1
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Barquera R, Del Castillo-Chávez O, Nägele K, Pérez-Ramallo P, Hernández-Zaragoza DI, Szolek A, Rohrlach AB, Librado P, Childebayeva A, Bianco RA, Penman BS, Acuña-Alonzo V, Lucas M, Lara-Riegos JC, Moo-Mezeta ME, Torres-Romero JC, Roberts P, Kohlbacher O, Warinner C, Krause J. Ancient genomes reveal insights into ritual life at Chichén Itzá. Nature 2024; 630:912-919. [PMID: 38867041 PMCID: PMC11208145 DOI: 10.1038/s41586-024-07509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/02/2024] [Indexed: 06/14/2024]
Abstract
The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1-4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
| | - Oana Del Castillo-Chávez
- Centro INAH Yucatán, Instituto Nacional de Antropología e Historia (INAH), Mérida, Yucatán, Mexico.
| | - Kathrin Nägele
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- University of the Basque Country (EHU), San Sebastián-Donostia, Spain
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology and Cultural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Diana Iraíz Hernández-Zaragoza
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - András Szolek
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Adam Benjamin Rohrlach
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Pablo Librado
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | - Raffaela Angelina Bianco
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Bridget S Penman
- The Zeeman Institute and the School of Life Sciences, University of Warwick, Coventry, UK
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mary Lucas
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | | | | | | | - Patrick Roberts
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
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2
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García-Vilchis B, Román-López TV, Ramírez-González D, López-Camaño XJ, Murillo-Lechuga V, Díaz-Téllez X, Sánchez-Moncada CI, Espinosa-Méndez IM, Zenteno-Morales D, Espinosa-Valdes ZX, Pradel-Jiménez S, Tapia-Atilano A, Zanabria-Pérez AV, Livas-Gangas F, Aldana-Assad O, Caballero-Sánchez U, Dominguez-Frausto CA, Rentería ME, Medina-Rivera A, Alcauter S, Ruiz-Contreras AE. TwinsMX: Exploring the Genetic and Environmental Influences on Health Traits in the Mexican Population. Twin Res Hum Genet 2024; 27:85-96. [PMID: 38699821 DOI: 10.1017/thg.2024.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
TwinsMX registry is a national research initiative in Mexico that aims to understand the complex interplay between genetics and environment in shaping physical and mental health traits among the country's population. With a multidisciplinary approach, TwinsMX aims to advance our knowledge of the genetic and environmental mechanisms underlying ethnic variations in complex traits and diseases, including behavioral, psychometric, anthropometric, metabolic, cardiovascular and mental disorders. With information gathered from over 2800 twins, this article updates the prevalence of several complex traits; and describes the advances and novel ideas we have implemented such as magnetic resonance imaging. The future expansion of the TwinsMX registry will enhance our comprehension of the intricate interplay between genetics and environment in shaping health and disease in the Mexican population. Overall, this report describes the progress in the building of a solid database that will allow the study of complex traits in the Mexican population, valuable not only for our consortium, but also for the worldwide scientific community, by providing new insights of understudied genetically admixed populations.
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Affiliation(s)
- Brisa García-Vilchis
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Talia V Román-López
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Diego Ramírez-González
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Xanat J López-Camaño
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Vanessa Murillo-Lechuga
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Xóchitl Díaz-Téllez
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | | | - Ian M Espinosa-Méndez
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Diego Zenteno-Morales
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Zaida X Espinosa-Valdes
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sofia Pradel-Jiménez
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Andrea Tapia-Atilano
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ana V Zanabria-Pérez
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Federica Livas-Gangas
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Oscar Aldana-Assad
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Ulises Caballero-Sánchez
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Miguel E Rentería
- Mental Health & Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Sarael Alcauter
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Alejandra E Ruiz-Contreras
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación en Psicobiología y Neurociencias. Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, México
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3
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Castillo A, Rondón F, Mantilla G, Gusmão L, Simão F. Maternal ancestry and lineages diversity of the Santander population from Colombia. Forensic Sci Res 2023; 8:241-248. [PMID: 38221971 PMCID: PMC10785602 DOI: 10.1093/fsr/owad032] [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: 06/30/2022] [Accepted: 09/20/2023] [Indexed: 01/16/2024] Open
Abstract
Santander, located in the Andean region of Colombia, is one of the 32 departments of the country. Its population was shaped by intercontinental admixture between autochthonous native Americans, European settlers, and African slaves. To establish forensic databases of haplotype frequencies, the evaluation of population substructure is crucial to capture the genetic diversity in admixed populations. Total control region mitochondrial deoxyribonucleic acid haplotypes were determined for 204 individuals born in the seven provinces across the department. The maternal native heritage is highly preserved in Santander genetic background, with 90% of the haplotypes belonging to haplogroups inside A2, B4, C1, and D. Most native lineages are found broadly across the American continent, while some sub-branches are concentrated in Central America and north South America. Subtle European (6%) and African (4%) input was detected. In pairwise comparisons between provinces, relatively high FST values were found in some cases, although not statistically significant. Nonetheless, when provinces were grouped according to the principal component analysis results, significant differences were detected between groups. The database on mitochondrial deoxyribonucleic acid control region haplotype frequencies established here can be further used for populational and forensic purposes.
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Affiliation(s)
- Adriana Castillo
- Department of Basic Sciences, Genetics Laboratory, Industrial University of Santander, 680002, Bucaramanga, Colombia
| | - Fernando Rondón
- Department of Basic Sciences, Genetics Laboratory, Industrial University of Santander, 680002, Bucaramanga, Colombia
| | - Gerardo Mantilla
- Department of Basic Sciences, Genetics Laboratory, Industrial University of Santander, 680002, Bucaramanga, Colombia
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, 20550-900, Rio de Janeiro, Brazil
| | - Filipa Simão
- DNA Diagnostic Laboratory, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, 20550-900, Rio de Janeiro, Brazil
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4
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Shen-Gunther J, Gunther RS, Cai H, Wang Y. A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping. Int J Mol Sci 2023; 24:13505. [PMID: 37686313 PMCID: PMC10488239 DOI: 10.3390/ijms241713505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA
| | - Rutger S. Gunther
- Nuclear Medicine & Molecular Imaging, Department of Radiology, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA;
| | - Hong Cai
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
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5
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Aizpurua-Iraola J, Rasal R, Prieto L, Comas D, Bonet N, Casals F, Calafell F, Vásquez P. Population analysis of complete mitogenomes for 334 samples from El Salvador. Forensic Sci Int Genet 2023; 66:102906. [PMID: 37364481 DOI: 10.1016/j.fsigen.2023.102906] [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: 03/22/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
The use of mitochondrial DNA (mtDNA) in the field of forensic genetics is widely spread mainly due to its advantages when identifying highly degraded samples. In this sense, massive parallel sequencing has made the analysis of the whole mitogenome more accessible, noticeably increasing the informativeness of mtDNA haplotypes. The civil war (1980-1992) in El Salvador caused many deaths and disappearances (including children) all across the country and the economic and social instability after the war forced many people to emigration. For this reason, different organizations have collected DNA samples from relatives with the aim of identifying missing people. Thus, we present a dataset containing 334 complete mitogenomes from the Salvadoran general population. To the best of our knowledge, this is the first publication of a nationwide forensic-quality complete mitogenome database of any Latin American country. We found 293 different haplotypes, with a random match probability of 0.0041 and 26.6 mean pairwise differences, which is similar to other Latin American populations, and which represent a marked improvement from the values obtained with just control region sequences. These haplotypes belong to 54 different haplogroups, being 91% of them of Native American origin. Over a third (35.9%) of the individuals carried at least a heteroplasmic site (excluding length heteroplasmies). Ultimately, the present database aims to represent mtDNA haplotype diversity in the general Salvadoran populations as a basis for the identification of people that disappeared during or after the civil war.
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Affiliation(s)
- Julen Aizpurua-Iraola
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Lourdes Prieto
- Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Comisaría General de Policía Científica. DNA Laboratory, Madrid, Spain
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, San Salvador, El Salvador
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Villa-Islas V, Izarraras-Gomez A, Larena M, Campos EMP, Sandoval-Velasco M, Rodríguez-Rodríguez JE, Bravo-Lopez M, Moguel B, Fregel R, Garfias-Morales E, Medina Tretmanis J, Velázquez-Ramírez DA, Herrera-Muñóz A, Sandoval K, Nieves-Colón MA, Zepeda García Moreno G, Villanea FA, Medina EFV, Aguayo-Haro R, Valdiosera C, Ioannidis AG, Moreno-Estrada A, Jay F, Huerta-Sanchez E, Moreno-Mayar JV, Sánchez-Quinto F, Ávila-Arcos MC. Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 2023; 380:eadd6142. [PMID: 37167382 DOI: 10.1126/science.add6142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled "ghost" populations.
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Affiliation(s)
- Viridiana Villa-Islas
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Alan Izarraras-Gomez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Maximilian Larena
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Cuidad de México, Mexico
| | | | - Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Barbara Moguel
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
- Centro de Geociencias, UNAM Juriquilla, Juriquilla, Querétaro, México
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Ernesto Garfias-Morales
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | | | | | | | - Karla Sandoval
- Equity and Gender Office of the Centre for Research and Advanced Studies (CODIGO-C), CINVESTAV, Mexico City, Mexico
| | - Maria A Nieves-Colón
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | | | - Fernando A Villanea
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Cristina Valdiosera
- Departamento de Historia, Geografía y Comunicaciones, Universidad de Burgos, Burgos, Spain
- Department of History and Archaeology, La Trobe University, Melbourne, Australia
| | - Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Flora Jay
- Laboratoire Interdisciplinaire des Sciences du Numérique, Université Paris-Saclay, CNRS, INRIA, 91400 Orsay, France
| | | | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
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7
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Aquilano E, de la Fuente C, Rodríguez Golpe D, Motti JMB, Bravi CM. Sequencing errors in Native American mitogenomes: impact on clade definitions, haplogroup assignation, and beyond. Mitochondrion 2023; 70:54-58. [PMID: 37003527 DOI: 10.1016/j.mito.2023.03.005] [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: 09/06/2022] [Revised: 03/09/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
Abstract
Available evidence allows the interpretation that some cases of absence of otherwise expected variation, based on phylogenetic expectations in mitogenomes of Native American origin, are due to artificial recombination rather than to homoplasy, while other more complex scenarios involving combination of original Cambridge Reference Sequence mistakes plus incomplete or incorrect scoring of variation are also showed. Several instances of mismatched control and coding regions as well as partially duplicated HV2 are observed in Peruvians, while intra-haplogroup chimaeras of different D1 subhaplogroups are referred to in Mexican Native Americans. A revised definition for haplogroup B2h is proposed, and preventive quality control measures are suggested.
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Affiliation(s)
- Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina
| | | | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina
| | - Josefina M B Motti
- Laboratorio de Ecología Evolutiva Humana (LEEH), Facultad de Ciencias Sociales (FACSO), Universidad Nacional del Centro de la Provincia de Buenos Aires-CONICET, Calle 508 #881, 7631 Quequén, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET-CICPBA-Universidad Nacional de La Plata, Calle 526 e/ 10 y 11, 1900 La Plata, Argentina.
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8
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Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample. Int J Mol Sci 2022; 23:ijms23126725. [PMID: 35743173 PMCID: PMC9223851 DOI: 10.3390/ijms23126725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.
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Avila E, Speransa PA, Lindholz CG, Kahmann A, Alho CS. Haplotype distribution in a forensic full mtDNA genome database of admixed Southern Brazilians and its association with self-declared ancestry and pigmentation traits. Forensic Sci Int Genet 2021; 57:102650. [PMID: 34972071 DOI: 10.1016/j.fsigen.2021.102650] [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: 10/22/2021] [Accepted: 12/01/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND The advent of massively parallel sequencing (MPS) applications focused on the generation of forensic-quality full mitochondrial genome sequences led to a popularization of the technique on a global scale. However, the lack of forensic-graded population databases has refrained a wider adoption of full genome sequences as the industry standard, despite its better discrimination capacity of individual maternal lineages. PURPOSE This work describes a forensic-oriented full mtDNA genome database comprised of 480 samples from a Southern Brazilian population. METHODS A collection of mitochondrial sequences were obtained from low-pass, full genome DNA sequencing results. The complete sample set was evaluated regarding haplotype composition and distribution. Summary statistics and forensic parameters were calculated and are presented for the database, with detailed information concerning the impact of removing genetic information in the form of specific variants or increasingly larger genomic regions. Interpopulational analysis comparing haplotypical diversity in Brazilian and 26 worldwide populations was also performed. The association between mitochondrial genetic variability and phenotypic diversity was also evaluated in populations, with self-declared ancestry and three distinct phenotypic pigmentation traits (eyes, skin and hair colors) as parameters. RESULTS The presented database can be used to evaluate mitochondrial-related genetic evidence, providing LR values of up to 20,465 for unobserved haplotypes. Haplotype distribution in Southern Brazil seems to be different than the remaining of the country, with a larger contribution of maternal lines with European origin. Despite association can be found between lighter and darker phenotypes or self-declared ancestry and haplotype distribution, prediction models cannot be reliably proposed due to the admixed nature of the Brazilian population. CONCLUSIONS The proposed database provides a basis for statistical calculation and frequency estimation of full mitochondrial genomes, and can be part of an integrated, representative, national database comprising most of the genetic diversity of maternal lineages in the country.
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Affiliation(s)
- Eduardo Avila
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Technical Scientific Section, Federal Police Department in Rio Grande do Sul State, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
| | - Pietro Augusto Speransa
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Catieli Gobetti Lindholz
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Alessandro Kahmann
- National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Institute of Mathematics, Statistics and Physics, Federal University of Rio Grande, Rio Grande, RS, Brazil.
| | - Clarice Sampaio Alho
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
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Rambaldi Migliore N, Colombo G, Capodiferro MR, Mazzocchi L, Chero Osorio AM, Raveane A, Tribaldos M, Perego UA, Mendizábal T, Montón AG, Lombardo G, Grugni V, Garofalo M, Ferretti L, Cereda C, Gagliardi S, Cooke R, Smith-Guzmán N, Olivieri A, Aram B, Torroni A, Motta J, Semino O, Achilli A. Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas. Genes (Basel) 2021; 12:genes12121921. [PMID: 34946870 PMCID: PMC8702192 DOI: 10.3390/genes12121921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022] Open
Abstract
The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.
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Affiliation(s)
- Nicola Rambaldi Migliore
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Giulia Colombo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Marco Rosario Capodiferro
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Lucia Mazzocchi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Ana Maria Chero Osorio
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Department of Math and Science, Southeastern Community College, West Burlington, IA 52655, USA
| | - Tomás Mendizábal
- Center for Historical, Anthropological and Cultural Research—AIP, Panama City 0816-07812, Panama;
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
| | - Alejandro García Montón
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Gianluca Lombardo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Viola Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Maria Garofalo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Luca Ferretti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Nicole Smith-Guzmán
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Bethany Aram
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ornella Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
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