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Bodner M, Perego UA, Gomez JE, Cerda-Flores RM, Rambaldi Migliore N, Woodward SR, Parson W, Achilli A. The Mitochondrial DNA Landscape of Modern Mexico. Genes (Basel) 2021; 12:genes12091453. [PMID: 34573435 PMCID: PMC8467843 DOI: 10.3390/genes12091453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/16/2022] Open
Abstract
Mexico is a rich source for anthropological and population genetic studies with high diversity in ethnic and linguistic groups. The country witnessed the rise and fall of major civilizations, including the Maya and Aztec, but resulting from European colonization, the population landscape has dramatically changed. Today, the majority of Mexicans do not identify themselves as Indigenous but as admixed, and appear to have very little in common with their pre-Columbian predecessors. However, when the maternally inherited mitochondrial (mt)DNA is investigated in the modern Mexican population, this is not the case. Control region sequences of 2021 samples deriving from all over the country revealed an overwhelming Indigenous American legacy, with almost 90% of mtDNAs belonging to the four major pan-American haplogroups A2, B2, C1, and D1. This finding supports a very low European contribution to the Mexican gene pool by female colonizers and confirms the effectiveness of employing uniparental markers as a tool to reconstruct a country’s history. In addition, the distinct frequency and dispersal patterns of Indigenous American and West Eurasian clades highlight the benefit such large and country-wide databases provide for studying the impact of colonialism from a female perspective and population stratification. The importance of geographical database subsets not only for forensic application is clearly demonstrated.
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Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Ugo A. Perego
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
- Department of Math and Science, Southeastern Community College, Burlington, IA 52655, USA
| | - J. Edgar Gomez
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
- FamilySearch Int., Salt Lake City, UT 84150, USA
| | | | - Nicola Rambaldi Migliore
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria;
- Forensic Science Program, Penn State University, University Park, State College, PA 16802, USA
- Correspondence: (W.P.); (A.A.)
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
- Correspondence: (W.P.); (A.A.)
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Measuring the impact of European colonization on Native American populations in Southern Brazil and Uruguay: Evidence from mtDNA. Am J Hum Biol 2019; 31:e23243. [DOI: 10.1002/ajhb.23243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/05/2019] [Accepted: 03/10/2019] [Indexed: 01/26/2023] Open
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Mizuno F, Wang L, Sugiyama S, Kurosaki K, Granados J, Gomez-Trejo C, Acuña-Alonzo V, Ueda S. Characterization of complete mitochondrial genomes of indigenous Mayans in Mexico. Ann Hum Biol 2017; 44:652-658. [PMID: 28724311 DOI: 10.1080/03014460.2017.1358393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND The authors have previously published the complete mitochondrial genome (mitogenome) sequences of two indigenous Mesoamerican populations, Mazahua (n = 25) and Zapotec (n = 88). METHODS This study determined the complete mitogenome sequences of nine unrelated individuals from the indigenous Maya population living in Mexico. RESULTS Their mitogenome sequences could be classified into either of the haplogroups A2 and C1. Surprisingly, there were no mitogenome sequences (haplotypes) that the Maya, Mazahua, and Zapotec people share in common. CONCLUSIONS This indicates that no genetic exchange, at least matrilineally, has occurred among them.
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Affiliation(s)
- Fuzuki Mizuno
- a Department of Legal Medicine , Toho University School of Medicine , Ota-ku , Tokyo , Japan.,b Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Bunkyo-ku , Tokyo , Japan
| | - Li Wang
- c School of Medicine, Hangzhou Normal University School of Medicine , Hangzhou , Zhejiang , China
| | - Saburo Sugiyama
- d Graduate School of International Cultural Studies, Cultural Symbiosis Research Institute , Aichi Prefectural University , Nagakute , Aichi , Japan
| | - Kunihiko Kurosaki
- a Department of Legal Medicine , Toho University School of Medicine , Ota-ku , Tokyo , Japan
| | - Julio Granados
- e Department of Transplants , Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , Mexico City , Mexico
| | - Celta Gomez-Trejo
- f Molecular Genetics Laboratory , National Institute of Anthropology and History , Mexico City , Mexico
| | - Víctor Acuña-Alonzo
- f Molecular Genetics Laboratory , National Institute of Anthropology and History , Mexico City , Mexico
| | - Shintaroh Ueda
- b Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Bunkyo-ku , Tokyo , Japan.,c School of Medicine, Hangzhou Normal University School of Medicine , Hangzhou , Zhejiang , China
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Mizuno F, Kumagai M, Kurosaki K, Hayashi M, Sugiyama S, Ueda S, Wang L. Imputation approach for deducing a complete mitogenome sequence from low-depth-coverage next-generation sequencing data: application to ancient remains from the Moon Pyramid, Mexico. J Hum Genet 2017; 62:631-635. [PMID: 28202952 DOI: 10.1038/jhg.2017.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 12/19/2022]
Abstract
It is considered that more than 15 depths of coverage are necessary for next-generation sequencing (NGS) data to obtain reliable complete nucleotide sequences of the mitogenome. However, it is difficult to satisfy this requirement for all nucleotide positions because of problems obtaining a uniform depth of coverage for poorly preserved materials. Thus, we propose an imputation approach that allows a complete mitogenome sequence to be deduced from low-depth-coverage NGS data. We used different types of mitogenome data files as panels for imputation: a worldwide panel comprising all the major haplogroups, a worldwide panel comprising sequences belonging to the estimated haplogroup alone, a panel comprising sequences from the population most closely related to an individual under investigation, and a panel comprising sequences belonging to the estimated haplogroup from the population most closely related to an individual under investigation. The number of missing nucleotides was drastically reduced in all the panels, but the contents obtained by imputation were quite different among the panels. The efficiency of the imputation method differed according to the panels used. The missing nucleotides were most credibly imputed using sequences of the estimated haplogroup from the population most closely related to the individual under investigation as a panel.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Saburo Sugiyama
- Graduate school of International Cultural Studies, Cultural Symbiosis Research Institute, Aichi Prefectural University, Aichi, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,School of Medicine, Hangzhou Normal University School of Medicine, Zhejiang, China
| | - Li Wang
- School of Medicine, Hangzhou Normal University School of Medicine, Zhejiang, China
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Guangxin E, Yong-Ju Z, Ri-Su N, Yue-Hui M, Jia-Hua Z, Li-Peng C, Xiao-Yu Q, Zhong-Quan Z, Ya-Wang S, Xin W, Yong-Fu H. Meta-analysis evidence of maternal lineages in Chinese Tibetan sheep using mtDNA D-loop panel. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:579-583. [PMID: 27159711 DOI: 10.3109/24701394.2016.1143469] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Tibetan sheep is an indigenous breed living in the entire Tibetan Plateau, and its origin and phylogenic relationships are still uncertain and controversial. In this study, we analyzed partial mtDNA D-loop sequences of 156 Chinese Tibetan sheep individuals from 12 distributed geographic ecotype populations. Phylogenetic analysis indicated that three maternal lineages (haplogroups A, B and C) were found in this breed and that Ovis vignei and Ovis ammon have possibly contributed to the original Tibetan sheep. The absence of haplogroups D and E in Tibetan sheep suggests that this breed did not originate in the Middle East, China.
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Affiliation(s)
- E Guangxin
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Zhao Yong-Ju
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Na Ri-Su
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Ma Yue-Hui
- b Institute of Animal Science , Chinese Academy of Agricultural Sciences (CAAS) , Beijing , China
| | - Zhang Jia-Hua
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Chen Li-Peng
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Qiu Xiao-Yu
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Zhao Zhong-Quan
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Sun Ya-Wang
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Wu Xin
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Huang Yong-Fu
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
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