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Ancient Components and Recent Expansion in the Eurasian Heartland: Insights into the Revised Phylogeny of Y-Chromosomes from Central Asia. Genes (Basel) 2022; 13:genes13101776. [PMID: 36292661 PMCID: PMC9601478 DOI: 10.3390/genes13101776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/04/2022] Open
Abstract
In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic studies in Central Asia. Here, we sequenced and analyzed the Y-chromosomes of 187 male individuals from Kazakh, Kyrgyz, Uzbek, Karakalpak, Hazara, Karluk, Tajik, Uyghur, Dungan, and Turkmen populations. High diversity and admixture from peripheral areas of Eurasia were observed among the paternal gene pool of these populations. This general pattern can be largely attributed to the activities of ancient people in four periods, including the Neolithic farmers, Indo-Europeans, Turks, and Mongols. Most importantly, we detected the consistent expansion of many minor lineages over the past thousand years, which may correspond directly to the formation of modern populations in these regions. The newly discovered sub-lineages and variants provide a basis for further studies of the contributions of minor lineages to the formation of modern populations in Central Asia.
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2
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Paz Sepúlveda PB, Mayordomo AC, Sala C, Sosa EJ, Zaiat JJ, Cuello M, Schwab M, Rodríguez Golpe D, Aquilano E, Santos MR, Dipierri JE, Alfaro Gómez EL, Bravi CM, Muzzio M, Bailliet G. Human Y chromosome sequences from Q Haplogroup reveal a South American settlement pre-18,000 years ago and a profound genomic impact during the Younger Dryas. PLoS One 2022; 17:e0271971. [PMID: 35976870 PMCID: PMC9385064 DOI: 10.1371/journal.pone.0271971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/11/2022] [Indexed: 11/18/2022] Open
Abstract
The settlement of the Americas has been the focus of incessant debate for more than 100 years, and open questions regarding the timing and spatial patterns of colonization still remain today. Phylogenetic studies with complete human Y chromosome sequences are used as a highly informative tool to investigate the history of human populations in a given time frame. To study the phylogenetic relationships of Native American lineages and infer the settlement history of the Americas, we analyzed Y chromosome Q Haplogroup, which is a Pan-American haplogroup and represents practically all Native American lineages in Mesoamerica and South America. We built a phylogenetic tree for Q Haplogroup based on 102 whole Y chromosome sequences, of which 13 new Argentine sequences were provided by our group. Moreover, 1,072 new single nucleotide polymorphisms (SNPs) that contribute to its resolution and diversity were identified. Q-M848 is known to be the most frequent autochthonous sub-haplogroup of the Americas. The present is the first genomic study of Q Haplogroup in which current knowledge on Q-M848 sub-lineages is contrasted with the historical, archaeological and linguistic data available. The divergence times, spatial structure and the SNPs found here as novel for Q-Z780, a less frequent sub-haplogroup autochthonous of the Americas, provide genetic support for a South American settlement before 18,000 years ago. We analyzed how environmental events that occurred during the Younger Dryas period may have affected Native American lineages, and found that this event may have caused a substantial loss of lineages. This could explain the current low frequency of Q-Z780 (also perhaps of Q-F4674, a third possible sub-haplogroup autochthonous of the Americas). These environmental events could have acted as a driving force for expansion and diversification of the Q-M848 sub-lineages, which show a spatial structure that developed during the Younger Dryas period.
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Affiliation(s)
- Paula B. Paz Sepúlveda
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - Andrea Constanza Mayordomo
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
- Programa de Cáncer Hereditario, Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Camila Sala
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - Ezequiel Jorge Sosa
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Jonathan Javier Zaiat
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Mariela Cuello
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - Marisol Schwab
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - María Rita Santos
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - José Edgardo Dipierri
- Instituto de Biología de la Altura, Facultad de Humanidades y Ciencias Sociales, Universidad Nacional de Jujuy, San Salvador de Jujuy, Jujuy, Argentina
| | - Emma L. Alfaro Gómez
- Instituto de Biología de la Altura, Facultad de Humanidades y Ciencias Sociales, Universidad Nacional de Jujuy, San Salvador de Jujuy, Jujuy, Argentina
- Instituto de Ecorregiones Andinas, Universidad Nacional de Jujuy, San Salvador de Jujuy, Jujuy, Argentina
| | - Claudio M. Bravi
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Marina Muzzio
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Graciela Bailliet
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
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3
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Wang Q, Zhao J, Ren Z, Sun J, He G, Guo J, Zhang H, Ji J, Liu Y, Yang M, Yang X, Chen J, Zhu K, Wang R, Li Y, Chen G, Huang J, Wang CC. Male-Dominated Migration and Massive Assimilation of Indigenous East Asians in the Formation of Muslim Hui People in Southwest China. Front Genet 2021; 11:618614. [PMID: 33505437 PMCID: PMC7834311 DOI: 10.3389/fgene.2020.618614] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
The origin and diversification of Muslim Hui people in China via demic or simple cultural diffusion is a long-going debate. We here generated genome-wide data at nearly 700,000 single nucleotide polymorphisms (SNPs) from 45 Hui and 14 Han Chinese individuals collected from Guizhou province in southwest China. We applied principal component analysis (PCA), ADMIXTURE, f-statistics, qpWave, and qpAdm analysis to infer the population genetic structure and admixture history. Our results revealed the Guizhou Hui people have a limited amount of West Eurasian related ancestry at a proportion of 6%, but show massive genetic assimilation with indigenous southern Han Chinese and Tibetan or Tungusic/Mongolic related northern East Asians. We also detected a high frequency of North Asia or Central Asia related paternal Y-chromosome but not maternal mtDNA lineages in Guizhou Hui. Our observation supports the cultural diffusion has played a vital role in the formation of Hui people and the migration of Hui people to southwest China was probably a sex-biased male-driven process.
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Affiliation(s)
- Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinwen Chen
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rui Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yingxiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | | | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
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Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas. Sci Rep 2020; 10:21428. [PMID: 33293675 PMCID: PMC7722846 DOI: 10.1038/s41598-020-78487-9] [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: 04/24/2020] [Accepted: 11/19/2020] [Indexed: 11/08/2022] Open
Abstract
Chuetas are a group of descendants of Majorcan Crypto-Jews (Balearic Islands, Spain) who were socially stigmatized and segregated by their Majorcan neighbours until recently; generating a community that, although after the seventeenth century no longer contained Judaic religious elements, maintained strong group cohesion, Jewishness consciousness, and endogamy. Collective memory fixed 15 surnames as a most important defining element of Chueta families. Previous studies demonstrated Chuetas were a differentiated population, with a considerable proportion of their original genetic make-up. Genetic data of Y-chromosome polymorphism and mtDNA control region showed, in Chuetas’ paternal lineages, high prevalence of haplogroups J2-M172 (33%) and J1-M267 (18%). In maternal lineages, the Chuetas hallmark is the presence of a new sub-branching of the rare haplogroup R0a2m as their modal haplogroup (21%). Genetic diversity in both Y-chromosome and mtDNA indicates the Chueta community has managed to avoid the expected heterogeneity decrease in their gene pool after centuries of isolation and inbreeding. Moreover, the composition of their uniparentally transmitted lineages demonstrates a remarkable signature of Middle Eastern ancestry—despite some degree of host admixture—confirming Chuetas have retained over the centuries a considerable degree of ancestral genetic signature along with the cultural memory of their Jewish origin.
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5
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Borda A, Gray K, Fu Y. Research data management in health and biomedical citizen science: practices and prospects. JAMIA Open 2020; 3:113-125. [PMID: 32607493 PMCID: PMC7309241 DOI: 10.1093/jamiaopen/ooz052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/09/2019] [Accepted: 09/30/2019] [Indexed: 12/25/2022] Open
Abstract
Background Public engagement in health and biomedical research is being influenced by the paradigm of citizen science. However, conventional health and biomedical research relies on sophisticated research data management tools and methods. Considering these, what contribution can citizen science make in this field of research? How can it follow research protocols and produce reliable results? Objective The aim of this article is to analyze research data management practices in existing biomedical citizen science studies, so as to provide insights for members of the public and of the research community considering this approach to research. Methods A scoping review was conducted on this topic to determine data management characteristics of health and bio medical citizen science research. From this review and related web searching, we chose five online platforms and a specific research project associated with each, to understand their research data management approaches and enablers. Results Health and biomedical citizen science platforms and projects are diverse in terms of types of work with data and data management activities that in themselves may have scientific merit. However, consistent approaches in the use of research data management models or practices seem lacking, or at least are not prevalent in the review. Conclusions There is potential for important data collection and analysis activities to be opaque or irreproducible in health and biomedical citizen science initiatives without the implementation of a research data management model that is transparent and accessible to team members and to external audiences. This situation might be improved with participatory development of standards that can be applied to diverse projects and platforms, across the research data life cycle.
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Affiliation(s)
- Ann Borda
- Health and Biomedical Informatics Centre, Melbourne Medical School, The University of Melbourne, Melbourne, Australia
| | - Kathleen Gray
- Health and Biomedical Informatics Centre, Melbourne Medical School, The University of Melbourne, Melbourne, Australia
| | - Yuqing Fu
- Health and Biomedical Informatics Centre, Melbourne Medical School, The University of Melbourne, Melbourne, Australia
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AlSafar HS, Al-Ali M, Elbait GD, Al-Maini MH, Ruta D, Peramo B, Henschel A, Tay GK. Introducing the first whole genomes of nationals from the United Arab Emirates. Sci Rep 2019; 9:14725. [PMID: 31604968 PMCID: PMC6789106 DOI: 10.1038/s41598-019-50876-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/20/2019] [Indexed: 12/30/2022] Open
Abstract
Whole Genome Sequencing (WGS) provides an in depth description of genome variation. In the era of large-scale population genome projects, the assembly of ethnic-specific genomes combined with mapping human reference genomes of underrepresented populations has improved the understanding of human diversity and disease associations. In this study, for the first time, whole genome sequences of two nationals of the United Arab Emirates (UAE) at >27X coverage are reported. The two Emirati individuals were predominantly of Central/South Asian ancestry. An in-house customized pipeline using BWA, Picard followed by the GATK tools to map the raw data from whole genome sequences of both individuals was used. A total of 3,994,521 variants (3,350,574 Single Nucleotide Polymorphisms (SNPs) and 643,947 indels) were identified for the first individual, the UAE S001 sample. A similar number of variants, 4,031,580 (3,373,501 SNPs and 658,079 indels), were identified for UAE S002. Variants that are associated with diabetes, hypertension, increased cholesterol levels, and obesity were also identified in these individuals. These Whole Genome Sequences has provided a starting point for constructing a UAE reference panel which will lead to improvements in the delivery of precision medicine, quality of life for affected individuals and a reduction in healthcare costs. The information compiled will likely lead to the identification of target genes that could potentially lead to the development of novel therapeutic modalities.
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Affiliation(s)
- Habiba S AlSafar
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mariam Al-Ali
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Gihan Daw Elbait
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | | | - Dymitr Ruta
- Etisalat-British Telecom Innovation Center, Abu Dhabi, United Arab Emirates
| | | | - Andreas Henschel
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,School of Psychiatry and Clinical Neurosciences, University of Western Australia, Nedlands, Australia. .,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.
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7
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Sun N, Ma PC, Yan S, Wen SQ, Sun C, Du PX, Cheng HZ, Deng XH, Wang CC, Wei LH. Phylogeography of Y-chromosome haplogroup Q1a1a-M120, a paternal lineage connecting populations in Siberia and East Asia. Ann Hum Biol 2019; 46:261-266. [PMID: 31208219 DOI: 10.1080/03014460.2019.1632930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Background: Previous studies have suggested that the human Y-chromosome haplogroup Q1a1a-M120, a widespread paternal lineage in East Asian populations, originated in South Siberia. However, much uncertainty remains regarding the origin, diversification, and expansion of this paternal lineage.Aim: To explore the origin and diffusion of paternal Q-M120 lineages in East Asia.Subjects and methods: The authors generated 26 new Y chromosome sequences of Q-M120 males and co-analysed 45 Y chromosome sequences of this haplogroup. A highly-revised phylogenetic tree of haplogroup Q-M120 with age estimates was reconstructed. Additionally, a comprehensive phylogeographic analysis of this lineage was performed including 15,007 samples from 440 populations in eastern Eurasia.Results: An ancient connection of this lineage with populations in Siberia was revealed. However, this paternal lineage experienced an in-situ expansion between 5000 and 3000 years ago in northwestern China. Ancient populations with high frequencies of Q-M120 were involved in the formation of ancient Huaxia populations before 2000 years ago; this haplogroup eventually became one of the founding paternal lineages of modern Han populations.Conclusion: This study provides a clear pattern of the origin and diffusion process of haplogroup Q1a1a-M120, as well as the role of this paternal lineage during the formation of ancient Huaxia populations and modern Han populations.
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Affiliation(s)
- Na Sun
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China
| | - Peng-Cheng Ma
- Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai, PR China.,B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China
| | - Shao-Qing Wen
- B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China.,Institute of Archaeological Science, Fudan University, Shanghai, PR China
| | - Chang Sun
- B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China.,Institute of Archaeological Science, Fudan University, Shanghai, PR China
| | - Pan-Xin Du
- B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China
| | - Hui-Zhen Cheng
- Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China.,Culture Development Institute of Xiamen University, Xiamen, PR China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China.,Laboratory for Anthropology and Human Development, Xiamen University, Xiamen, PR China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China.,B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China.,Culture Development Institute of Xiamen University, Xiamen, PR China.,Laboratory for Anthropology and Human Development, Xiamen University, Xiamen, PR China
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8
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Grugni V, Raveane A, Ongaro L, Battaglia V, Trombetta B, Colombo G, Capodiferro MR, Olivieri A, Achilli A, Perego UA, Motta J, Tribaldos M, Woodward SR, Ferretti L, Cruciani F, Torroni A, Semino O. Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas. BMC Biol 2019; 17:3. [PMID: 30674303 PMCID: PMC6345020 DOI: 10.1186/s12915-018-0622-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America by an ancestral Beringian population, from which two well-differentiated components originated and subsequently mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analysis of the Y-chromosome haplogroup Q, which is the only Pan-American haplogroup and accounts for virtually all Native American Y chromosomes in Mesoamerica and South America. RESULTS Our analyses of 1.5 Mb of 152 Y chromosomes, 34 re-sequenced in this work, support a "coastal and inland routes scenario" for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand years ago (kya), followed by a period of constant population size from 8 to 3 kya, after which a secondary sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainly revealed by haplogroup Q-Z780, suggest an entrance in South America prior to 15 kya. During the global constant population size phase, local South American hints of growth were registered by different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steady population growth and a single cohesive culture diffusion as it occurred in Europe. CONCLUSIONS We established and dated a detailed haplogroup Q phylogeny that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ugo A Perego
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Jorge Motta
- Secretaría Nacional de Ciencia, Tecnología e Innovación (SENACYT), Panama City, Panama
| | - Maribel Tribaldos
- Department of Health Technology Assessment and Economic Evaluation, Panama City, Panama
| | | | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.
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9
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Pinotti T, Bergström A, Geppert M, Bawn M, Ohasi D, Shi W, Lacerda DR, Solli A, Norstedt J, Reed K, Dawtry K, González-Andrade F, Paz-Y-Miño C, Revollo S, Cuellar C, Jota MS, Santos JE, Ayub Q, Kivisild T, Sandoval JR, Fujita R, Xue Y, Roewer L, Santos FR, Tyler-Smith C. Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders. Curr Biol 2018; 29:149-157.e3. [PMID: 30581024 DOI: 10.1016/j.cub.2018.11.029] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/03/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15-25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1-4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation ("Beringian Standstill" [8, 9]) for 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.
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Affiliation(s)
- Thomaz Pinotti
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil; The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Anders Bergström
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Maria Geppert
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matt Bawn
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martin de Porres, 15009 Lima, Peru; The Earlham Institute, NR4 7UG Norwich, UK
| | - Dominique Ohasi
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil
| | - Wentao Shi
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China
| | - Daniela R Lacerda
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil
| | - Arne Solli
- Q Nordic Independent Researchers; Department of Archaeology, History, Cultural Studies and Religion (AHKR), University of Bergen, Norway
| | | | | | | | - Fabricio González-Andrade
- Translational Medicine Unit, Central University of Ecuador, Faculty of Medical Sciences, Iquique N14-121 y Sodiro-Itchimbía, Sector El Dorado, 170403 Quito, Ecuador
| | - Cesar Paz-Y-Miño
- Universidad de las Americas, Av. de los Granados E12-41, 170513 Quito, Ecuador
| | - Susana Revollo
- Universidad Mayor de San Andrés, Av. Villazón 1995, 2008 La Paz, Bolivia
| | - Cinthia Cuellar
- Universidad Mayor de San Andrés, Av. Villazón 1995, 2008 La Paz, Bolivia
| | - Marilza S Jota
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil
| | - José E Santos
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil
| | - Qasim Ayub
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia; School of Science, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Toomas Kivisild
- Department of Archaeology and Anthropology, University of Cambridge, CB2 1QH Cambridge, UK; Estonian Biocentre, 51010 Tartu, Estonia
| | - José R Sandoval
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martin de Porres, 15009 Lima, Peru
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martin de Porres, 15009 Lima, Peru
| | - Yali Xue
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Fabrício R Santos
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil.
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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Arias L, Schröder R, Hübner A, Barreto G, Stoneking M, Pakendorf B. Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia. Mol Biol Evol 2018; 35:2719-2735. [PMID: 30169717 PMCID: PMC6231495 DOI: 10.1093/molbev/msy169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the nonrecombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences, only 925 of which were previously described. The NRY and mtDNA data showed different sex-specific demographic histories: female effective population size has been larger than that of males through time, which might reflect larger variance in male reproductive success. Both markers show an increase in lineage diversification beginning ∼5,000 years ago, which may reflect the intensification of agriculture, technological innovations, and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, we find similar excesses of NRY versus mtDNA between-population divergence at both the local and continental scale, suggesting long-term stability of female versus male migration. We also find evidence of the impact of sociocultural practices on diversity patterns. Finally, our study highlights the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between sexes.
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Affiliation(s)
- Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Laboratorio de Genética Molecular Humana, Departamento de Biología, Universidad del Valle, Cali, Colombia
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guillermo Barreto
- Laboratorio de Genética Molecular Humana, Departamento de Biología, Universidad del Valle, Cali, Colombia
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences. Eur J Hum Genet 2018; 26:1687-1696. [PMID: 29991739 DOI: 10.1038/s41431-018-0211-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 05/25/2018] [Accepted: 06/12/2018] [Indexed: 11/08/2022] Open
Abstract
The expansion of modern humans to the American continent after the Last Glacial Maximum led the way to the present-day distribution of American aborigines. Recent advances in autosomal DNA research and expanded testing of mtDNA lineages has provided a clearer picture of the number and timing of founding lineages. However, both autosomal DNA and mtDNA research have provided unresolved competing theories between the short-term and the long-term models of the Beringian standstill hypothesis. Further, the source of founding paternal lineages of American aborigines and their relationship with ancient Siberia populations remains ambiguous. In this study, we reanalyzed a 7.0 Mbp region of 132 paternal Y-chromosome sequences, including 39 newly reported ones, of male samples from American aborigines and Eurasian populations. Among Eurasian samples, we identified Y-chromosome branches that are most closely related to known American aborigine founding lineages, that is, Q1-L804 links to Q1-M3, Q1-L330 links to Q1-Z780, Q1-M120 links to Q1-B143, and C2-F1756 links to C2-P39. The revised phylogenetic tree and age estimates indicate a narrow timeframe (~15.3-14.3 kya) for the upper time limit of human entry to the American continent. Our analysis suggests that the in situ differentiation of Q-M242 in Central Eurasia and South Siberia region gave rise to numerous sub-lineages older than 15.3 kya, and the founding of Paleo-Indian paternal lineages is part of the great Q1-L53 diffusion throughout the Eurasia after the Last Glacial Maximum. The results of our study will assist in future studies of the history of modern populations in Eurasia and the Americas.
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12
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Huang YZ, Pamjav H, Flegontov P, Stenzl V, Wen SQ, Tong XZ, Wang CC, Wang LX, Wei LH, Gao JY, Jin L, Li H. Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia. Mol Genet Genomics 2018; 293:107-117. [PMID: 28884289 PMCID: PMC5846874 DOI: 10.1007/s00438-017-1363-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/27/2017] [Indexed: 12/17/2022]
Abstract
The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245. Through NETWORK and BATWING analyses, we found that the subclades of haplogroup Q continued to disperse from Central Asia and Southern Siberia during the past 10,000 years. Apart from its migration through the Beringia to the Americas, haplogroup Q also moved from Asia to the south and to the west during the Neolithic period, and subsequently to the whole of Eurasia and part of Africa.
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Affiliation(s)
- Yun-Zhi Huang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Horolma Pamjav
- National Center of Forensic Experts and Research, Budapest, 1087, Hungary
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 71000, Ostrava, Czech Republic
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russian Federation
| | - Vlastimil Stenzl
- Institute of Criminalistics, Police of the Czech Republic, 17089, Prague, Czech Republic
| | - Shao-Qing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xin-Zhu Tong
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, 361005, China
| | - Ling-Xiang Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lan-Hai Wei
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Institut National des Langues et Civilisations Orientales, 75013, Paris, France
| | - Jing-Yi Gao
- Faculty of Arts and Humanities, University of Tartu, 50090, Tartu, Estonia
- Faculty of Central European Studies, Beijing International Studies University, Beijing, 100024, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hui Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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13
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Abstract
The properties of the human Y chromosome - namely, male specificity, haploidy and escape from crossing over - make it an unusual component of the genome, and have led to its genetic variation becoming a key part of studies of human evolution, population history, genealogy, forensics and male medical genetics. Next-generation sequencing (NGS) technologies have driven recent progress in these areas. In particular, NGS has yielded direct estimates of mutation rates, and an unbiased and calibrated molecular phylogeny that has unprecedented detail. Moreover, the availability of direct-to-consumer NGS services is fuelling a rise of 'citizen scientists', whose interest in resequencing their own Y chromosomes is generating a wealth of new data.
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14
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Affiliation(s)
- Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, 22030, USA.
- Research Centre for Medical Genetics, Moskvorechie, 1, Moscow, Russia.
| | - Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia
- Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia
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