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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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2
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Iwanycki Ahlstrand N, Gopalakrishnan S, Vieira FG, Bieker VC, Meudt HM, Dunbar-Co S, Rothfels CJ, Martinez-Swatson KA, Maldonado C, Hassemer G, Shipunov A, Bowers MD, Gardner E, Xu M, Ghorbani A, Amano M, Grace OM, Pringle JS, Bishop M, Manzanilla V, Cotrim H, Blaney S, Zubov D, Choi HK, Yesil Y, Bennett B, Vimolmangkang S, El-Seedi HR, Staub PO, Li Z, Boldbaatar D, Hislop M, Caddy LJ, Muasya AM, Saslis-Lagoudakis CH, Gilbert MTP, Zerega NJC, Rønsted N. Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes. Front Plant Sci 2022; 13:838166. [PMID: 35755675 PMCID: PMC9218338 DOI: 10.3389/fpls.2022.838166] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species' establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.
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Affiliation(s)
| | - Shyam Gopalakrishnan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Filipe G. Vieira
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Vanessa C. Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | | | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | | | - Carla Maldonado
- Herbario Nacional de Bolivia, Universidad Mayor de San Andres, La Paz, Bolivia
| | | | - Alexey Shipunov
- Department of Biology, Minot University, Minot, ND, United States
| | - M. Deane Bowers
- Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
| | - Elliot Gardner
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Chicago, IL, United States
- Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
| | - Maonian Xu
- Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
| | - Abdolbaset Ghorbani
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Makoto Amano
- Natural History Museum and Institute, Chiba, Japan
| | - Olwen M. Grace
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Madonna Bishop
- Memorial University Botanical Garden, St. John’s, NL, Canada
| | | | - Helena Cotrim
- Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Sean Blaney
- Atlantic Canada Conservation Data Centre, Sackville, NB, Canada
| | | | - Hong-Keun Choi
- Department of Life Sciences, Ajou University, Suweon, South Korea
| | - Yeter Yesil
- Department of Pharmaceutical Botany, Istanbul University, Istanbul, Turkey
| | - Bruce Bennett
- Yukon Conservation Data Centre, Yukon Territory, YT, Canada
| | - Sornkanok Vimolmangkang
- Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand
| | - Hesham R. El-Seedi
- Pharmacognosy Group, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Peter O. Staub
- Department of Biomedical Science, University of Cagliari, Cagliari, Italy
| | - Zhu Li
- Chinese Academy of Sciences, Beijing, China
| | - Delgerbat Boldbaatar
- Department of Liver Center, National University of Mongolia, Ulaanbaatar, Mongolia
| | | | - Laura J. Caddy
- Botanical Garden, The University of British Columbia, Vancouver, BC, Canada
| | - A. Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | | | | | - Nyree J. C. Zerega
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Chicago, IL, United States
- Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
| | - Nina Rønsted
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- National Tropical Botanic Garden, Kaua‘i, HI, United States
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3
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Liu X, Schjøtt SR, Granquist SM, Rosing-Asvid A, Dietz R, Teilmann J, Galatius A, Cammen K, O Corry-Crowe G, Harding K, Härkönen T, Hall A, Carroll EL, Kobayashi Y, Hammill M, Stenson G, Frie AK, Lydersen C, Kovacs KM, Andersen LW, Hoffman JI, Goodman SJ, Vieira FG, Heller R, Moltke I, Tange Olsen M. Origin and expansion of the world's most widespread pinniped: range-wide population genomics of the harbour seal (Phoca vitulina). Mol Ecol 2022; 31:1682-1699. [PMID: 35068013 PMCID: PMC9306526 DOI: 10.1111/mec.16365] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Received: 10/04/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonised virtually the whole of the Northern Hemisphere. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic SNPs from 286 individuals sampled from 22 localities across the species' range. Our results point to a Northeast Pacific origin, colonisation of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonise and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.
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Affiliation(s)
- Xiaodong Liu
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | | | - Sandra M Granquist
- Icelandic Seal Centre, Höfðabraut 6, 530, Hvammstangi, Iceland.,Marine and Freshwater Research Institute, Institute of Freshwater Fisheries Fornubúðir 5, 220, Hafnarfjörður, Iceland
| | | | - Rune Dietz
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Jonas Teilmann
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Anders Galatius
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | | | - Greg O Corry-Crowe
- Wildlife Evolution and Behavior Program, Florida Atlantic University, USA
| | - Karin Harding
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
| | | | - Ailsa Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, UK, KY16 8LB
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Yumi Kobayashi
- Laboratory of Animal Ecology, Research Faculty of Agriculture, Hokkaido University, Japan
| | - Mike Hammill
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, P.O. Box 1000, Mont-Joli, QC, Canada
| | - Garry Stenson
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, P.O. Box 5667, St. John's NL, Canada
| | | | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | | | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, 33501, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Simon J Goodman
- School of Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Filipe G Vieira
- Center for Genomic Medicine, Copenhagen University Hospitalet, Denmark
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Denmark
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4
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Sinding MHS, Ciucani MM, Ramos-Madrigal J, Carmagnini A, Rasmussen JA, Feng S, Chen G, Vieira FG, Mattiangeli V, Ganjoo RK, Larson G, Sicheritz-Pontén T, Petersen B, Frantz L, Gilbert MTP, Bradley DG. Kouprey ( Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience 2021; 24:103226. [PMID: 34712923 PMCID: PMC8531564 DOI: 10.1016/j.isci.2021.103226] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Received: 04/13/2021] [Revised: 08/11/2021] [Accepted: 10/01/2021] [Indexed: 12/30/2022] Open
Abstract
The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so. We generated two genomes from the likely extinct kouprey (Bos sauveli) Extensive mt and nuclear-genome-wide incomplete lineage sorting across wild Asian Bos Initial polytomic diversification of the wild Asian Bos—kouprey, banteng, and gaur
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Affiliation(s)
| | | | | | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Jacob Agerbo Rasmussen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Guangji Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - M. Thomas P. Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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5
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Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, Westbury MV, de Manuel M, Margaryan A, Ciucani MM, Vieira FG, Patramanis Y, Kalthoff DC, Timmons Z, Sicheritz-Pontén T, Dalén L, Ryder OA, Zhang G, Marquès-Bonet T, Moodley Y, Gilbert MTP. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). Mol Ecol 2021; 30:6355-6369. [PMID: 34176179 PMCID: PMC9291831 DOI: 10.1111/mec.16043] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 01/08/2023]
Abstract
Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.
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Affiliation(s)
| | - Shyam Gopalakrishnan
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,DTU Bioinformatics, Kongens Lyngby, Hovedstaden, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - Ashot Margaryan
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Marta M Ciucani
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Filipe G Vieira
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Zena Timmons
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Thomas Sicheritz-Pontén
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,BGI-Shenzhen, Shenzhen, China
| | - Tomás Marquès-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain.,National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - M Thomas P Gilbert
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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6
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Hansen AR, Borgwardt L, Rasmussen ÅK, Godballe C, Poulsen MM, Vieira FG, Mathiesen JS, Rossing M. Germline RET Leu56Met Variant Is Likely Not Causative of Multiple Endocrine Neoplasia Type 2. Front Endocrinol (Lausanne) 2021; 12:764512. [PMID: 34925234 PMCID: PMC8672160 DOI: 10.3389/fendo.2021.764512] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
Activating variants in the receptor tyrosine kinase REarranged during Transfection (RET) cause multiple endocrine neoplasia type 2 (MEN 2), an autosomal dominantly inherited cancer-susceptibility syndrome. The variant c.166C>A, p.Leu56Met in RET was recently reported in two patients with medullary thyroid cancer (MTC). The presence of a pheochromocytoma in one of the patients, suggested a possible pathogenic role of the variant in MEN 2A. Here, we present clinical follow up of a Danish RET Leu56Met cohort. Patients were evaluated for signs of MEN 2 according to a set of predefined criteria. None of the seven patients in our cohort exhibited evidence of MEN 2. Furthermore, we found the Leu56Met variant in our in-house diagnostic cohort with an allele frequency of 0.59%, suggesting that it is a common variant in the population. Additionally, none of the patients who harbored the allele were listed in the Danish MTC and MEN 2 registries. In conclusion, our findings do not support a pathogenic role of the Leu56Met variant in MEN 2.
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Affiliation(s)
- Anna Reimer Hansen
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Line Borgwardt
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Åse Krogh Rasmussen
- Department of Endocrinology and Metabolism, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christian Godballe
- Department of Otorhinolaryngology, Head & Neck Surgery and Audiology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Morten Møller Poulsen
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Filipe G. Vieira
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jes Sloth Mathiesen
- Department of Otorhinolaryngology, Head & Neck Surgery and Audiology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maria Rossing
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Maria Rossing,
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7
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Sinding MHS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Carøe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jørgensen MP, Dietz R, Sonne C, Meldgaard M, Dalén L, Larson G, Petersen B, Sicheritz-Pontén T, Bachmann L, Wiig Ø, Marques-Bonet T, Hansen AJ, Gilbert MTP. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition. Science 2020; 368:1495-1499. [PMID: 32587022 DOI: 10.1126/science.aaz8599] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/06/2020] [Indexed: 12/18/2022]
Abstract
Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
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Affiliation(s)
- Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Natural History Museum, University of Oslo, Oslo, Norway.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | | | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Filipe G Vieira
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,BioArch, Department of Archaeology, University of York, York, UK
| | | | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emilie U Andersen-Ranberg
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Clinical Veterinary Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter D Jordan
- Arctic Centre and Groningen Institute of Archaeology, University of Groningen, Netherlands
| | - Elena Y Pavlova
- Arctic and Antarctic Research Institute, St. Petersburg, Russia
| | | | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Varvara V Ivanova
- VNIIOkeangeologia Research Institute (The All-Russian Research Institute of Geology and Mineral Resources of the World Ocean), St. Petersburg, Russia
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Danish Institute for Advanced Study (D-IAS), University of Southern Denmark, Odense, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Francis Crick Institute, London, UK
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sanne Eline Wennerberg
- Ministry of Fisheries, Hunting and Agriculture, Government of Greenland, Nuuk, Greenland
| | | | - Rune Dietz
- Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
| | - Christian Sonne
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark.,Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Morten Meldgaard
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Bent Petersen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Pontén
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain. .,Catalan Institution of Research and Advanced Studies, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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8
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Gopalakrishnan S, Sinding MHS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Carøe C, de Manuel Montero M, Kuderna L, Serres A, González-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP. Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Curr Biol 2019; 29:4152. [PMID: 31794747 PMCID: PMC6892301 DOI: 10.1016/j.cub.2019.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Fox EA, Wright AE, Fumagalli M, Vieira FG. ngsLD: evaluating linkage disequilibrium using genotype likelihoods. Bioinformatics 2019; 35:3855-3856. [DOI: 10.1093/bioinformatics/btz200] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 12/27/2018] [Accepted: 03/20/2019] [Indexed: 12/21/2022] Open
Abstract
Abstract
Motivation
Linkage disequilibrium (LD) measures the correlation between genetic loci and is highly informative for association mapping and population genetics. As many studies rely on called genotypes for estimating LD, their results can be affected by data uncertainty, especially when employing a low read depth sequencing strategy. Furthermore, there is a manifest lack of tools for the analysis of large-scale, low-depth and short-read sequencing data from non-model organisms with limited sample sizes.
Results
ngsLD addresses these issues by estimating LD directly from genotype likelihoods in a fast, reliable and user-friendly implementation. This method makes use of the full information available from sequencing data and provides accurate estimates of linkage disequilibrium patterns compared with approaches based on genotype calling. We conducted a case study to investigate how LD decays over physical distance in two avian species.
Availability and implementation
The methods presented in this work were implemented in C/C and are freely available for non-commercial use from https://github.com/fgvieira/ngsLD.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emma A Fox
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Filipe G Vieira
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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10
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Alves JM, Carneiro M, Cheng JY, Lemos de Matos A, Rahman MM, Loog L, Campos PF, Wales N, Eriksson A, Manica A, Strive T, Graham SC, Afonso S, Bell DJ, Belmont L, Day JP, Fuller SJ, Marchandeau S, Palmer WJ, Queney G, Surridge AK, Vieira FG, McFadden G, Nielsen R, Gilbert MTP, Esteves PJ, Ferrand N, Jiggins FM. Parallel adaptation of rabbit populations to myxoma virus. Science 2019; 363:1319-1326. [PMID: 30765607 DOI: 10.1126/science.aau7285] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/10/2018] [Accepted: 02/01/2019] [Indexed: 12/18/2022]
Abstract
In the 1950s the myxoma virus was released into European rabbit populations in Australia and Europe, decimating populations and resulting in the rapid evolution of resistance. We investigated the genetic basis of resistance by comparing the exomes of rabbits collected before and after the pandemic. We found a strong pattern of parallel evolution, with selection on standing genetic variation favoring the same alleles in Australia, France, and the United Kingdom. Many of these changes occurred in immunity-related genes, supporting a polygenic basis of resistance. We experimentally validated the role of several genes in viral replication and showed that selection acting on an interferon protein has increased the protein's antiviral effect.
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Affiliation(s)
- Joel M Alves
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK. .,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal.,Palaeogenomics and Bio-Archaeology Research Network Research Laboratory for Archaeology and History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Jade Y Cheng
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Ana Lemos de Matos
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Masmudur M Rahman
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Liisa Loog
- Palaeogenomics and Bio-Archaeology Research Network Research Laboratory for Archaeology and History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK.,Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.,Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA.,Department of Archaeology, University of York, King's Manor, York YO1 7EP, UK
| | - Anders Eriksson
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Tanja Strive
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia.,Centre for Invasive Species Solutions, University of Canberra, Bruce, ACT 2601, Australia
| | - Stephen C Graham
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Diana J Bell
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Laura Belmont
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Jonathan P Day
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Susan J Fuller
- School of Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | | | - William J Palmer
- The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Guillaume Queney
- ANTAGENE, Wildlife Genetics Laboratory, La Tour de Salvagny (Lyon), France
| | - Alison K Surridge
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Grant McFadden
- The Biodesign Institute, Center for Immunotherapy, Vaccines, and Virotherapy, Arizona State University, Tempe, AZ 85287-5401, USA
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark.,Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park 2006, South Africa
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
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11
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Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MHS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP. Erratum to: Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience 2018; 7:5232643. [PMID: 30535251 PMCID: PMC6284137 DOI: 10.1093/gigascience/giy151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Sarah Siu Tze Mak
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7,1350 Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7,1350 Copenhagen, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7,1350 Copenhagen, Denmark.,DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | | | - Shanlin Liu
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7,1350 Copenhagen, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7,1350 Copenhagen, Denmark.,Natural History Museum, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway.,The Qimmeq Project, University of Greenland, Manutooq 1, PO Box 1061, 3905 Nuussuaq, Greenland
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | | | - Shujin Fu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7,1350 Copenhagen, Denmark
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, ul. Kulakovskogo 48, 677980 Yakutsk, Russia
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Thomas Sicheritz-Pontén
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen 518083, China
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7,1350 Copenhagen, Denmark.,Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, 6102 Perth, Australia.,Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
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12
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Gopalakrishnan S, Sinding MHS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Carøe C, Montero MDM, Kuderna L, Serres A, González-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP. Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Curr Biol 2018; 28:3441-3449.e5. [PMID: 30344120 PMCID: PMC6224481 DOI: 10.1016/j.cub.2018.08.041] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [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: 10/09/2017] [Revised: 04/30/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022]
Abstract
The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a "ghost" basal canid lineage.
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Affiliation(s)
- Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Natural History Museum, University of Oslo, Oslo, Norway; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; University of Greenland, Manuutoq 1, Nuuk, Greenland
| | - Jazmín Ramos-Madrigal
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jose A Samaniego Castruita
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Aitor Serres
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | | | - Yan-Hu Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 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
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA
| | - Carlos Fernandes
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM-CNRS-IRD-EPHE, Université de Montpellier, Montpellier, France
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Prospekt, St. Petersburg 199034, Russia
| | - Jane Budd
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Eli Knispel Rueness
- Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Claudio Sillero
- Wildlife Conservation Research Unit, Zoology, University of Oxford, Tubney House, Tubney OX13 5QL, UK; IUCN SSC Canid Specialist Group, Oxford, UK
| | - Mads Peter Heide-Jørgensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Ponten
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; University of Greenland, Manuutoq 1, Nuuk, Greenland
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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13
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Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MHS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience 2018; 6:1-13. [PMID: 28854615 PMCID: PMC5570000 DOI: 10.1093/gigascience/gix049] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [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] [Received: 03/05/2017] [Accepted: 06/20/2017] [Indexed: 12/30/2022] Open
Abstract
Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction–amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
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Affiliation(s)
- Sarah Siu Tze Mak
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | | | - Shanlin Liu
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Natural History Museum, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway.,The Qimmeq Project, University of Greenland, Manutooq 1, PO Box 1061, 3905 Nuussuaq, Greenland
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | | | - Shujin Fu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, ul. Kulakovskogo 48, 677980 Yakutsk, Russia
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Thomas Sicheritz-Pontén
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen 518083, China
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, 6102 Perth, Australia.,Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
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14
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Hernández Y, Bernstein R, Pagan P, Vargas L, McCaig W, Ramrattan G, Akther S, Larracuente A, Di L, Vieira FG, Qiu WG. BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines. BMC Bioinformatics 2018; 19:76. [PMID: 29499649 PMCID: PMC5833151 DOI: 10.1186/s12859-018-2074-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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] [Received: 04/12/2017] [Accepted: 02/20/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl ( http://bioperl.org ) to make many of the well-designed, robust, and routinely used biological classes available for a wider base of end users. RESULTS Designed as standard utilities for UNIX-family operating systems, BpWrapper makes functionality of some of the most popular BioPerl modules readily accessible on the command line to novice as well as to experienced bioinformatics practitioners. The initial release of BpWrapper includes four utilities with concise command-line user interfaces, bioseq, bioaln, biotree, and biopop, specialized for manipulation of molecular sequences, sequence alignments, phylogenetic trees, and DNA polymorphisms, respectively. Over a hundred methods are currently available as command-line options and new methods are easily incorporated. Performance of BpWrapper utilities lags that of precompiled utilities while equivalent to that of other utilities based on BioPerl. BpWrapper has been tested on BioPerl Release 1.6, Perl versions 5.10.1 to 5.25.10, and operating systems including Apple macOS, Microsoft Windows, and GNU/Linux. Release code is available from the Comprehensive Perl Archive Network (CPAN) at https://metacpan.org/pod/Bio::BPWrapper . Source code is available on GitHub at https://github.com/bioperl/p5-bpwrapper . CONCLUSIONS BpWrapper improves on existing sequence utilities by following the design principles of Unix text utilities such including a concise user interface, extensive command-line options, and standard input/output for serialized operations. Further, dozens of novel methods for manipulation of sequences, alignments, and phylogenetic trees, unavailable in existing utilities (e.g., EMBOSS, Newick Utilities, and FAST), are provided. Bioinformaticians should find BpWrapper useful for rapid prototyping of workflows on the command-line without creating custom scripts for comparative genomics and other bioinformatics applications.
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Affiliation(s)
- Yözen Hernández
- Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA.,Graduate Program in Bioinformatics, Boston University, Boston, MA, 02215, USA
| | - Rocky Bernstein
- Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA
| | - Pedro Pagan
- Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA
| | - Levy Vargas
- Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA
| | - William McCaig
- Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA
| | - Girish Ramrattan
- Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA
| | - Saymon Akther
- Graduate Center, City University of New York, New York, 10016, USA
| | - Amanda Larracuente
- Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA
| | - Lia Di
- Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Wei-Gang Qiu
- Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA. .,Graduate Center, City University of New York, New York, 10016, USA. .,Department of Physiology and Biophysics & Institute for Computational Biomedicine, Weil Cornell Medical College, New York, NY, 10021, USA.
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15
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Wright AE, Fumagalli M, Cooney CR, Bloch NI, Vieira FG, Buechel SD, Kolm N, Mank JE. Male-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture. Evol Lett 2018; 2:52-61. [PMID: 30283664 PMCID: PMC6089503 DOI: 10.1002/evl3.39] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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] [Received: 12/04/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 12/20/2022] Open
Abstract
Many genes are subject to contradictory selection pressures in males and females, and balancing selection resulting from sexual conflict has the potential to substantially increase standing genetic diversity in populations and thereby act as an important force in adaptation. However, the underlying causes of sexual conflict, and the potential for resolution, remains hotly debated. Using transcriptome‐resequencing data from male and female guppies, we use a novel approach, combining patterns of genetic diversity and intersexual divergence in allele frequency, to distinguish the different scenarios that give rise to sexual conflict, and how this conflict may be resolved through regulatory evolution. We show that reproductive fitness is the main source of sexual conflict, and this is resolved via the evolution of male‐biased expression. Furthermore, resolution of sexual conflict produces significant differences in genetic architecture between males and females, which in turn lead to specific alleles influencing sex‐specific viability. Together, our findings suggest an important role for sexual conflict in shaping broad patterns of genome diversity, and show that regulatory evolution is a rapid and efficient route to the resolution of conflict.
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Affiliation(s)
- Alison E Wright
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus Imperial College London London United Kingdom
| | - Christopher R Cooney
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Natasha I Bloch
- Department of Genetics, Evolution and Environment University College London London United Kingdom
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | | | - Niclas Kolm
- Department of Zoology Stockholm University Stockholm Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment University College London London United Kingdom.,Department of Organismal Biology Uppsala University Uppsala Sweden
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16
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Barnett R, Sinding MHS, Vieira FG, Mendoza MLZ, Bonnet M, Araldi A, Kienast I, Zambarda A, Yamaguchi N, Henschel P, Gilbert MTP. No longer locally extinct? Tracing the origins of a lion ( Panthera leo) living in Gabon. CONSERV GENET 2018; 19:611-618. [PMID: 31007636 PMCID: PMC6448349 DOI: 10.1007/s10592-017-1039-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/16/2017] [Indexed: 12/22/2022]
Abstract
Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread population declines in what has hitherto been seen as a common species, robust to anthropogenic disturbance. Here we use non-invasive methods to recover complete mitochondrial genomes from single hair samples collected in the field in order to explore the identity of the Gabonese Plateaux Batéké lion. Comparison of the mitogenomes against a comprehensive dataset of African lion sequences that includes relevant geographically proximate lion populations from both contemporary and ancient sources, enabled us to identify the Plateaux Batéké lion as a close maternal relative to now extirpated populations found in Gabon and nearby Congo during the twentieth century, and to extant populations of Southern Africa. Our study demonstrates the relevance of ancient DNA methods to field conservation work, and the ability of trace field samples to provide copious genetic information about free-ranging animals.
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Affiliation(s)
- Ross Barnett
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mikkel-Holder S. Sinding
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Natural History Museum, University of Oslo, Blindern, P.O. Box 1172, 0318 Oslo, Norway
| | - Filipe G. Vieira
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Matthieu Bonnet
- The Aspinall Foundation, Port Lympne Wild Animal Park, Hythe, Kent CT21 4PD UK
| | - Alessandro Araldi
- The Aspinall Foundation, Port Lympne Wild Animal Park, Hythe, Kent CT21 4PD UK
| | - Ivonne Kienast
- Congo Program, Wildlife Conservation Society, Brazzaville, Congo
| | - Alice Zambarda
- The Aspinall Foundation, Port Lympne Wild Animal Park, Hythe, Kent CT21 4PD UK
| | - Nobuyuki Yamaguchi
- Department of Biological and Environmental Sciences, Qatar University, Doha, Qatar
| | - Philipp Henschel
- Panthera, 8 West 40th Street, 18th Floor, New York, NY 10018 USA
- Institut de Recherche en Ecologie Tropicale, CENAREST, BP 842 Libreville, Gabon
| | - M. Thomas P. Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- NTNU University Museum, 7491 Trondheim, Norway
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17
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Wang H, Vieira FG, Crawford JE, Chu C, Nielsen R. Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice. Genome Res 2017; 27:1029-1038. [PMID: 28385712 PMCID: PMC5453317 DOI: 10.1101/gr.204800.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/21/2017] [Indexed: 12/30/2022]
Abstract
The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 435 wild rice accessions. We show that most modern wild rice is heavily admixed with domesticated rice through both pollen- and seed-mediated gene flow. In fact, much presumed wild rice may simply represent different stages of feralized domesticated rice. In line with this hypothesis, many presumed wild rice varieties show remnants of the effects of selective sweeps in previously identified domestication genes, as well as evidence of recent selection in flowering genes possibly associated with the feralization process. Furthermore, there is a distinct geographical pattern of gene flow from aus, indica, and japonica varieties into colocated wild rice. We also show that admixture from aus and indica is more recent than gene flow from japonica, possibly consistent with an earlier spread of japonica varieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow.
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Affiliation(s)
- Hongru Wang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Filipe G Vieira
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Jacob E Crawford
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA
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18
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Sánchez Barreiro F, Vieira FG, Martin MD, Haile J, Gilbert MTP, Wales N. Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes. Mol Ecol Resour 2016; 17:209-220. [DOI: 10.1111/1755-0998.12610] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/17/2016] [Accepted: 08/29/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Fátima Sánchez Barreiro
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
| | - Filipe G. Vieira
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
| | - Michael D. Martin
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
- NTNU University Museum; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
| | - James Haile
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
- PalaeoBARN; Research Lab for Archaeology and the History of Art; University of Oxford; Oxford OX1 3QY UK
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
- NTNU University Museum; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
- Trace and Environmental DNA Laboratory; Department of Environment and Agriculture; Curtin University; GPO Box U1987, Perth WA 6845 Australia
| | - Nathan Wales
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen K Denmark
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19
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Júnior PAAM, Vieira FG, Magalhães CA, Ribeiro JS, Rios IG. Numerical method to digital photoelasticity using plane polariscope. Opt Express 2016; 24:12617-12624. [PMID: 27410283 DOI: 10.1364/oe.24.012617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This research aims to find a new way to get the intensity equations for the phase-shifting model in digital photoelasticity. The procedure is based on the rotation of the analyzer itself. From the intensity equations, the isoclinic and isochromatic equations parameters are deduced by applying a new numerical technique. This approach can be done to calculate how many images allow the resolution of the polariscope. Each image indicates the stress forces in the object. In this study the plane polariscope was used. The amount of images will determinate the number of errors and uncertainties of the study, due to the observation that the veracity of the equations increases considerably with a large amout of images. Several analyses are performed with different amounts of photographic images. The results showed the possibility to measure stress forces with high precision using plane polariscopes.
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20
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Vieira FG, Albrechtsen A, Nielsen R. Estimating IBD tracts from low coverage NGS data. Bioinformatics 2016; 32:2096-102. [DOI: 10.1093/bioinformatics/btw212] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/12/2016] [Indexed: 11/13/2022] Open
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21
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Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SMS, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJP, Park Y, Rozas J, Benton R, Pedra JHF, Nelson DR, Unger MF, Tubio JMC, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nat Commun 2016; 7:10507. [PMID: 26856261 PMCID: PMC4748124 DOI: 10.1038/ncomms10507] [Citation(s) in RCA: 328] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 12/12/2015] [Indexed: 01/06/2023] Open
Abstract
Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
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Affiliation(s)
- Monika Gulia-Nuss
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Andrew B. Nuss
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jason M. Meyer
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Daniel E. Sonenshine
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginina 23529, USA
| | - R. Michael Roe
- Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Robert M. Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
- Swiss Institute of Bioinformatics, Geneva 1211, Switzerland
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David B. Sattelle
- Centre for Respiratory Biology, UCL Respiratory Department, Division of Medicine, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC-CSIC-UCLM-JCCM, Ronda de Toledo sn, Ciudad Real 13005, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, 250 McElroy Hall, Stillwater, Oklahama 74078, USA
| | - Jose M. Ribeiro
- Laboratory of Malaria and Vector Research, NIAID, Rockville, Maryland 20852, USA
| | - Karine Megy
- VectorBase/EMBL-EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | - Sergey Koren
- J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | | | | | | | | | - Shelby Bidwell
- J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Martin P. Hammond
- VectorBase/EMBL-EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Sarah Young
- Genome Sequencing and Analysis Program, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Qiandong Zeng
- Genome Sequencing and Analysis Program, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Jenica L. Abrudan
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Francisca C. Almeida
- Departament de Genètica & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona E-08028, Spain
| | - Nieves Ayllón
- SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC-CSIC-UCLM-JCCM, Ronda de Toledo sn, Ciudad Real 13005, Spain
| | - Ketaki Bhide
- Bioinformatics Core, Purdue University, West Lafayette, Indiana 47907, USA
| | - Brooke W. Bissinger
- Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Elena Bonzon-Kulichenko
- Vascular Physiopathology, Centro Nacional de Investigaciones Cardiovasculares, Madrid 28029, Spain
| | - Steven D. Buckingham
- Centre for Respiratory Biology, UCL Respiratory Department, Division of Medicine, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK
| | - Daniel R. Caffrey
- Department of Medicine, Division of Infectious Diseases, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Melissa J. Caimano
- Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Vincent Croset
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Timothy Driscoll
- Genetics, Bioinformatics, and Computational Biology Program, Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Don Gilbert
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Joseph J. Gillespie
- Genetics, Bioinformatics, and Computational Biology Program, Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Gloria I. Giraldo-Calderón
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jeffrey M. Grabowski
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
- Department Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - David Jiang
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Sayed M. S. Khalil
- Department of Microbial Molecular Biology, Agricultural Genetic Engineering Research Institute, Giza 12619, Egypt
| | - Donghun Kim
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Katherine M. Kocan
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, 250 McElroy Hall, Stillwater, Oklahama 74078, USA
| | - Juraj Koči
- Department of Entomology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Richard J. Kuhn
- Department Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Timothy J. Kurtti
- Department of Entomology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Kristin Lees
- Department of Neurosystems, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Emma G. Lang
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Ryan C. Kennedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA
| | - Hyeogsun Kwon
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Rushika Perera
- Department Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Yumin Qi
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Justin D. Radolf
- Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Joyce M. Sakamoto
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Alejandro Sánchez-Gracia
- Departament de Genètica & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona E-08028, Spain
| | - Maiara S. Severo
- Department of Entomology, Center for Disease Vector Research, University of California, Riverside, California 92506, USA
| | - Neal Silverman
- Department of Medicine, Division of Infectious Diseases, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Ladislav Šimo
- Department of Entomology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Marta Tojo
- Department of Pathology, Cambridge Genomic Services, University of Cambridge, Cambridge CB2 1QP, UK
- Department of Physiology, School of Medicine-CIMUS-Instituto de Investigaciones Sanitarias, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Cristian Tornador
- Department of Experimental and Health Sciences, Universidad Pompeu Fabra, Barcelona 08003, Spain
| | - Janice P. Van Zee
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jesús Vázquez
- Vascular Physiopathology, Centro Nacional de Investigaciones Cardiovasculares, Madrid 28029, Spain
| | - Filipe G. Vieira
- Departament de Genètica & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona E-08028, Spain
| | - Margarita Villar
- SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC-CSIC-UCLM-JCCM, Ronda de Toledo sn, Ciudad Real 13005, Spain
| | - Adam R. Wespiser
- Department of Medicine, Division of Infectious Diseases, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Yunlong Yang
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Jiwei Zhu
- Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, USA
| | | | - Stephen C. Barker
- Parasitology Section, School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Renfu Shao
- GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4556, Australia
| | - Evgeny M. Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
- Swiss Institute of Bioinformatics, Geneva 1211, Switzerland
| | - Frank Hauser
- Department of Biology, Center for Functional and Comparative Insect Genomics, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Cornelis J. P. Grimmelikhuijzen
- Department of Biology, Center for Functional and Comparative Insect Genomics, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Julio Rozas
- Departament de Genètica & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona E-08028, Spain
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Joao H. F. Pedra
- Department of Entomology, Center for Disease Vector Research, University of California, Riverside, California 92506, USA
| | - David R. Nelson
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Maria F. Unger
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jose M. C. Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Martin Shumway
- J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Granger Sutton
- J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | | | - Daniel Lawson
- VectorBase/EMBL-EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stephen K. Wikel
- Department of Medical Sciences, Frank H. Netter MD School of Medicine at Quinnipiac University, Hamden, Connecticut 06518, USA
| | | | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland 21201, USA
| | - Frank H. Collins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Bruce Birren
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Elisabet Caler
- J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Catherine A. Hill
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
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22
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Martin MD, Vieira FG, Ho SYW, Wales N, Schubert M, Seguin-Orlando A, Ristaino JB, Gilbert MTP. Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans. Mol Biol Evol 2016; 33:478-91. [PMID: 26576850 PMCID: PMC4866541 DOI: 10.1093/molbev/msv241] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed, as does the New World center of origin of the species itself. Both Mexico and South America have been proposed, generating considerable controversy. Here, we readdress the pathogen's origins using a genomic data set encompassing 71 globally sourced modern and historical samples of P. infestans and the hybrid species P. andina, a close relative known only from the Andean highlands. Previous studies have suggested that the nuclear DNA lineage behind the initial outbreaks in Europe in 1845 is now extinct. Analysis of P. andina's phased haplotypes recovered eight haploid genome sequences, four of which represent a previously unknown basal lineage of P. infestans closely related to the famine-era lineage. Our analyses further reveal that clonal lineages of both P. andina and historical P. infestans diverged earlier than modern Mexican lineages, casting doubt on recent claims of a Mexican center of origin. Finally, we use haplotype phasing to demonstrate that basal branches of the clade comprising Mexican samples are occupied by clonal isolates collected from wild Solanum hosts, suggesting that modern Mexican P. infestans diversified on Solanum tuberosum after a host jump from a wild species and that the origins of P. infestans are more complex than was previously thought.
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Affiliation(s)
- Michael D Martin
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Department of Integrative Biology, Center for Theoretical Evolutionary Genomics, University of California, Berkeley
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jean B Ristaino
- Department of Plant Pathology, North Carolina State University
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
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23
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Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L. Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse. Curr Biol 2015; 25:2577-83. [PMID: 26412128 DOI: 10.1016/j.cub.2015.08.032] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/06/2015] [Accepted: 08/14/2015] [Indexed: 12/22/2022]
Abstract
Przewalski's horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [1]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [2-4]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878-1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Melinda A Yang
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Matteo Fumagalli
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Hákon Jónsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Gila Kahila Bar-Gal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, Rehovot 76100, Israel
| | - Anders Albrechtsen
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen 2200N, Denmark
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Bent Petersen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark
| | - Aurélien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Andaine Seguin-Orlando
- National High-Throughput DNA Sequencing Centre, University of Copenhagen, Copenhagen 1353K, Denmark
| | - Kim Magnussen
- National High-Throughput DNA Sequencing Centre, University of Copenhagen, Copenhagen 1353K, Denmark
| | - Antoine Fages
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Belen Lorente-Galdos
- ICREA at the Institut de Biologia Evolutiva (CSIC-University Pompeu Fabra), Barcelona 08003, Spain
| | - Sagi Polani
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, Rehovot 76100, Israel
| | - Cynthia Steiner
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | | | | | - Claudia Feh
- Station Biologique de la Tour du Valat, Arles 13200, France
| | - Charles L Greenblatt
- Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin 10315, Germany
| | - Natalia I Abramson
- Zoological Institute of the Russian Academy of Sciences, Saint-Petersburg 199034, Russia
| | | | - Renate Schafberg
- Martin-Luther-University Halle-Wittenberg, Museum of Domesticated Animals "Julius Kühn", Halle 06108, Germany
| | - Alexei Tikhonov
- Zoological Institute of the Russian Academy of Sciences, Saint-Petersburg 199034, Russia; Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk 677980, Russia
| | - Thomas Sicheritz-Ponten
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Tomas Marques-Bonet
- ICREA at the Institut de Biologia Evolutiva (CSIC-University Pompeu Fabra), Barcelona 08003, Spain; Centro Nacional de Analisis Genomico (CNAG-CRG), Barcelona 08023, Spain
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | - Molly McCue
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches 1580, Switzerland
| | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern 3001, Switzerland
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark; Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde, 31000 Toulouse, France.
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24
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Vieira FG, Lassalle F, Korneliussen TS, Fumagalli M. Improving the estimation of genetic distances from Next-Generation Sequencing data. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12511] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Filipe G. Vieira
- Centre for GeoGenetics and Evogenomics Section; Natural History Museum of Denmark; University of Copenhagen; DK-2100 Copenhagen Denmark
| | - Florent Lassalle
- Department of Genetics, Evolution and Environment; UCL Genetics Institute; University College London; Gower Street London WC1E 6BT UK
| | - Thorfinn S. Korneliussen
- Centre for GeoGenetics and Evogenomics Section; Natural History Museum of Denmark; University of Copenhagen; DK-2100 Copenhagen Denmark
| | - Matteo Fumagalli
- Department of Genetics, Evolution and Environment; UCL Genetics Institute; University College London; Gower Street London WC1E 6BT UK
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25
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Librado P, Vieira FG, Sánchez-Gracia A, Kolokotronis SO, Rozas J. Mycobacterial phylogenomics: an enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families. Genome Biol Evol 2014; 6:1454-65. [PMID: 24904011 PMCID: PMC4079203 DOI: 10.1093/gbe/evu117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Species of the genus Mycobacterium differ in several features, from geographic ranges, and degree of pathogenicity, to ecological and host preferences. The recent availability of several fully sequenced genomes for a number of these species enabled the comparative study of the genetic determinants of this wide lifestyle diversity. Here, we applied two complementary phylogenetic-based approaches using information from 19 Mycobacterium genomes to obtain a more comprehensive view of the evolution of this genus. First, we inferred the phylogenetic relationships using two new approaches, one based on a Mycobacterium-specific amino acid substitution matrix and the other on a gene content dissimilarity matrix. Then, we utilized our recently developed gain-and-death stochastic models to study gene turnover dynamics in this genus in a maximum-likelihood framework. We uncovered a scenario that differs markedly from traditional 16S rRNA data and improves upon recent phylogenomic approaches. We also found that the rates of gene gain and death are high and unevenly distributed both across species and across gene families, further supporting the utility of the new models of rate heterogeneity applied in a phylogenetic context. Finally, the functional annotation of the most expanded or contracted gene families revealed that the transposable elements and the fatty acid metabolism-related gene families are the most important drivers of gene content evolution in Mycobacterium.
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Affiliation(s)
- Pablo Librado
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Filipe G Vieira
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, SpainDepartment of Integrative Biology, University of California, Berkeley
| | - Alejandro Sánchez-Gracia
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sergios-Orestis Kolokotronis
- Department of Biological Sciences, Fordham UniversitySackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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26
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Abstract
SUMMARY Next-generation sequencing technologies produce short reads that are either de novo assembled or mapped to a reference genome. Genotypes and/or single-nucleotide polymorphisms are then determined from the read composition at each site, which become the basis for many downstream analyses. However, for low sequencing depths, e.g. , there is considerable statistical uncertainty in the assignment of genotypes because of random sampling of homologous base pairs in heterozygotes and sequencing or alignment errors. Recently, several probabilistic methods have been proposed to account for this uncertainty and make accurate inferences from low quality and/or coverage sequencing data. We present ngsTools, a collection of programs to perform population genetics analyses from next-generation sequencing data. The methods implemented in these programs do not rely on single-nucleotide polymorphism or genotype calling and are particularly suitable for low sequencing depth data. AVAILABILITY Programs included in ngsTools are implemented in C/C++ and are freely available for noncommercial use at https://github.com/mfumagalli/ngsTools. CONTACT mfumagalli82@gmail.com SUPPLEMENTARY INFORMATION Supplementary materials are available at Bioinformatics online.
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Affiliation(s)
- Matteo Fumagalli
- Department of Integrative Biology, Department of Statistics, University of California, Berkeley, CA 94720, USA and Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
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Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R. Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Res 2013; 23:1852-61. [PMID: 23950147 PMCID: PMC3814885 DOI: 10.1101/gr.157388.113] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Most methods for next-generation sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy–Weinberg equilibrium (HWE) as a prior. However, many organisms including those that are domesticated, partially selfing, or with asexual life cycles show strong deviations from HWE. For such species, and specially for low-coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual before calling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an expectation-maximization (EM) algorithm. We assess the impact of taking inbreeding into account when calling genotypes or estimating the site frequency spectrum (SFS), and demonstrate a marked increase in accuracy on low-coverage highly inbred samples. We demonstrate the applicability and efficacy of these methods in both simulated and real data sets.
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Affiliation(s)
- Filipe G Vieira
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
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28
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Vieira FG, Forêt S, He X, Rozas J, Field LM, Zhou JJ. Unique features of odorant-binding proteins of the parasitoid wasp Nasonia vitripennis revealed by genome annotation and comparative analyses. PLoS One 2012; 7:e43034. [PMID: 22952629 PMCID: PMC3428353 DOI: 10.1371/journal.pone.0043034] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/16/2012] [Indexed: 12/22/2022] Open
Abstract
Insects are the most diverse group of animals on the planet, comprising over 90% of all metazoan life forms, and have adapted to a wide diversity of ecosystems in nearly all environments. They have evolved highly sensitive chemical senses that are central to their interaction with their environment and to communication between individuals. Understanding the molecular bases of insect olfaction is therefore of great importance from both a basic and applied perspective. Odorant binding proteins (OBPs) are some of most abundant proteins found in insect olfactory organs, where they are the first component of the olfactory transduction cascade, carrying odorant molecules to the olfactory receptors. We carried out a search for OBPs in the genome of the parasitoid wasp Nasonia vitripennis and identified 90 sequences encoding putative OBPs. This is the largest OBP family so far reported in insects. We report unique features of the N. vitripennis OBPs, including the presence and evolutionary origin of a new subfamily of double-domain OBPs (consisting of two concatenated OBP domains), the loss of conserved cysteine residues and the expression of pseudogenes. This study also demonstrates the extremely dynamic evolution of the insect OBP family: (i) the number of different OBPs can vary greatly between species; (ii) the sequences are highly diverse, sometimes as a result of positive selection pressure with even the canonical cysteines being lost; (iii) new lineage specific domain arrangements can arise, such as the double domain OBP subfamily of wasps and mosquitoes.
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Affiliation(s)
- Filipe G. Vieira
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xiaoli He
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Linda M. Field
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
- * E-mail:
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29
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Abstract
MOTIVATION The comparative analysis of gene gain and loss rates is critical for understanding the role of natural selection and adaptation in shaping gene family sizes. Studying complete genome data from closely related species allows accurate estimation of gene family turnover rates. Current methods and software tools, however, are not well designed for dealing with certain kinds of functional elements, such as microRNAs or transcription factor binding sites. RESULTS Here, we describe BadiRate, a new software tool to estimate family turnover rates, as well as the number of elements in internal phylogenetic nodes, by likelihood-based methods and parsimony. It implements two stochastic population models, which provide the appropriate statistical framework for testing hypothesis, such as lineage-specific gene family expansions or contractions. We have assessed the accuracy of BadiRate by computer simulations, and have also illustrated its functionality by analyzing a representative empirical dataset. AVAILABILITY BadiRate software and documentation is available from http://www.ub.edu/softevol/badirate.
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Affiliation(s)
- P Librado
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
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Vieira FG, Rozas J. Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system. Genome Biol Evol 2011; 3:476-90. [PMID: 21527792 PMCID: PMC3134979 DOI: 10.1093/gbe/evr033] [Citation(s) in RCA: 310] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chemoreception is a biological process essential for the survival of animals, as it allows the recognition of important volatile cues for the detection of food, egg-laying substrates, mates, or predators, among other purposes. Furthermore, its role in pheromone detection may contribute to evolutionary processes, such as reproductive isolation and speciation. This key role in several vital biological processes makes chemoreception a particularly interesting system for studying the role of natural selection in molecular adaptation. Two major gene families are involved in the perireceptor events of the chemosensory system: the odorant-binding protein (OBP) and chemosensory protein (CSP) families. Here, we have conducted an exhaustive comparative genomic analysis of these gene families in 20 Arthropoda species. We show that the evolution of the OBP and CSP gene families is highly dynamic, with a high number of gains and losses of genes, pseudogenes, and independent origins of subfamilies. Taken together, our data clearly support the birth-and-death model for the evolution of these gene families with an overall high gene turnover rate. Moreover, we show that the genome organization of the two families is significantly more clustered than expected by chance and, more important, that this pattern appears to be actively maintained across the Drosophila phylogeny. Finally, we suggest the homologous nature of the OBP and CSP gene families, dating back their most recent common ancestor after the terrestrialization of Arthropoda (380--450 Ma) and we propose a scenario for the origin and diversification of these families.
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Affiliation(s)
- Filipe G Vieira
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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31
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Zhou JJ, Vieira FG, He XL, Smadja C, Liu R, Rozas J, Field LM. Genome annotation and comparative analyses of the odorant-binding proteins and chemosensory proteins in the pea aphid Acyrthosiphon pisum. Insect Mol Biol 2010; 19 Suppl 2:113-22. [PMID: 20482644 DOI: 10.1111/j.1365-2583.2009.00919.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) are two families of small water-soluble proteins, abundant in the aqueous fluid surrounding olfactory receptor neurons in insect antennae. OBPs are involved in the first step of olfactory signal transduction, carrying airborne semiochemicals to the odorant receptors and can be classified into three groups: Classic OBPs, Plus-C OBPs and Atypical OBPs. Here, we identified and annotated genes encoding putative OBPs and CSPs in the pea aphid Acyrthosiphon pisum using bioinformatics. This identified genes encoding 13 Classic and two Plus-C OBPs and 13 CSPs. Homologous OBP sequences were also identified in nine other aphid species, allowing us to compare OBPs across several aphid and non-aphid species. We show that, although OBP sequences are divergent within a species and between different orders, there is a high similarity between orthologs within a range of aphid species. Furthermore, the phylogenetic relationships between OBP orthologs reflect the divergence of aphid evolution lineages. Our results support the 'birth-and-death' model as the major mechanism explaining aphid OBP sequence evolution, with the main force acting on the evolution being purifying selection.
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Affiliation(s)
- J-J Zhou
- Department of Biological Chemistry, Harpenden, Hertfordshire, UK
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Vieira FG, Sánchez-Gracia A, Rozas J. Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution. Genome Biol 2008; 8:R235. [PMID: 18039354 PMCID: PMC2258175 DOI: 10.1186/gb-2007-8-11-r235] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 06/08/2007] [Accepted: 11/08/2007] [Indexed: 01/18/2023] Open
Abstract
The comparative analysis of the odorant binding protein family in 12 Drosophila genomes allowed the identification of 595 putative family member genes and revealed insights into the evolution of this family in these species. Background Chemoreception is a widespread mechanism that is involved in critical biologic processes, including individual and social behavior. The insect peripheral olfactory system comprises three major multigene families: the olfactory receptor (Or), the gustatory receptor (Gr), and the odorant-binding protein (OBP) families. Members of the latter family establish the first contact with the odorants, and thus constitute the first step in the chemosensory transduction pathway. Results Comparative analysis of the OBP family in 12 Drosophila genomes allowed the identification of 595 genes that encode putative functional and nonfunctional members in extant species, with 43 gene gains and 28 gene losses (15 deletions and 13 pseudogenization events). The evolution of this family shows tandem gene duplication events, progressive divergence in DNA and amino acid sequence, and prevalence of pseudogenization events in external branches of the phylogenetic tree. We observed that the OBP arrangement in clusters is maintained across the Drosophila species and that purifying selection governs the evolution of the family; nevertheless, OBP genes differ in their functional constraints levels. Finally, we detect that the OBP repertoire evolves more rapidly in the specialist lineages of the Drosophila melanogaster group (D. sechellia and D. erecta) than in their closest generalists. Conclusion Overall, the evolution of the OBP multigene family is consistent with the birth-and-death model. We also found that members of this family exhibit different functional constraints, which is indicative of some functional divergence, and that they might be involved in some of the specialization processes that occurred through the diversification of the Drosophila genus.
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Affiliation(s)
- Filipe G Vieira
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av, Diagonal 645, Barcelona 08028, Spain.
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Cangussu SD, Vieira FG, Rossoni RB. Sexual dimorphism and seasonal variation in submandibular gland histology of Bolomys lasiurus (Rodentia, Muridae). J Morphol 2002; 254:320-7. [PMID: 12386901 DOI: 10.1002/jmor.10041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Wild rodents (Bolomys lasiurus) of both sexes were caught in a cerrado grassland area during the dry (July-September) and rainy (January-March) seasons of Brazil. Fasted animals were perfused with Karnovsky fixative through the left ventricle, under ether anesthesia, and the submandibular gland was processed for embedding in historesin. Histological and histometric data show sexual dimorphism at both seasons. In the volume percentage of the granular convoluted tubules (GCT) and their secretory granules, the males exhibited higher values. The absolute volume occupied by these structures, however, was dimorphic only in the rainy season. The diameter of the GCT, the height of its epithelium, and its total length were also greater in males during the rainy season. The absolute volumes of the acini and of the ductal tree were identical in both sexes in the dry and rainy seasons but the acinar diameter increased in the males and females during the rainy season. The sexual dimorphism and the seasonal variations now described in the B. lasiurus submandibular glands could be explained by the augmented reproductive activity of the males in the rainy period.
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Affiliation(s)
- S D Cangussu
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, 30161-970 Belo Horizonte MG, Brazil
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