sequences. Applying the newly updated mtDNA tree to the previously reported northern Asian and eastern Asian mtDNA data sets has resolved the status of the poorly classified mtDNA types and allowed us to obtain the coalescence age estimates of the nodes of interest using different calibrated rates. Our findings confirm our previous conclusion that northern Asian maternal gene pool consists of predominantly post-LGM components of eastern Asian ancestry, though some genetic lineages may have a pre-LGM/LGM origin.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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26
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Ballantyne KN, van Oven M, Ralf A, Stoneking M, Mitchell RJ, van Oorschot RAH, Kayser M. MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Sci Int Genet 2011; 6:425-36. [PMID: 21940232 DOI: 10.1016/j.fsigen.2011.08.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/18/2011] [Accepted: 08/25/2011] [Indexed: 01/22/2023]
Abstract
Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for Oceania introduced here with those we developed earlier for all other continental regions, global matrilineal bio-geographic ancestry assignment from DNA is now achievable in a highly efficient way that is also suitable for applications with limited material such as forensic case work.
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Affiliation(s)
- Kaye N Ballantyne
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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