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Sandoval-Velasco M, Jagadeesan A, Ramos-Madrigal J, Ávila-Arcos MC, Fortes-Lima CA, Watson J, Johannesdóttir E, Cruz-Dávalos DI, Gopalakrishnan S, Moreno-Mayar JV, Niemann J, Renaud G, Robson Brown KA, Bennett H, Pearson A, Helgason A, Gilbert MTP, Schroeder H. The ancestry and geographical origins of St Helena's liberated Africans. Am J Hum Genet 2023; 110:1825. [PMID: 37802045 PMCID: PMC10577070 DOI: 10.1016/j.ajhg.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023] Open
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2
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Sandoval-Velasco M, Jagadeesan A, Ramos-Madrigal J, Ávila-Arcos MC, Fortes-Lima CA, Watson J, Johannesdóttir E, Cruz-Dávalos DI, Gopalakrishnan S, Moreno-Mayar JV, Niemann J, Renaud G, Robson Brown KA, Bennett H, Pearson A, Helgason A, Gilbert MTP, Schroeder H. The ancestry and geographical origins of St Helena's liberated Africans. Am J Hum Genet 2023; 110:1590-1599. [PMID: 37683613 PMCID: PMC10502851 DOI: 10.1016/j.ajhg.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/10/2023] Open
Abstract
The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.
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Affiliation(s)
- Marcela Sandoval-Velasco
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Anuradha Jagadeesan
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - Jazmín Ramos-Madrigal
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla, 76230 Santiago de Querétaro, México
| | - Cesar A Fortes-Lima
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Judy Watson
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Erna Johannesdóttir
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Diana I Cruz-Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Shyam Gopalakrishnan
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Jonas Niemann
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology Bioinformatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | - Helena Bennett
- St Helena National Trust, Broadway House, Mainstreet, Jamestown, St Helena
| | - Andrew Pearson
- Environmental Dimension Partnership, Atlantic Wharf, CF10 4HF Cardiff, UK
| | - Agnar Helgason
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - M Thomas P Gilbert
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Gopalakrishnan S, Ebenesersdóttir SS, Lundstrøm IKC, Turner-Walker G, Moore KHS, Luisi P, Margaryan A, Martin MD, Ellegaard MR, Magnússon ÓÞ, Sigurðsson Á, Snorradóttir S, Magnúsdóttir DN, Laffoon JE, van Dorp L, Liu X, Moltke I, Ávila-Arcos MC, Schraiber JG, Rasmussen S, Juan D, Gelabert P, de-Dios T, Fotakis AK, Iraeta-Orbegozo M, Vågene ÅJ, Denham SD, Christophersen A, Stenøien HK, Vieira FG, Liu S, Günther T, Kivisild T, Moseng OG, Skar B, Cheung C, Sandoval-Velasco M, Wales N, Schroeder H, Campos PF, Guðmundsdóttir VB, Sicheritz-Ponten T, Petersen B, Halgunset J, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Willerslev E, Balloux F, Marques-Bonet T, Lalueza-Fox C, Nielsen R, Stefánsson K, Helgason A, Gilbert MTP. The population genomic legacy of the second plague pandemic. Curr Biol 2022; 32:4743-4751.e6. [PMID: 36182700 DOI: 10.1016/j.cub.2022.09.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/15/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th-19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.
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Affiliation(s)
- Shyam Gopalakrishnan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark.
| | - S Sunna Ebenesersdóttir
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
| | - Inge K C Lundstrøm
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Gordon Turner-Walker
- National Yunlin University of Science & Technology, 123 University Road, Section 3, 64002 Douliu, Yun-Lin County, Taiwan; Department of Archaeology and Anthropology, National Museum of Natural Science, 1 Guanqian Road, North District Taichung City 404023, Taiwan
| | | | - Pierre Luisi
- Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina; Microbial Paleogenomics Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Ashot Margaryan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Michael D Martin
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Martin Rene Ellegaard
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | | | | | | | | | - Jason E Laffoon
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), Universidad Nacional Autónoma de México (UNAM), 3001 Boulevard Juriquilla, 76230 Querétaro, Mexico
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., San Diego, CA, USA
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Toni de-Dios
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anna K Fotakis
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Miren Iraeta-Orbegozo
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Åshild J Vågene
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | | | - Axel Christophersen
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Filipe G Vieira
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Shanlin Liu
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Torsten Günther
- Evolutionsbiologisk Centrum EBC, Norbyv. 18A, 752 36 Uppsala, Sweden
| | - Toomas Kivisild
- KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Ole Georg Moseng
- Department of Business, History and Social Sciences, University of South-Eastern Norway, Notodden, Norway
| | - Birgitte Skar
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Christina Cheung
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; EA - Eco-anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
| | - Marcela Sandoval-Velasco
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Nathan Wales
- Department of Archaeology, Kings Manor and Principals House, University of York, Exhibition Square, York YO1 7EP, UK
| | - Hannes Schroeder
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Paula F Campos
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
| | - Valdís B Guðmundsdóttir
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
| | - Bent Petersen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
| | | | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark; The Globe Institute, Lundbeck Foundation Center for Geogenetics, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Eske Willerslev
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Francois Balloux
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Museu de Ciències Naturals de Barcelona, 08019 Barcelona, Spain
| | - Rasmus Nielsen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720-3140, USA
| | - Kári Stefánsson
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Agnar Helgason
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
| | - M Thomas P Gilbert
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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5
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Guzmán-Solís AA, Villa-Islas V, Bravo-López MJ, Sandoval-Velasco M, Wesp JK, Gómez-Valdés JA, Moreno-Cabrera MDLL, Meraz A, Solís-Pichardo G, Schaaf P, TenOever BR, Blanco-Melo D, Ávila Arcos MC. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade. eLife 2021; 10:e68612. [PMID: 34350829 PMCID: PMC8423449 DOI: 10.7554/elife.68612] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
After the European colonization of the Americas, there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover the diversity of viral pathogens during this period, we designed an enrichment assay targeting ancient DNA (aDNA) from viruses of clinical importance and applied it to DNA extracts from individuals found in a Colonial hospital and a Colonial chapel (16th-18th century) where records suggest that victims of epidemics were buried during important outbreaks in Mexico City. This allowed us to reconstruct three ancient human parvovirus B19 genomes and one ancient human hepatitis B virus genome from distinct individuals. The viral genomes are similar to African strains, consistent with the inferred morphological and genetic African ancestry of the hosts as well as with the isotopic analysis of the human remains, suggesting an origin on the African continent. This study provides direct molecular evidence of ancient viruses being transported to the Americas during the transatlantic slave trade and their subsequent introduction to New Spain. Altogether, our observations enrich the discussion about the etiology of infectious diseases during the Colonial period in Mexico.
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Affiliation(s)
- Axel A Guzmán-Solís
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoQuerétaroMexico
| | - Viridiana Villa-Islas
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoQuerétaroMexico
| | - Miriam J Bravo-López
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoQuerétaroMexico
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health, University of CopenhagenCopenhagenDenmark
| | - Julie K Wesp
- Department of Sociology and Anthropology, North Carolina State UniversityRaleighUnited States
| | | | | | - Alejandro Meraz
- Instituto Nacional de Antropología e HistoriaMexico CityMexico
| | - Gabriela Solís-Pichardo
- Laboratorio Universitario de Geoquímica Isotópica (LUGIS), Instituto de Geología, Universidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Peter Schaaf
- LUGIS, Instituto de Geofísica, Universidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Benjamin R TenOever
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Daniel Blanco-Melo
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research CenterSeattle, WAUnited States
| | - María C Ávila Arcos
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoQuerétaroMexico
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6
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Westbury MV, Barnett R, Sandoval-Velasco M, Gower G, Vieira FG, de Manuel M, Hansen AJ, Yamaguchi N, Werdelin L, Marques-Bonet T, Gilbert MTP, Lorenzen ED. A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives. Open Res Eur 2021; 1:25. [PMID: 35098251 PMCID: PMC7612286 DOI: 10.12688/openreseurope.13104.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/03/2022]
Abstract
Background: The evolutionary relationships of Felidae during their Early-Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths. Methods: Here, we sequenced a draft nuclear genome of Smilodon populator, dated to 13,182 ± 90 cal BP, making this the oldest palaeogenome from South America to date, a region known to be problematic for ancient DNA preservation. We analysed this genome, together with genomes from other extinct and extant cats to investigate their phylogenetic relationships. Results: We confirm a deep divergence (~20.65 Ma) within sabre-toothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae. Conclusions: Given that some species traditionally assigned to Pseudaelurus originated in the Early Miocene ~20 Ma, this indicates that some species of Pseudaelurus may be younger than the lineages they purportedly gave rise to, further supporting the hypothesis that Pseudaelurus was paraphyletic.
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Affiliation(s)
- Michael V Westbury
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Ross Barnett
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | | | - Graham Gower
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Filipe Garrett Vieira
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Eline D Lorenzen
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
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7
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Bravo-Lopez M, Villa-Islas V, Rocha Arriaga C, Villaseñor-Altamirano AB, Guzmán-Solís A, Sandoval-Velasco M, Wesp JK, Alcantara K, López-Corral A, Gómez-Valdés J, Mejía E, Herrera A, Meraz-Moreno A, Moreno-Cabrera MDLL, Moreno-Estrada A, Nieves-Colón MA, Olvera J, Pérez-Pérez J, Iversen KH, Rasmussen S, Sandoval K, Zepeda G, Ávila-Arcos MC. Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190580. [PMID: 33012233 PMCID: PMC7702795 DOI: 10.1098/rstb.2019.0580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
The 'red complex' is an aggregate of three oral bacteria (Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient T.forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from the Pre-Hispanic to the Colonial period in Mexico. We recovered twelve partial ancient T. forsythia genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the T. forsythia ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa. This study highlights the potential for studying ancient T. forsythia genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Viridiana Villa-Islas
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Carolina Rocha Arriaga
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Ana B. Villaseñor-Altamirano
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Axel Guzmán-Solís
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Julie K. Wesp
- Department of Sociology and Anthropology, North Carolina State University, Raleigh, NC 27695, USA
| | - Keitlyn Alcantara
- Department of Anthropology, Indiana University-Bloomington, Bloomington, IN 47405, USA
| | - Aurelio López-Corral
- Department of Archeology, National Institute of Anthropology and History, Tlaxcala, 90000, Mexico
| | | | - Elizabeth Mejía
- National Institute of Anthropology and History, Querétaro, 76000, Mexico
| | - Alberto Herrera
- National Institute of Anthropology and History, Querétaro, 76000, Mexico
| | | | | | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Maria A. Nieves-Colón
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Joel Olvera
- Graduate Program of Physical Anthropology, National School of Anthropology and History, Mexico City, 14030, Mexico
| | - Julia Pérez-Pérez
- National School of Anthropology and History, Mexico City, 14030, Mexico
| | - Katrine Højholt Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Gabriela Zepeda
- National Institute of Anthropology and History, Guanajuato, 36250, Mexico
| | - María C. Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
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8
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Barnett R, Westbury MV, Sandoval-Velasco M, Vieira FG, Jeon S, Zazula G, Martin MD, Ho SYW, Mather N, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Zepeda-Mendoza ML, Antunes A, Baez AC, De Cahsan B, Larson G, O'Brien SJ, Eizirik E, Johnson WE, Koepfli KP, Wilting A, Fickel J, Dalén L, Lorenzen ED, Marques-Bonet T, Hansen AJ, Zhang G, Bhak J, Yamaguchi N, Gilbert MTP. Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens. Curr Biol 2020; 30:5018-5025.e5. [PMID: 33065008 PMCID: PMC7762822 DOI: 10.1016/j.cub.2020.09.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/10/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022]
Abstract
Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6, 7, 8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11, 12, 13, 14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage. Nuclear genome and exome analyses of extinct scimitar-toothed cat, Homotherium latidens Homotherium was a highly divergent lineage from all living cat species (∼22.5 Ma) Genetic adaptations to cursorial and diurnal hunting behaviors Relatively high levels of genetic diversity in this individual
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Affiliation(s)
- Ross Barnett
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark.
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Filipe Garrett Vieira
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism and Culture, Government of Yukon, PO Box 2703, Whitehorse, YT Y1A 2C6, Canada
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Niklas Mather
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, Barcelona 08003, Spain
| | - M Lisandra Zepeda-Mendoza
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; School of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Porto 4169-007, Portugal
| | - Aldo Carmona Baez
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Binia De Cahsan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, 49 Kronverkskiy Pr., St. Petersburg 197101, Russia; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 8000 North Ocean Drive. Ft Lauderdale, FL 33004, USA
| | - Eduardo Eizirik
- Laboratory of Genomics and Molecular Biology, Escola de Ciências da Saúde e da Vida, PUCRS, Porto Alegre, RS, Brazil; INCT Ecologia, Evolução e Conservação da Biodiversidade (INCT-EECBio), Goiânia, GO, Brazil; Instituto Pró-Carnívoros, Atibaia, SP, Brazil
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA; The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD 20746-2863, USA; Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam 14476, Germany
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm SE-10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden
| | - Eline D Lorenzen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, Barcelona 08003, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats, ICREA, Barcelona 08003, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyola del Vallès, Barcelona 08193, Spain
| | - Anders J Hansen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Clinomics, Inc., Ulsan 44919, Republic of Korea; Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark.
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9
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Sandoval-Velasco M, Rodríguez JA, Perez Estrada C, Zhang G, Lieberman Aiden E, Marti-Renom MA, Gilbert MTP, Smith O. Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform. Gigascience 2020; 9:giaa087. [PMID: 32845983 PMCID: PMC7448675 DOI: 10.1093/gigascience/giaa087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/15/2020] [Accepted: 07/23/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Hi-C experiments couple DNA-DNA proximity with next-generation sequencing to yield an unbiased description of genome-wide interactions. Previous methods describing Hi-C experiments have focused on the industry-standard Illumina sequencing. With new next-generation sequencing platforms such as BGISEQ-500 becoming more widely available, protocol adaptations to fit platform-specific requirements are useful to give increased choice to researchers who routinely generate sequencing data. RESULTS We describe an in situ Hi-C protocol adapted to be compatible with the BGISEQ-500 high-throughput sequencing platform. Using zebra finch (Taeniopygia guttata) as a biological sample, we demonstrate how Hi-C libraries can be constructed to generate informative data using the BGISEQ-500 platform, following circularization and DNA nanoball generation. Our protocol is a modification of an Illumina-compatible method, based around blunt-end ligations in library construction, using un-barcoded, distally overhanging double-stranded adapters, followed by amplification using indexed primers. The resulting libraries are ready for circularization and subsequent sequencing on the BGISEQ series of platforms and yield data similar to what can be expected using Illumina-compatible approaches. CONCLUSIONS Our straightforward modification to an Illumina-compatible in situHi-C protocol enables data generation on the BGISEQ series of platforms, thus expanding the options available for researchers who wish to utilize the powerful Hi-C techniques in their research.
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Affiliation(s)
- Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Juan Antonio Rodríguez
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Baldiri i Reixach, 4-8, 08028 Barcelona, Spain
| | - Cynthia Perez Estrada
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Computer Science and Computational Applied Mathematics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Baldiri i Reixach, 4-8, 08028 Barcelona, Spain
- Centre for Genomic Regulation, Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain
- Pompeu Fabra University, Doctor Aiguader 88, Barcelona 08003, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
| | - Oliver Smith
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
- Micropathology Ltd, University of Warwick Science Park, Coventry CV4 7EZ, UK
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10
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Nägele K, Posth C, Iraeta Orbegozo M, Chinique de Armas Y, Hernández Godoy ST, González Herrera UM, Nieves-Colón MA, Sandoval-Velasco M, Mylopotamitaki D, Radzeviciute R, Laffoon J, Pestle WJ, Ramos-Madrigal J, Lamnidis TC, Schaffer WC, Carr RS, Day JS, Arredondo Antúnez C, Rangel Rivero A, Martínez-Fuentes AJ, Crespo-Torres E, Roksandic I, Stone AC, Lalueza-Fox C, Hoogland M, Roksandic M, Hofman CL, Krause J, Schroeder H. Genomic insights into the early peopling of the Caribbean. Science 2020; 369:456-460. [PMID: 32499399 DOI: 10.1126/science.aba8697] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/31/2022]
Abstract
The Caribbean was one of the last regions of the Americas to be settled by humans, but where they came from and how and when they reached the islands remain unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200 and 400 calibrated years before the present and found evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detected genetic differences between the early settlers and the newcomers from South America, with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas.
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Affiliation(s)
- Kathrin Nägele
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Miren Iraeta Orbegozo
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Silvia Teresita Hernández Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | | | - Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Marcela Sandoval-Velasco
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorothea Mylopotamitaki
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rita Radzeviciute
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jason Laffoon
- Faculty of Archaeology, Leiden University, Leiden, Netherlands
| | | | - Jazmin Ramos-Madrigal
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - William C Schaffer
- Liberal Arts Department, Phoenix College, Phoenix, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Robert S Carr
- Archaeological and Historical Conservancy Inc., Davie, FL, USA
| | - Jane S Day
- Research Atlantica Inc., Boca Raton, FL, USA
| | | | - Armando Rangel Rivero
- Museo Antropológico Montané, Facultad de Biología, Universidad de La Habana, Havana, Cuba
| | | | - Edwin Crespo-Torres
- Departamento de Sociología y Antropología, Universidad de Puerto Rico Rio Piedras, San Juan, Puerto Rico
| | - Ivan Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, Spanish National Research Council (CSIC)-Universitat Pompeu Fabra, Barcelona, Spain
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Leiden, Netherlands.,Royal Netherlands Institute of Southeast Asian and Caribbean Studies, Leiden, Netherlands
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Corinne L Hofman
- Faculty of Archaeology, Leiden University, Leiden, Netherlands.,Royal Netherlands Institute of Southeast Asian and Caribbean Studies, Leiden, Netherlands
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Faculty of Archaeology, Leiden University, Leiden, Netherlands
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11
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de Manuel M, Barnett R, Sandoval-Velasco M, Yamaguchi N, Garrett Vieira F, Zepeda Mendoza ML, Liu S, Martin MD, Sinding MHS, Mak SST, Carøe C, Liu S, Guo C, Zheng J, Zazula G, Baryshnikov G, Eizirik E, Koepfli KP, Johnson WE, Antunes A, Sicheritz-Ponten T, Gopalakrishnan S, Larson G, Yang H, O'Brien SJ, Hansen AJ, Zhang G, Marques-Bonet T, Gilbert MTP. The evolutionary history of extinct and living lions. Proc Natl Acad Sci U S A 2020; 117:10927-10934. [PMID: 32366643 PMCID: PMC7245068 DOI: 10.1073/pnas.1919423117] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lions are one of the world's most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species.
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Affiliation(s)
- Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Ross Barnett
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia;
| | - Filipe Garrett Vieira
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - M Lisandra Zepeda Mendoza
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
- School of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, B15 2TT Edgbaston, Birmingham, United Kingdom
| | | | - Michael D Martin
- Norwegian University of Science and Technology (NTNU) University Museum, 7012 Trondheim, Norway
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Sarah S T Mak
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Shanlin Liu
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
- BGI-Shenzhen, 518083 Shenzhen, China
| | | | - Jiao Zheng
- BGI-Shenzhen, 518083 Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, 518083 Shenzhen, China
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism and Culture, Government of Yukon, Y1A 2C6 Whitehorse, Yukon, Canada
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Eduardo Eizirik
- Laboratory of Genomics and Molecular Biology, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS 90619-900, Brazil
- Instituto Nacional de Ciência e Tecnologia - Ecologia Evolução e Conservação da Biodiversidade (INCT-EECBio), Goiânia, GO 74690-900, Brazil
- Instituto Pró-Carnívoros, Atibaia, SP 12945-010, Brazil
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD 20746-2863
- Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Agostinho Antunes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Thomas Sicheritz-Ponten
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, OX1 3QY Oxford, United Kingdom
| | - Huanming Yang
- BGI-Shenzhen, 518083 Shenzhen, China
- James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO (Information Technologies, Mechanics and Optics) University, 197101 St. Petersburg, Russia;
- Guy Harvey Oceanographic Center Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft. Lauderdale, FL 33004
| | - Anders J Hansen
- Section for GeoGenetics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Guojie Zhang
- BGI-Shenzhen, 518083 Shenzhen, China
- Section for Ecology and Evolution, Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain;
- Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation (CNAG-CRG), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark;
- Norwegian University of Science and Technology (NTNU) University Museum, 7012 Trondheim, Norway
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12
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van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Mol Biol Evol 2020; 37:773-785. [PMID: 31697387 PMCID: PMC7038659 DOI: 10.1093/molbev/msz264] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Adrien Rieux
- CIRAD, UMR PVBMT, St. Pierre de la Réunion, France
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Fregel
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Spain
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Population Health and Immunity Division, Walter & Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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13
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Gelabert P, Sandoval-Velasco M, Serres A, de Manuel M, Renom P, Margaryan A, Stiller J, de-Dios T, Fang Q, Feng S, Mañosa S, Pacheco G, Ferrando-Bernal M, Shi G, Hao F, Chen X, Petersen B, Olsen RA, Navarro A, Deng Y, Dalén L, Marquès-Bonet T, Zhang G, Antunes A, Gilbert MTP, Lalueza-Fox C. Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet. Curr Biol 2019; 30:108-114.e5. [PMID: 31839456 DOI: 10.1016/j.cub.2019.10.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/03/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022]
Abstract
As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. The cause of its extinction remains contentious: besides excessive mortality associated to habitat destruction and active hunting, their survival could have been negatively affected by its range having become increasingly patchy [2] or by the exposure to poultry pathogens [3, 4]. In addition, the Carolina parakeet showed a predilection for cockleburs, an herbaceous plant that contains a powerful toxin, carboxyatractyloside, or CAT [5], which did not seem to affect them but made the birds notoriously toxic to most predators [3]. To explore the demographic history of this bird, we generated the complete genomic sequence of a preserved specimen held in a private collection in Espinelves (Girona, Spain), as well as of a close extant relative, Aratinga solstitialis. We identified two non-synonymous genetic changes in two highly conserved proteins known to interact with CAT that could underlie a specific dietary adaptation to this toxin. Our genomic analyses did not reveal evidence of a dramatic past demographic decline in the Carolina parakeet; also, its genome did not exhibit the long runs of homozygosity that are signals of recent inbreeding and are typically found in endangered species. As such, our results suggest its extinction was an abrupt process and thus likely solely attributable to human causes.
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Affiliation(s)
- Pere Gelabert
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Aitor Serres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Pere Renom
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ashot Margaryan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Shenzhen 518083, China
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Shenzhen 518083, China
| | - Santi Mañosa
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Facultat de Biologia, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Manuel Ferrando-Bernal
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guolin Shi
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Fei Hao
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Xianqing Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Semeling Road, 08100 Kedah, Malaysia
| | - Remi-André Olsen
- ScieLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Frescativägen 40, SE-17121 Solna, Sweden
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08036 Barcelona, Spain
| | - Yuan Deng
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Shenzhen 518083, China
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 40, 10405 Stockholm, Sweden
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08036 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, c. de les Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; NTNU University Museum, Erling Skakkes gate 47c, 7012 Trondheim, Norway.
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain.
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Thomas JE, Carvalho GR, Haile J, Rawlence NJ, Martin MD, Ho SYW, Sigfússon AÞ, Jósefsson VA, Frederiksen M, Linnebjerg JF, Samaniego Castruita JA, Niemann J, Sinding MHS, Sandoval-Velasco M, Soares AER, Lacy R, Barilaro C, Best J, Brandis D, Cavallo C, Elorza M, Garrett KL, Groot M, Johansson F, Lifjeld JT, Nilson G, Serjeanston D, Sweet P, Fuller E, Hufthammer AK, Meldgaard M, Fjeldså J, Shapiro B, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLife 2019; 8:e47509. [PMID: 31767056 PMCID: PMC6879203 DOI: 10.7554/elife.47509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/22/2019] [Indexed: 01/23/2023] Open
Abstract
The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
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Affiliation(s)
- Jessica E Thomas
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
| | - James Haile
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Michael D Martin
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Simon YW Ho
- School of Life and Environmental SciencesUniversity of SydneySydneyAustralia
| | | | | | | | | | | | - Jonas Niemann
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Mikkel-Holger S Sinding
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Greenland Institute of Natural ResourcesNuukGreenland
| | | | - André ER Soares
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Robert Lacy
- Department of Conservation ScienceChicago Zoological SocietyBrookfieldUnited States
| | | | - Juila Best
- Department of Archaeology, Anthropology and Forensic Science, Faculty of Science and TechnologyBournemouth UniversityPooleUnited Kingdom
- School of History, Archaeology and ReligionCardiff UniversityCardiffUnited Kingdom
| | | | - Chiara Cavallo
- Amsterdam Centre for Ancient Studies and ArchaeologyUniversity of AmsterdamAmsterdamNetherlands
| | - Mikelo Elorza
- Arqueología PrehistóricaSociedad de Ciencias AranzadiSan SebastiánSpain
| | - Kimball L Garrett
- Natural History Museum of Los Angeles CountyLos AngelesUnited States
| | - Maaike Groot
- Institut für Prähistorische ArchäologieFreie Universität BerlinBerlinGermany
| | | | | | - Göran Nilson
- Gothenburg Museum of Natural HistoryGothenburgSweden
| | - Dale Serjeanston
- Humanities ArchaeologyUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Paul Sweet
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkUnited States
| | | | | | | | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural SciencesUniversity of PotsdamPotsdamGermany
| | - John R Stewart
- Faculty of Science and TechnologyBournemouth UniversityDorsetUnited Kingdom
| | - M Thomas P Gilbert
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Michael Knapp
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
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15
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de-Dios T, van Dorp L, Gelabert P, Carøe C, Sandoval-Velasco M, Fregel R, Escosa R, Aranda C, Huijben S, Balloux F, Gilbert MTP, Lalueza-Fox C. Genetic affinities of an eradicated European Plasmodium falciparum strain. Microb Genom 2019; 5. [PMID: 31454309 PMCID: PMC6807384 DOI: 10.1099/mgen.0.000289] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Malaria was present in most of Europe until the second half of the 20th century, when it was eradicated through a combination of increased surveillance and mosquito control strategies, together with cross-border and political collaboration. Despite the severe burden of malaria on human populations, it remains contentious how the disease arrived and spread in Europe. Here, we report a partial Plasmodium falciparum nuclear genome derived from a set of antique medical slides stained with the blood of malaria-infected patients from Spain’s Ebro Delta, dating to the 1940s. Our analyses of the genome of this now eradicated European P. falciparum strain confirms stronger phylogeographical affinity to present-day strains in circulation in central south Asia, rather than to those in Africa. This points to a longitudinal, rather than a latitudinal, spread of malaria into Europe. In addition, this genome displays two derived alleles in the pfmrp1 gene that have been associated with drug resistance. Whilst this could represent standing variation in the ancestral P. falciparum population, these mutations may also have arisen due to the selective pressure of quinine treatment, which was an anti-malarial drug already in use by the time the sample we sequenced was mounted on a slide.
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Affiliation(s)
- Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Christian Carøe
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad of La Laguna, 38206 La Laguna, Spain.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), 43580 Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, 08980 Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - François Balloux
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - M Thomas P Gilbert
- Norwegian University of Science and Technology (NTNU) University Museum, N-7491 Trondheim, Norway.,Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1353 Copenhagen, Denmark
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Ebenesersdóttir SS, Sandoval-Velasco M, Gunnarsdóttir ED, Jagadeesan A, Guðmundsdóttir VB, Thordardóttir EL, Einarsdóttir MS, Moore KHS, Sigurðsson Á, Magnúsdóttir DN, Jónsson H, Snorradóttir S, Hovig E, Møller P, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Cavalleri GL, Gilbert E, Lalueza-Fox C, Walser JW, Kristjánsdóttir S, Gopalakrishnan S, Árnadóttir L, Magnússon ÓÞ, Gilbert MTP, Stefánsson K, Helgason A. Ancient genomes from Iceland reveal the making of a human population. Science 2018; 360:1028-1032. [PMID: 29853688 DOI: 10.1126/science.aar2625] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/25/2018] [Indexed: 12/14/2022]
Abstract
Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.
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Affiliation(s)
- S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland. .,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Marcela Sandoval-Velasco
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Ellen D Gunnarsdóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Anuradha Jagadeesan
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Valdís B Guðmundsdóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Elísabet L Thordardóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Margrét S Einarsdóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Pål Møller
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Human Medicine, Universität Witten/Herdecke, Witten, Germany.,Research Group Inherited Cancer, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark.,Danish Headache Center, Department of Neurology, Copenhagen University hospital, DK-2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark
| | - Gianpiero L Cavalleri
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, Ireland
| | - Edmund Gilbert
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, Ireland
| | | | - Joe W Walser
- National Museum of Iceland, Reykjavik, Iceland.,Department of Archaeology, University of Iceland, Reykjavik, Iceland
| | - Steinunn Kristjánsdóttir
- National Museum of Iceland, Reykjavik, Iceland.,Department of Archaeology, University of Iceland, Reykjavik, Iceland
| | - Shyam Gopalakrishnan
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | | | | | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.,Norwegian University of Science and Techonology, University Museum, 7491 Trondheim, Norway
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland. .,Faculity of Medicine, University of Iceland, Reykjavik, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland. .,Department of Anthropology, University of Iceland, Reykjavik, Iceland
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17
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Olalde I, Schroeder H, Sandoval-Velasco M, Vinner L, Lobón I, Ramirez O, Civit S, García Borja P, Salazar-García DC, Talamo S, María Fullola J, Xavier Oms F, Pedro M, Martínez P, Sanz M, Daura J, Zilhão J, Marquès-Bonet T, Gilbert MTP, Lalueza-Fox C. A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures. Mol Biol Evol 2015; 32:3132-42. [PMID: 26337550 PMCID: PMC4652622 DOI: 10.1093/molbev/msv181] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the Danube River into Central Europe. Although genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400-year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter–gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.
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Affiliation(s)
- Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Marcela Sandoval-Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Irene Lobón
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Oscar Ramirez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Sergi Civit
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Pablo García Borja
- Departament de Prehistòria i Arqueologia, Universitat de València, València, Spain
| | - Domingo C Salazar-García
- Departament de Prehistòria i Arqueologia, Universitat de València, València, Spain Department of Archaeology, University of Cape Town, Cape Town, South Africa LAMPEA UMR 7269, Maison Méditerranéenne des Sciences de l'Homme (MMSH), Aix-en-Provence, France Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Josep María Fullola
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Xavier Oms
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Mireia Pedro
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Pablo Martínez
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain Col·Lectiu per a la Investigació de la Prehistòria i l'Arqueologia del Garraf-Ordal, CIPAG, Begues, Spain
| | - Montserrat Sanz
- Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal
| | - Joan Daura
- Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal GRQ, Grup de Recerca del Quaternari, Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - João Zilhão
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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