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Wilson LA, Marr M, Logie C, Beckmann K, Lurz P, Ogden R, Milne E, Everest DJ. Squirrelpox in a red squirrel in Fife. Vet Rec 2024; 194:312. [PMID: 38639234 DOI: 10.1002/vetr.4182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Affiliation(s)
- L A Wilson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG
| | - M Marr
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG
| | - C Logie
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG
| | - K Beckmann
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG
| | - Pww Lurz
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG
| | - R Ogden
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG
| | - E Milne
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG
| | - D J Everest
- APHA Weybridge, Addlestone, Surrey, KT15 3NB
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2
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Gose MA, Humble E, Brownlow A, Wall D, Rogan E, Sigurðsson GM, Kiszka JJ, Thøstesen CB, IJsseldijk LL, Ten Doeschate M, Davison NJ, Øien N, Deaville R, Siebert U, Ogden R. Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): Implications for conservation amid climate-driven range shifts. Heredity (Edinb) 2024; 132:192-201. [PMID: 38302666 PMCID: PMC10997624 DOI: 10.1038/s41437-024-00672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.
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Affiliation(s)
- Marc-Alexander Gose
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.
| | - Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Dave Wall
- Irish Whale and Dolphin Group (IWDG), Kilrush, Ireland
| | - Emer Rogan
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | | | - Jeremy J Kiszka
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, FL, USA
| | | | - Lonneke L IJsseldijk
- Division of Pathology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Mariel Ten Doeschate
- Scottish Marine Animal Stranding Scheme, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Nils Øien
- Institute of Marine Research (IMR), Bergen, Norway
| | - Rob Deaville
- Institute of Zoology, Zoological Society of London, London, UK
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
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3
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Au WC, Dures SG, Ishida Y, Green CE, Zhao K, Ogden R, Roca AL. Lion Localizer: A software tool for inferring the provenance of lions (Panthera leo) using mitochondrial DNA. J Hered 2024; 115:166-172. [PMID: 37952226 DOI: 10.1093/jhered/esad072] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
The illegal poaching of lions for their body parts poses a severe threat to lion populations across Africa. Poaching accounts for 35% of all human-caused lion deaths, with 51% attributed to retaliatory killings following livestock predation. In nearly half of the retaliatory killings, lion body parts are removed, suggesting that high demand for lion body parts may fuel killings attributed to human-lion conflict. Trafficked items are often confiscated in transit or destination countries far from their country of origin. DNA from lion parts may in some cases be the only available means for examining their geographic origins. In this paper, we present the Lion Localizer, a full-stack software tool that houses a comprehensive database of lion mitochondrial DNA (mtDNA) sequences sourced from previously published studies. The database covers 146 localities from across the African continent and India, providing information on the potential provenance of seized lion body parts. Lion mtDNA sequences of 350 or 1,140 bp corresponding to the cytochrome b region can be generated from lion products and queried against the Lion Localizer database. Using the query sequence, the Lion Localizer generates a listing of exact or partial matches, which are displayed on an interactive map of Africa. This allows for the rapid identification of potential regions and localities where lions have been or are presently being targeted by poachers. By examining the potential provenance of lion samples, the Lion Localizer serves as a valuable resource in the fight against lion poaching. The software is available at https://lionlocalizer.org.
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Affiliation(s)
- Wesley C Au
- School of Information Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Simon G Dures
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Cory E Green
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Kai Zhao
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Rob Ogden
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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4
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Cetkovská E, Brandlová K, Ogden R, Černá Bolfíková B. Evaluation of the Impact of Population Management on the Genetic Parameters of Selected Spiral-Horned Antelopes. Biology (Basel) 2024; 13:104. [PMID: 38392322 PMCID: PMC10886411 DOI: 10.3390/biology13020104] [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] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
The rapid loss of biodiversity and the associated reduction and fragmentation of habitats means that ex situ populations have become an important part of species conservation. These populations, which are often established from a small number of founders, require careful management to avoid the negative effects of genetic drift and inbreeding. Although the inclusion of molecular data is recommended, their availability for captive breeding management remains limited. The aim of this study was to evaluate the relationship between the levels of genetic diversity in six spiral-horned antelope taxa bred under human care and their respective management strategies, conservation status, demography, and geographic origin, using 10 nuclear DNA microsatellite loci and mitochondrial control region DNA sequences. Our findings include associations between genetic diversity and management intensity but also with the diversity and contribution of wild populations to captive founders, with some populations apparently composed of animals from divergent wild lineages elevating captive genetic diversity. When population sizes are large, the potential advantages of maximizing genetic diversity in widely outcrossed populations may need careful consideration with respect to the potential disruption of adaptive diversity. Genetic data serve as a robust tool for managing captive populations, yet their interpretation necessitates a comprehensive understanding of species biology and history.
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Affiliation(s)
- Ema Cetkovská
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Karolína Brandlová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
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5
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Abecasis D, Ogden R, Winkler AC, Gandra M, Khallahi B, Diallo M, Cabrera-Castro R, Weiller Y, Erzini K, Afonso P, Assis J. Multidisciplinary estimates of connectivity and population structure suggest the use of multiple units for the conservation and management of meagre, Argyrosomus regius. Sci Rep 2024; 14:873. [PMID: 38195638 PMCID: PMC10776566 DOI: 10.1038/s41598-023-50869-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024] Open
Abstract
Information on population structure and connectivity of targeted species is key for proper implementation of spatial conservation measures. We used a combination of genomics, biophysical modelling, and biotelemetry to infer the population structure and connectivity of Atlantic meagre, an important fisheries resource throughout its distribution. Genetic samples from previously identified Atlantic spawning locations (Gironde, Tejo, Guadalquivir, Banc d'Arguin) and two additional regions (Algarve and Senegal) were analysed using genome-wide SNP-genotyping and mitochondrial DNA analyses. Biophysical models were conducted to investigate larval dispersal and connectivity from the known Atlantic spawning locations. Additionally, thirteen fish were double-tagged with biotelemetry transmitters off the Algarve (Portugal) to assess movement patterns and connectivity of adult individuals. This multidisciplinary approach provided a robust overview of meagre population structure and connectivity in the Atlantic. Nuclear SNP-genotyping showed a clear differentiation between the European and African populations, with significant isolation of the few known Atlantic spawning sites. The limited level of connectivity between these subpopulations is potentially driven by adults, capable of wide-ranging movements and connecting sites 500 km apart, as evidenced by tagging studies, whilst larval dispersal inferred by modelling is much more limited (average of 52 km; 95% of connectivity events up to 174 km). Our results show sufficient evidence of population structure, particularly between Africa and Europe but also within Europe, for the meagre to be managed as separate stocks. Additionally, considering the low degree of larvae connectivity, the implementation of marine protected areas in key spawning sites could be crucial towards species sustainability.
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Affiliation(s)
- D Abecasis
- CCMAR, Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal.
| | - R Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - A C Winkler
- CCMAR, Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
| | - M Gandra
- CCMAR, Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
| | - B Khallahi
- Institut Mauritanien de Recherches Océanographiques et des Pêches (IMROP), BP 22, Nouadhibou, Cansado, Mauritania
| | - M Diallo
- Conservation and Research of West African Aquatic Mammals (COREWAM), Dakar, Senegal
| | - R Cabrera-Castro
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Campus de Excelencia Internacional del Mar (CEIMAR), Avda. República Saharaui, s/n, Puerto Real, 11510, Cádiz, Spain
- Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEIMAR), Avda. República Saharaui, S/N, Puerto Real, 11510, Cádiz, Spain
| | - Y Weiller
- Parc naturel marin de l'estuaire de La Gironde et de la mer des Pertuis, OFB, 17320, Marennes, France
| | - K Erzini
- CCMAR, Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
| | - P Afonso
- Ocean Sciences Institute (Okeanos), University of the Azores, 9901-862, Horta, Portugal
- Institute of Marine Research (IMAR), 9901-862, Horta, Portugal
| | - J Assis
- CCMAR, Centre of Marine Sciences, University of Algarve, 8005-139, Faro, Portugal
- Faculty of Bioscience and Aquaculture, Nord Universitet, Bodø, Norway
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6
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Humble E, Hosegood J, Carvalho G, de Bruyn M, Creer S, Stevens GMW, Armstrong A, Bonfil R, Deakos M, Fernando D, Froman N, Peel LR, Pollett S, Ponzo A, Stewart JD, Wintner S, Ogden R. Comparative population genomics of manta rays has global implications for management. Mol Ecol 2023. [PMID: 37994168 DOI: 10.1111/mec.17220] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonization, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.
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Affiliation(s)
- Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
- The Manta Trust, Catemwood House, Dorset, UK
| | - Jane Hosegood
- The Manta Trust, Catemwood House, Dorset, UK
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
| | - Gary Carvalho
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
| | - Mark de Bruyn
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
- Australian Research Centre for Human Evolution, Griffith University, Nathan, Queensland, Australia
| | - Simon Creer
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
| | | | - Amelia Armstrong
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Ramon Bonfil
- Océanos Vivientes AC, Mexico City, Mexico
- Consejo Nacional de Humanidades Ciencia y Tecnología (CONAHCyT), Mexico City, Mexico
- El Colegio de la Frontera Sur, Unidad Chetumal, Chetumal, Mexico
| | - Mark Deakos
- Hawai'i Association for Marine Education and Research, Lahaina, USA
| | - Daniel Fernando
- The Manta Trust, Catemwood House, Dorset, UK
- Blue Resources Trust, Colombo, Sri Lanka
| | - Niv Froman
- The Manta Trust, Catemwood House, Dorset, UK
| | - Lauren R Peel
- The Manta Trust, Catemwood House, Dorset, UK
- Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
- School of Biological Sciences, Oceans Institute and Oceans Graduate School, The University of Western Australia, Crawley, Western Australia, Australia
| | | | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Dorset, UK
- Ocean Ecology Lab, Marine Mammal Institute, Department of Fisheries, Wildlife & Conservation Sciences, Oregon State University, Newport, Oregon, USA
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
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Sitam FT, Salgado‐Lynn M, Denel A, Panjang E, McEwing R, Lightson A, Ogden R, Maruji NA, Yahya NK, Ngau C, Mohd Kulaimi NA, Ithnin H, Rovie‐Ryan J, Abu Bakar MS, Ewart KM. Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics. Ecol Evol 2023; 13:e10373. [PMID: 37593756 PMCID: PMC10427774 DOI: 10.1002/ece3.10373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 08/19/2023] Open
Abstract
The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species, occurring across much of Southeast Asia and in southern China. It is classified as Critically Endangered and is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations but also poses a potential disease risk to other species, including humans and livestock. Here, we aimed to investigate the species' phylogeography across its distribution to improve our understanding of the species' evolutionary history, elucidate any taxonomic uncertainties and enhance the species' conservation genetic management and potential wildlife forensics applications. We sequenced mtDNA genomes from 23 wild Sunda pangolins of known provenance originating from Malaysia to fill sampling gaps in previous studies, particularly in Borneo. To conduct phylogenetic and population genetic analyses of Sunda pangolins across their range, we integrated these newly generated mitochondrial genomes with previously generated mtDNA and nuclear DNA data sets (RAD-seq SNP data). We identified an evolutionarily distinct mtDNA lineage in north Borneo, estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time from the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. These findings are consistent with the 'out of Borneo hypothesis', whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex and highlight the critical need for additional georeferenced samples to accurately apportion its range-wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.
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Affiliation(s)
- Frankie T. Sitam
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Milena Salgado‐Lynn
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
- Organisms and Environment Division, Cardiff School of BiosciencesCardiff UniversityCardiffUK
| | - Azroie Denel
- Sarawak Forestry Corporation (SFC)KuchingMalaysia
| | - Elisa Panjang
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Organisms and Environment Division, Cardiff School of BiosciencesCardiff UniversityCardiffUK
| | | | | | - Rob Ogden
- TRACE Wildlife Forensics NetworkEdinburghUK
- Royal (Dick) School of Veterinary Studies and the Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Nur Alwanie Maruji
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
- Sabah Wildlife Department (SWD)Kota KinabaluMalaysia
| | - Nurhartini Kamalia Yahya
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
| | - Cosmas Ngau
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Noor Azleen Mohd Kulaimi
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Hartini Ithnin
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | | | | | - Kyle M. Ewart
- TRACE Wildlife Forensics NetworkEdinburghUK
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
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Humble E, Stoffel MA, Dicks K, Ball AD, Gooley RM, Chuven J, Pusey R, Remeithi MA, Koepfli KP, Pukazhenthi B, Senn H, Ogden R. Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx. Proc Natl Acad Sci U S A 2023; 120:e2210756120. [PMID: 37098062 PMCID: PMC10160979 DOI: 10.1073/pnas.2210756120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
In an age of habitat loss and overexploitation, small populations, both captive and wild, are increasingly facing the effects of isolation and inbreeding. Genetic management has therefore become a vital tool for ensuring population viability. However, little is known about how the type and intensity of intervention shape the genomic landscape of inbreeding and mutation load. We address this using whole-genome sequence data of the scimitar-horned oryx (Oryx dammah), an iconic antelope that has been subject to contrasting management strategies since it was declared extinct in the wild. We show that unmanaged populations are enriched for long runs of homozygosity (ROH) and have significantly higher inbreeding coefficients than managed populations. Additionally, despite the total number of deleterious alleles being similar across management strategies, the burden of homozygous deleterious genotypes was consistently higher in unmanaged groups. These findings emphasize the risks associated with deleterious mutations through multiple generations of inbreeding. As wildlife management strategies continue to diversify, our study reinforces the importance of maintaining genome-wide variation in vulnerable populations and has direct implications for one of the largest reintroduction attempts in the world.
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Affiliation(s)
- Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Martin A Stoffel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Kara Dicks
- RZSS WildGenes, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, United Kingdom
| | - Alex D Ball
- RZSS WildGenes, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, United Kingdom
| | - Rebecca M Gooley
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630 and Washington, DC 20008
| | - Justin Chuven
- Terrestrial & Marine Biodiversity Sector, Environment Agency - Abu Dhabi, United Arab Emirates
- US Fish and Wildlife Service, CO 80612
| | - Ricardo Pusey
- Terrestrial & Marine Biodiversity Sector, Environment Agency - Abu Dhabi, United Arab Emirates
| | - Mohammed Al Remeithi
- Terrestrial & Marine Biodiversity Sector, Environment Agency - Abu Dhabi, United Arab Emirates
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630 and Washington, DC 20008
| | - Budhan Pukazhenthi
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630 and Washington, DC 20008
| | - Helen Senn
- RZSS WildGenes, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, United Kingdom
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
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9
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Hoban S, Bruford MW, da Silva JM, Funk WC, Frankham R, Gill MJ, Grueber CE, Heuertz M, Hunter ME, Kershaw F, Lacy RC, Lees C, Lopes-Fernandes M, MacDonald AJ, Mastretta-Yanes A, McGowan PJK, Meek MH, Mergeay J, Millette KL, Mittan-Moreau CS, Navarro LM, O'Brien D, Ogden R, Segelbacher G, Paz-Vinas I, Vernesi C, Laikre L. Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework. CONSERV GENET 2023; 24:181-191. [PMID: 36683963 PMCID: PMC9841145 DOI: 10.1007/s10592-022-01492-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/30/2022] [Indexed: 01/18/2023]
Abstract
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.
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Affiliation(s)
- Sean Hoban
- The Morton Arboretum, Center for Tree Science, Lisle, USA.,The University of Chicago, Chicago, USA
| | | | - Jessica M da Silva
- South African National Biodiversity Institute, Pretoria, South Africa.,Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Richard Frankham
- School of Natural Sciences, Macquarie University, Sydney, NSW Australia
| | - Michael J Gill
- NatureServe, Biodiversity Indicators Program, Arlington, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Francine Kershaw
- Oceans Division, Natural Resources Defense Council, NewYork, USA
| | - Robert C Lacy
- Chicago Zoological Society, Species Conservation Toolkit Initiative, Brookfield, USA
| | - Caroline Lees
- Conservation Planning Specialist Group, IUCN SSC, Auckland, New Zealand
| | | | - Anna J MacDonald
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Australia
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Mexico City, Mexico.,Consejo Nacional de Ciencia Y Tecnología (CONACYT), Mexico City, Mexico
| | - Philip J K McGowan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Mariah H Meek
- Department of Integrative Biology; Ecology, Evolution, and Behavior Program, Michigan State University, AgBio Research, Lansing, USA
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Katie L Millette
- Group on Earth Observations Biodiversity Observation Network (GEO BON), McGill University, Montreal, Canada
| | - Cinnamon S Mittan-Moreau
- Kellogg Biological Station; Ecology and Evolutionary Biology, Michigan State University, Lansing, USA
| | | | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, Midlothian, United Kingdom
| | | | - Ivan Paz-Vinas
- Department of Biology, Colorado State University, Fort Collins, USA
| | | | - Linda Laikre
- Department of Zoology, Stockholm University, Stockholm, Sweden
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10
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O'Brien D, Laikre L, Hoban S, Bruford MW, Ekblom R, Fischer MC, Hall J, Hvilsom C, Hollingsworth PM, Kershaw F, Mittan CS, Mukassabi T, Ogden R, Segelbacher G, Shaw RE, Vernesi C, MacDonald AJ. Bringing together approaches to reporting on within species genetic diversity. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Linda Laikre
- Division of Population Genetics Department of Zoology Stockholm University Stockholm Sweden
| | - Sean Hoban
- Center for Tree Science Lisle Illinois USA
| | | | - Robert Ekblom
- Wildlife Analysis Unit Swedish Environmental Protection Agency Stockholm Sweden
| | | | | | | | | | | | - Cinnamon S. Mittan
- Ecology and Evolutionary Biology Program Michigan State University East Lansing Michigan USA
| | - Tarek A. Mukassabi
- University of Benghazi Department of Botany, Faculty of Sciences Benghazi Libya
| | - Rob Ogden
- Royal (DIck) School of Veterinary Studies and the Roslin Institute University of Edinburgh Edinburgh UK
| | - Gernot Segelbacher
- Wildlife Ecology and Management University Freiburg Freiburg im Breisgau Germany
| | - Robyn E. Shaw
- Environmental and Conservation Sciences Murdoch University Perth Australia
| | - Cristiano Vernesi
- Forest Ecology Unit Research and Innovation Centre ‐ Fondazione Edmund Mach San Michele all'Adige Italy
| | - Anna J. MacDonald
- Australian Antarctic Division Department of Agriculture, Water and the Environment Kingston Tasmania Australia
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11
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Kershaw F, Bruford MW, Funk WC, Grueber CE, Hoban S, Hunter ME, Laikre L, MacDonald AJ, Meek MH, Mittan C, O´Brien D, Ogden R, Shaw RE, Vernesi C, Segelbacher G. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Conservat Sci and Prac 2022. [DOI: 10.1111/csp2.12635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
| | | | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado USA
| | - Catherine E. Grueber
- School of Life and Environmental Sciences, The University of Sydney New South Wales Australia
| | - Sean Hoban
- The Morton Arboretum, Center for Tree Science Lisle Illinois USA
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville Florida USA
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics Stockholm University Stockholm Sweden
| | - Anna J. MacDonald
- Research School of Biology The Australian National University Canberra Acton Australia
| | - Mariah H. Meek
- Department of Integrative Biology, AgBio Research, and Ecology, Evolution, and Behavior Program Michigan State University East Lansing Michigan USA
| | - Cinnamon Mittan
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh Edinburgh UK
| | - Robyn E. Shaw
- Environmental and Conservation Sciences Murdoch University Perth Australia
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre‐Fondazione Edmund Mach San Michele all’Adige Trentino Italy
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12
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Vasiljevic N, Morf NV, Senn J, Pérez‐Espona S, Mattucci F, Mucci N, Moore‐Jones G, Pisano SRR, Kratzer A, Ogden R. Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization. Ecol Evol 2022; 12:e8626. [PMID: 35222977 PMCID: PMC8858214 DOI: 10.1002/ece3.8626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 11/12/2022] Open
Abstract
In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement.
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Affiliation(s)
- Nina Vasiljevic
- Zurich Institute of Forensic Medicine University of Zurich Switzerland
| | - Nadja V. Morf
- Zurich Institute of Forensic Medicine University of Zurich Switzerland
| | - Josef Senn
- Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Sílvia Pérez‐Espona
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Midlothian UK
| | - Federica Mattucci
- ISPRA‐Istituto Superiore per la Protezione e la Ricerca Ambientale Area per la Genetica della Conservazione BIO‐CGE Bologna Italy
| | - Nadia Mucci
- ISPRA‐Istituto Superiore per la Protezione e la Ricerca Ambientale Area per la Genetica della Conservazione BIO‐CGE Bologna Italy
| | - Gaia Moore‐Jones
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse‐Faculty University of Bern Bern Switzerland
| | - Simone Roberto Rolando Pisano
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse‐Faculty University of Bern Bern Switzerland
| | - Adelgunde Kratzer
- Zurich Institute of Forensic Medicine University of Zurich Switzerland
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Midlothian UK
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13
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Williams KT, Weigel KA, Coblentz WK, Esser NM, Schlesser H, Hoffman PC, Ogden R, Su H, Akins MS. Effect of diet energy level and genomic residual feed intake on bred Holstein dairy heifer growth and feed efficiency. J Dairy Sci 2022; 105:2201-2214. [PMID: 34998546 DOI: 10.3168/jds.2020-19982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 11/08/2021] [Indexed: 11/19/2022]
Abstract
The objective of this study was to determine growth, feed intake, and feed efficiency of postbred dairy heifers with different genomic residual feed intake (RFI) predicted as a lactating cow when offered diets differing in energy density. Postbred Holstein heifers (n = 128, ages 14-20 mo) were blocked by initial weight (high, medium-high, medium-low, and low) with 32 heifers per block. Each weight block was sorted by RFI (high or low) to obtain 2 pens of heifers with high and low genomically predicted RFI within each block (8 heifers per pen). Low RFI heifers were expected to have greater feed efficiency than high RFI heifers. Dietary treatments consisted of a higher energy control diet based on corn silage and alfalfa haylage [HE; 62.7% total digestible nutrients, 11.8% crude protein, and 45.6% neutral detergent fiber; dry matter (DM) basis], and a lower energy diet diluted with straw (LE; 57.0% total digestible nutrients, 11.7% crude protein, and 50.1% neutral detergent fiber; DM basis). Each pen within a block was randomly allocated a diet treatment to obtain a 2 × 2 factorial arrangement (2 RFI levels and 2 dietary energy levels). Diets were offered in a 120-d trial. Dry matter intake by heifers was affected by diet (11.0 vs. 10.0 kg/d for HE and LE, respectively) but not by RFI or the interaction of RFI and diet. Daily gain was affected by the interaction of RFI and diet, with low RFI heifers gaining more than high RFI heifers when fed LE (0.94 vs. 0.85 kg/d for low and high RFI, respectively), but no difference for RFI groups when fed HE (1.16 vs. 1.19 kg/d for low and high RFI, respectively). Respective feed efficiencies were improved for low RFI compared with high RFI heifers when fed LE (10.6 vs. 11.8 kg of feed DM/kg of gain), but no effect of RFI was found when fed HE (9.4 vs. 9.5 kg of DM/kg of gain for high and low RFI, respectively). No effect of RFI or diet on first-lactation performance through 150 DIM was observed. Based on these results, the feed efficiency of heifers having different genomic RFI may be dependent on diet energy level, whereby low RFI heifers utilized the LE diet more efficiently. The higher fiber straw (LE) diet controlled intake and maintained more desirable heifer weight gains. This suggests that selection for improved RFI in lactating cows may improve feed efficiency in growing heifers when fed to meet growth goals of 0.9 to 1.0 kg of gain/d.
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Affiliation(s)
- K T Williams
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison 53706
| | - K A Weigel
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison 53706
| | - W K Coblentz
- USDA Dairy Forage Research Center, Marshfield, WI 54449
| | - N M Esser
- Marshfield Agricultural Research Station, University of Wisconsin-Madison, Marshfield 54449
| | - H Schlesser
- Marathon County Extension, University of Wisconsin-Madison, Wausau 54403
| | - P C Hoffman
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison 53706; Vita Plus Corporation, Madison, WI 53713
| | - R Ogden
- USDA Dairy Forage Research Center, Marshfield, WI 54449
| | - H Su
- Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China 100193
| | - M S Akins
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison 53706.
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14
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Mead D, Ogden R, Meredith A, Peniche G, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Holmes N, Wright V, Loose M, Quail MA, McCarthy SA, Howe K, Chow W, Torrance J, Collins J, Challis R, Durbin R, Blaxter M. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758. Wellcome Open Res 2021; 6:112. [PMID: 34671705 PMCID: PMC8499043 DOI: 10.12688/wellcomeopenres.16631.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Accepted: 05/05/2021] [Indexed: 11/26/2022] Open
Abstract
We present a genome assembly from an individual female
Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.
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Affiliation(s)
- Dan Mead
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Owlstone Medical, Cambridge Science Park, Cambridge, CB4 0GJ, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Sciences and Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Anna Meredith
- Royal (Dick) School of Veterinary Sciences and Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK.,Melbourne Veterinary School, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Gabriela Peniche
- Royal (Dick) School of Veterinary Sciences and Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Michelle Smith
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Craig Corton
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jason Skelton
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Jale Doulcan
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Achilles Therapeutics plc, London, W6 8PW, UK
| | - Nadine Holmes
- Deep Seq, University of Nottingham, Nottingham, NG7 2UH, UK
| | | | - Matt Loose
- Deep Seq, University of Nottingham, Nottingham, NG7 2UH, UK
| | | | - Shane A McCarthy
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - William Chow
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - James Torrance
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Joanna Collins
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Richard Durbin
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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15
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Hoban S, Bruford MW, Funk WC, Galbusera P, Griffith MP, Grueber CE, Heuertz M, Hunter ME, Hvilsom C, Stroil BK, Kershaw F, Khoury CK, Laikre L, Lopes-Fernandes M, MacDonald AJ, Mergeay J, Meek M, Mittan C, Mukassabi TA, O'Brien D, Ogden R, Palma-Silva C, Ramakrishnan U, Segelbacher G, Shaw RE, Sjögren-Gulve P, Veličković N, Vernesi C. Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible. Bioscience 2021; 71:964-976. [PMID: 34475806 PMCID: PMC8407967 DOI: 10.1093/biosci/biab054] [Citation(s) in RCA: 37] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.
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Affiliation(s)
- Sean Hoban
- The Morton Arboretum, Center for Tree Science, Lisle, Illinois, United States
| | | | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, United States
| | - Peter Galbusera
- Royal Zoological Society of Antwerp, Centre for Research and Conservation, Antwerp, Belgium
| | | | - Catherine E Grueber
- University of Sydney's School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Myriam Heuertz
- INRAE, and the University of Bordeaux, Biogeco, Cestas, France
| | - Margaret E Hunter
- US Geological Survey's Wetland and Aquatic Research Center, Gainesville, Florida, United States
| | | | - Belma Kalamujic Stroil
- University of Sarajevo Institute for Genetic Engineering and Biotechnology, Laboratory for Molecular Genetics of Natural Resources, Sarajevo, Bosnia and Herzegovina
| | - Francine Kershaw
- Natural Resources Defense Council, New York, New York, United States
| | - Colin K Khoury
- International Center for Tropical Agriculture, Cali, Colombia
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | | | - Anna J MacDonald
- Australian National University, John Curtin School of Medical Research and Research School of Biology, Canberra, Australia
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Mariah Meek
- Michigan State University Department of Integrative Biology, AgBio Research, Ecology, Evolution, and Behavior Program, East Lansing, Michigan, United States
| | - Cinnamon Mittan
- Cornell University's Department of Ecology and Evolutionary Biology, Ithaca, New York, United States
| | - Tarek A Mukassabi
- University of Benghazi Department of Botany, Faculty of Sciences, Benghazi, Libya
| | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and with the Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Scotland, United Kingdom
| | | | - Uma Ramakrishnan
- Department of Ecology and Evolution, National Centre for Biological Sciences, Bangalore, India
| | - Gernot Segelbacher
- Chair of wildlife ecology and management, University Freiburg, Freiburg, Germany
| | - Robyn E Shaw
- Department of Environmental and Conservation Sciences, Murdoch University, Perth, Australia
| | - Per Sjögren-Gulve
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, Stockholm, Sweden
| | - Nevena Veličković
- University of Novi Sad's Faculty of Sciences, Department of Biology and Ecology, Novi Sad, Serbia
| | - Cristiano Vernesi
- Forest Ecology and Biogeochemical Fluxes Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Italy
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16
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Naito‐Liederbach AM, Sato Y, Nakajima N, Maeda T, Inoue T, Yamazaki T, Ogden R, Inoue‐Murayama M. Genetic diversity of the endangered Japanese golden eagle at neutral and functional loci. Ecol Res 2021. [DOI: 10.1111/1440-1703.12246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Yu Sato
- Wildlife Research Center Kyoto University Kyoto Japan
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Roslin UK
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies National Institute for Environmental Studies Tsukuba Japan
| | - Taku Maeda
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health Morioka Japan
| | - Takehiko Inoue
- Asian Raptor Research and Conservation Network Yasu Japan
| | - Toru Yamazaki
- Asian Raptor Research and Conservation Network Yasu Japan
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Roslin UK
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17
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Laguardia A, Gobush K, Bourgeois S, Strindberg S, Abitsi G, Ebouta F, Fay J, Gopalaswamy A, Maisels F, Ogden R, White L, Stokes E. Assessing the feasibility of density estimation methodologies for African forest elephant at large spatial scales. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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18
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Laikre L, Hohenlohe PA, Allendorf FW, Bertola LD, Breed MF, Bruford MW, Funk WC, Gajardo G, González-Rodríguez A, Grueber CE, Hedrick PW, Heuertz M, Hunter ME, Johannesson K, Liggins L, MacDonald AJ, Mergeay J, Moharrek F, O’Brien D, Ogden R, Orozco-terWengel P, Palma-Silva C, Pierson J, Paz-Vinas I, Russo IRM, Ryman N, Segelbacher G, Sjögren-Gulve P, Waits LP, Vernesi C, Hoban S. Correction to: Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01376-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A correction to this paper has been published: https://doi.org/10.1007/s10592-021-01376-9
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19
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Vasiljevic N, Lim M, Humble E, Seah A, Kratzer A, Morf NV, Prost S, Ogden R. Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification. Forensic Sci Int Genet 2021; 53:102493. [PMID: 33770699 DOI: 10.1016/j.fsigen.2021.102493] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/09/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022]
Abstract
Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.
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Affiliation(s)
- Nina Vasiljevic
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
| | - Marisa Lim
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK
| | - Adeline Seah
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Adelgunde Kratzer
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Nadja V Morf
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany; South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK; TRACE Wildlife Forensics Network, Edinburgh, UK
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20
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Abstract
Abstract
The pink cockatoo (Lophochroa leadbeateri; or Major Mitchell’s cockatoo) is one of Australia’s most iconic bird species. Two subspecies based on morphology are separated by a biogeographical divide, the Eyrean Barrier. Testing the genetic basis for this subspecies delineation, clarifying barriers to gene flow and identifying any cryptic genetic diversity will likely have important implications for conservation and management. Here, we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA data to conduct the first range-wide genetic assessment of the species. The aims were to investigate the phylogeography of the pink cockatoo, to characterize conservation units and to reassess subspecies boundaries. We found consistent but weak genetic structure between the two subspecies based on nuclear SNPs. However, phylogenetic analysis of nuclear SNPs and mitochondrial DNA sequence data did not recover reciprocally monophyletic groups, indicating incomplete evolutionary separation between the subspecies. Consequently, we have proposed that the two currently recognized subspecies be treated as separate management units rather than evolutionarily significant units. Given that poaching is suspected to be a threat to this species, we assessed the utility of our data for wildlife forensic applications. We demonstrated that a subspecies identification test could be designed using as few as 20 SNPs.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, ACT, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
- Centre for Forensic Science, University of Technology Sydney, Broadway, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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21
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Hosegood J, Humble E, Ogden R, de Bruyn M, Creer S, Stevens GMW, Abudaya M, Bassos-Hull K, Bonfil R, Fernando D, Foote AD, Hipperson H, Jabado RW, Kaden J, Moazzam M, Peel LR, Pollett S, Ponzo A, Poortvliet M, Salah J, Senn H, Stewart JD, Wintner S, Carvalho G. Phylogenomics and species delimitation for effective conservation of manta and devil rays. Mol Ecol 2020; 29:4783-4796. [PMID: 33164287 DOI: 10.1111/mec.15683] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.
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Affiliation(s)
- Jane Hosegood
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Emily Humble
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.,TRACE Wildlife Forensics Network, Edinburgh, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Guy M W Stevens
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | | | - Kim Bassos-Hull
- Mote Marine Laboratory, The Center for Shark Research, Sarasota, FL, USA
| | | | - Daniel Fernando
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Blue Resources Trust, Colombo, Sri Lanka
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, Trondheim, Norway
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Jennifer Kaden
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | | | - Lauren R Peel
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,The Australian Institute of Marine Science, Crawley, WA, Australia.,Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
| | - Stephen Pollett
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | | | - Jehad Salah
- Ministry of Agriculture Directorate General of Fisheries, Gaza City, Palestine
| | - Helen Senn
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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22
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Sato Y, Ogden R, Kishida T, Nakajima N, Maeda T, Inoue-Murayama M. Population history of the golden eagle inferred from whole-genome sequencing of three of its subspecies. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe application of evolutionary genetic research to investigate the potential for endangered species to adapt to changing environments is important for conservation biology. Effective population size (Ne) is informative for understanding adaptive potential as it refers to the genetic variation in breeding individuals who have contributed to contemporary and historic population diversity. We reconstruct fluctuations in Ne in three golden eagle subspecies (Japanese, Scottish, North American) using the pairwise sequential Markovian coalescent (PSMC) model based on whole-genome sequence data. Our results indicate the timing of subspeciation events and suggest significant ongoing demographic reductions since the start of the Last Glacial Period. Importantly, we find evidence for gene flow from continental populations into the ancestral Japanese population resulting in a short, sharp recovery in genetic diversity. Timing agrees with the palaeogeographic estimates of land bridge connections between the Japanese archipelago and Asian continent and matches a similar Ne spike in the Scottish population, but not in the North American population. Given contemporary declines in isolated Japanese and UK island populations, our study highlights a concerning loss of local genetic diversity, but also indicates the likely response of populations to genetic reinforcement from neighbouring subspecies, increasing management options and encouraging a range-wide species conservation approach.
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Affiliation(s)
- Yu Sato
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, University of Edinburgh, UK
| | - Takushi Kishida
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Museum of Natural and Environmental History, Shizuoka, Japan
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
| | - Taku Maeda
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Morioka, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
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23
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Humble E, Dobrynin P, Senn H, Chuven J, Scott AF, Mohr DW, Dudchenko O, Omer AD, Colaric Z, Lieberman Aiden E, Al Dhaheri SS, Wildt D, Oliaji S, Tamazian G, Pukazhenthi B, Ogden R, Koepfli KP. Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild. Mol Ecol Resour 2020; 20:1668-1681. [PMID: 32365406 DOI: 10.1111/1755-0998.13181] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 01/04/2023]
Abstract
Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a large-scale and long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.
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Affiliation(s)
- Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Pavel Dobrynin
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA.,Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Helen Senn
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Justin Chuven
- Terrestrial & Marine Biodiversity Sector, Environment Agency, Abu Dhabi, United Arab Emirates
| | - Alan F Scott
- Genetic Resources Core Facility, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David W Mohr
- Genetic Resources Core Facility, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | | | - David Wildt
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Shireen Oliaji
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gaik Tamazian
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia
| | - Budhan Pukazhenthi
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
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24
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Hartvig I, So T, Changtragoon S, Tran HT, Bouamanivong S, Ogden R, Senn H, Vieira FG, Turner F, Talbot R, Theilade I, Nielsen LR, Kjær ED. Conservation genetics of the critically endangered Siamese rosewood (Dalbergia cochinchinensis): recommendations for management and sustainable use. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01279-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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25
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Abstract
Seafood is one of the most traded food commodities in the world with demand steadily increasing [1]. There is, however, a rising concern over the vulnerability of seafood supply chains to species mislabelling and fraud [1,2]. DNA methods have been widely used to detect species mislabelling and a recent meta-analysis of 4500 seafood product tests from 51 publications found an average of 30 percent were not the species stated on the label or menu [3]. This high rate poses a serious threat to consumer trust, reputations of seafood businesses and the sustainability of fishery resources. Seafood certification schemes may help reduce this problem. Here, we use DNA barcoding [4] to validate the species identity of 1402 certified seafood products derived from 27 species across 18 countries and find that in over 99% of cases species labelling was correct.
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Affiliation(s)
- Jaco Barendse
- Marine Stewardship Council, 1 Snow Hill, London, EC1A 2DH, UK; Sustainability Research Unit (SRU), Nelson Mandela University, George Campus, South Africa
| | - Alison Roel
- Marine Stewardship Council, 1 Snow Hill, London, EC1A 2DH, UK
| | - Catherine Longo
- Marine Stewardship Council, 1 Snow Hill, London, EC1A 2DH, UK
| | | | - Lucy M I Webster
- Science and Advice for Scottish Agriculture (SASA), Roddinglaw Road, Edinburgh, EH12 9FJ, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, UK; TRACE Wildlife Forensics Network, Edinburgh, EH12 6LE, UK
| | - Francis Neat
- Marine Stewardship Council, 1 Snow Hill, London, EC1A 2DH, UK.
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26
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Ewart KM, Johnson RN, Ogden R, Joseph L, Frankham GJ, Lo N. Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species. Mol Ecol Resour 2019; 19:1578-1592. [PMID: 31484222 DOI: 10.1111/1755-0998.13082] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq™ ). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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27
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Bercovitch FB, Berry PSM, Dagg A, Deacon F, Doherty JB, Lee DE, Mineur F, Muller Z, Ogden R, Seymour R, Shorrocks B, Tutchings A. How many species of giraffe are there? Curr Biol 2019; 27:R136-R137. [PMID: 28222287 DOI: 10.1016/j.cub.2016.12.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a recent paper in Current Biology, Fennessy and colleagues [1] conclude that there are four species of giraffe and that their numbers are declining in Africa. Giraffes (Giraffa camelopardalis) are presently classified as one species, with nine subspecies, which are considered 'Vulnerable' on the IUCN Red List [2]. The present consensus of one species divided into nine subspecies has previously been questioned (Supplemental information), and Fennessy and colleagues [1] provide another viewpoint on giraffe taxonomy. The fundamental reason for different taxonomic interpretations is that they are based upon different datasets that adopt different statistical techniques and follow different criteria for nomenclature.
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Affiliation(s)
- Fred B Bercovitch
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan; Department of Animal, Wildlife, and Grassland Sciences, University of the Free State, Bloemfontein, South Africa; IUCN, Species Survival Commission, Giraffe and Okapi Specialist Group.
| | | | - Anne Dagg
- IUCN, Species Survival Commission, Giraffe and Okapi Specialist Group; Department of Independent Studies, University of Waterloo, Ontario, Canada
| | - Francois Deacon
- Department of Animal, Wildlife, and Grassland Sciences, University of the Free State, Bloemfontein, South Africa; IUCN, Species Survival Commission, Giraffe and Okapi Specialist Group
| | - John B Doherty
- IUCN, Species Survival Commission, Giraffe and Okapi Specialist Group; Reticulated Giraffe Project, Nairobi, Kenya; School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - Derek E Lee
- IUCN, Species Survival Commission, Giraffe and Okapi Specialist Group; Wild Nature Institute, Hanover, NH, USA
| | - Frédéric Mineur
- Reticulated Giraffe Project, Nairobi, Kenya; School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - Zoe Muller
- IUCN, Species Survival Commission, Giraffe and Okapi Specialist Group; Giraffe Research and Conservation Trust, Nairobi, Kenya; School of Biological Sciences, University of Bristol, Bristol, UK
| | - Rob Ogden
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Russell Seymour
- IUCN, Species Survival Commission, Giraffe and Okapi Specialist Group; Reticulated Giraffe Project, Nairobi, Kenya
| | - Bryan Shorrocks
- Environment Department, University of York, Heslington, York, UK; Department of Biology, University of Leeds, Leeds, UK
| | - Andy Tutchings
- IUCN, Species Survival Commission, Giraffe and Okapi Specialist Group
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28
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Masters A, Ogden R, Wetton JH, Dawnay N. Defining end user requirements for a field-based molecular detection system for wildlife forensic investigations. Forensic Sci Int 2019; 301:231-239. [PMID: 31181408 DOI: 10.1016/j.forsciint.2019.05.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/17/2019] [Indexed: 11/29/2022]
Abstract
The increasing use of non-laboratory-based DNA and protein detection methods promise to provide rapid investigative intelligence and support sample prioritisation. Primarily developed for human forensic or medical applications, current systems may also show utility in the field of wildlife forensic science. However, it is currently unknown whether the requirements of the wildlife forensic community can be met by current non-laboratory based tools. Given the diverse array of stakeholders and sample types commonly encountered, it is necessary to first identify the needs of the community and then try and map their needs to current instrumentation. By using a market research style questionnaire, this study identified key requirements for a non-laboratory-based system following feedback from the wildlife forensic community. Data showed that there is strong support for field-based detection methods while highlighting concerns including contamination risks and reduced quality assurance associated with non-laboratory testing. Key species and applications were identified alongside hurdles to implementation and adoption. Broadly, the requirements align with many of the developmental drivers that have led to the rise of in-field portable detection instrumentation, specifically rapid detection within one hour, ease-of-use, and ≥95% accuracy. Several existing platforms exist that met some of the identified requirements but not all. With further collaboration between industry partners and the wildlife forensic community it is possible that new field-based systems can be developed and applied routinely.
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Affiliation(s)
- Alice Masters
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Rob Ogden
- Royal School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK; TRACE Wildlife Forensics Network, Edinburgh, EH12 6LE, UK
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK.
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29
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Bourgeois S, Kaden J, Senn H, Bunnefeld N, Jeffery KJ, Akomo-Okoue EF, Ogden R, McEwing R. Improving cost-efficiency of faecal genotyping: New tools for elephant species. PLoS One 2019; 14:e0210811. [PMID: 30699177 PMCID: PMC6353156 DOI: 10.1371/journal.pone.0210811] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 06/01/2018] [Accepted: 01/02/2019] [Indexed: 11/18/2022] Open
Abstract
Despite the critical need for non-invasive tools to improve monitoring of wildlife populations, especially for endangered and elusive species, faecal genetic sampling has not been adopted as regular practice, largely because of the associated technical challenges and cost. Substantial work needs to be undertaken to refine sample collection and preparation methods in order to improve sample set quality and provide cost-efficient tools that can effectively support wildlife management. In this study, we collected an extensive set of forest elephant (Loxodonta cyclotis) faecal samples throughout Gabon, Central Africa, and prepared them for genotyping using 107 single-nucleotide polymorphism assays. We developed a new quantitative polymerase chain reaction (PCR) assay targeting a 130-bp nuclear DNA fragment and demonstrated its suitability for degraded samples in all three elephant species. Using this assay to compare the efficacy of two sampling methods for faecal DNA recovery, we found that sampling the whole surface of a dung pile with a swab stored in a small tube of lysis buffer was a convenient method producing high extraction success and DNA yield. We modelled the influence of faecal quality and storage time on DNA concentration in order to provide recommendations for optimized collection and storage. The maximum storage time to ensure 75% success was two months for samples collected within 24 hours after defecation and extended to four months for samples collected within one hour. Lastly, the real-time quantitative PCR assay allowed us to predict genotyping success and pre-screen DNA samples, thus further increasing the cost-efficiency of our approach. We recommend combining the validation of an efficient sampling method, the build of in-country DNA extraction capacity for reduced storage time and the development of species-specific quantitative PCR assays in order to increase the cost-efficiency of routine non-invasive DNA analyses and expand the use of next-generation markers to non-invasive samples.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- * E-mail:
| | - Jenny Kaden
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
| | - Helen Senn
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
| | - Nils Bunnefeld
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- Institut de Recherche en Écologie Tropicale, Libreville, Gabon
| | | | - Rob Ogden
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
| | - Ross McEwing
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
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30
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do Prado FD, Vera M, Hermida M, Bouza C, Pardo BG, Vilas R, Blanco A, Fernández C, Maroso F, Maes GE, Turan C, Volckaert FAM, Taggart JB, Carr A, Ogden R, Nielsen EE, Martínez P. Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot ( Scophthalmus maximus). Evol Appl 2018; 11:1322-1341. [PMID: 30151043 PMCID: PMC6099829 DOI: 10.1111/eva.12628] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 10/18/2017] [Accepted: 02/23/2018] [Indexed: 12/16/2022] Open
Abstract
Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double-digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.
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Affiliation(s)
- Fernanda Dotti do Prado
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
- CAPES FoundationMinistry of Education of BrazilBrasíliaBrazil
| | - Manuel Vera
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Belén G. Pardo
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Román Vilas
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Francesco Maroso
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Gregory E. Maes
- Laboratory of Biodiversity and Evolutionary GenomicsUniversity of LeuvenLeuvenBelgium
- Center for Human GeneticsUZ Leuven‐Genomics Core, KU LeuvenLeuvenBelgium
- Comparative Genomics CentreCollege of Science and EngineeringJames Cook UniversityTownsvilleQLDAustralia
| | - Cemal Turan
- Faculty of Marine Science and TechnologyIskenderun Technical UniversityIskenderunTurkey
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary GenomicsUniversity of LeuvenLeuvenBelgium
- Center for Human GeneticsUZ Leuven‐Genomics Core, KU LeuvenLeuvenBelgium
- Comparative Genomics CentreCollege of Science and EngineeringJames Cook UniversityTownsvilleQLDAustralia
| | | | | | - Rob Ogden
- Trace Wildlife Forensics NetworkRoyal Zoological Society of ScotlandEdinburghUK
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Paulino Martínez
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
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Maroso F, Hillen JEJ, Pardo BG, Gkagkavouzis K, Coscia I, Hermida M, Franch R, Hellemans B, Van Houdt J, Simionati B, Taggart JB, Nielsen EE, Maes G, Ciavaglia SA, Webster LMI, Volckaert FAM, Martinez P, Bargelloni L, Ogden R. Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species. Mar Genomics 2018; 39:64-72. [PMID: 29496460 DOI: 10.1016/j.margen.2018.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/29/2023]
Abstract
The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2.5 × 1012 bases in total), using a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use of a reference genome and a posteriori genotype correction improved genotyping precision. Individual read coverage was a key variable for reproducibility; variance in sequencing depth between loci in the same individual was also identified as an important factor and found to correlate to tag length. A comparison of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select and improve approaches to the analysis of large datasets based on RAD-like methodologies.
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Affiliation(s)
- F Maroso
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy.
| | - J E J Hillen
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - B G Pardo
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - K Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - I Coscia
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium; School of Environmental and Life Science, Rm 332, Peel Building, University of Salford, Salford M5 4WT, UK
| | - M Hermida
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - R Franch
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - B Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - J Van Houdt
- Department of Human Genetics, University of Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium
| | - B Simionati
- BMR Genomics, Via Redipuglia 21a, Padova, Italy
| | - J B Taggart
- Division of Environmental and Evolutionary Biology, School of Biology and Biochemistry, The Queen's University of Belfast, Belfast BT7 INN, UK
| | - E E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - G Maes
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium; Department of Human Genetics, University of Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium; Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Marine and Environmental Sciences, Faculty of Science and Engineering, James Cook University, Townsville, 4811, QLD, Australia
| | - S A Ciavaglia
- Science and Advice for Scottish Agriculture, Roddinglaw Road, Edinburgh EH12 9FJ, UK
| | - L M I Webster
- Science and Advice for Scottish Agriculture, Roddinglaw Road, Edinburgh EH12 9FJ, UK
| | - F A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - P Martinez
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - L Bargelloni
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - R Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
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Bourgeois S, Senn H, Kaden J, Taggart JB, Ogden R, Jeffery KJ, Bunnefeld N, Abernethy K, McEwing R. Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant. Ecol Evol 2018; 8:2207-2217. [PMID: 29468037 PMCID: PMC5817121 DOI: 10.1002/ece3.3854] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 08/27/2017] [Revised: 12/17/2017] [Accepted: 12/29/2017] [Indexed: 12/14/2022] Open
Abstract
The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field. As such, genetic monitoring is being increasingly implemented to complement or replace more burdensome field techniques. Single-nucleotide polymorphisms (SNPs) are particularly cost-effective and informative markers that can be used for a range of practical applications, including population census, assessment of human impact on social and genetic structure, and investigation of the illegal wildlife trade. SNP resources for elephants are scarce, but next-generation sequencing provides the opportunity for rapid, inexpensive generation of SNP markers in nonmodel species. Here, we sourced forest elephant DNA from 23 samples collected from 10 locations within Gabon, Central Africa, and applied double-digest restriction-site-associated DNA (ddRAD) sequencing to discover 31,851 tags containing SNPs that were reduced to a set of 1,365 high-quality candidate SNP markers. A subset of 115 candidate SNPs was then selected for assay design and validation using 56 additional samples. Genotyping resulted in a high conversion rate (93%) and a low per allele error rate (0.07%). This study provides the first panel of 107 validated SNP markers for forest elephants. This resource presents great potential for new genetic tools to produce reliable data and underpin a step-change in conservation policies for this elusive species.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs NationauxLibrevilleGabon
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Helen Senn
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - Jenny Kaden
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - John B. Taggart
- Aquaculture Pathfoot BuildingUniversity of StirlingStirlingUK
| | - Rob Ogden
- TRACE Wildlife Forensics NetworkEdinburghUK
- Royal (Dick) School of Veterinary Studies & The Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs NationauxLibrevilleGabon
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
| | - Nils Bunnefeld
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Katharine Abernethy
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
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33
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Murray-Dickson G, Ghazali M, Ogden R, Brown R, Auliya M. Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds' most traded snake species. PLoS One 2017; 12:e0182049. [PMID: 28817588 PMCID: PMC5560690 DOI: 10.1371/journal.pone.0182049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 04/19/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022] Open
Abstract
As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python's native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley's modification of Wallace's line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans.
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Affiliation(s)
- Gillian Murray-Dickson
- Royal Zoological Society of Scotland (RZSS) WildGenes Laboratory, Edinburgh, United Kingdom
- * E-mail:
| | - Muhammad Ghazali
- Royal Zoological Society of Scotland (RZSS) WildGenes Laboratory, Edinburgh, United Kingdom
| | - Rob Ogden
- Trace Wildlife Forensics Network, Edinburgh, United Kingdom
| | - Rafe Brown
- KU Biodiversity Institute, 1345 Jayhawk Blvd, Dyche, Lawrence, KS, United States of America
| | - Mark Auliya
- Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
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Ito H, Ogden R, Langenhorst T, Inoue-Murayama M. Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations. Zoo Biol 2016; 36:87-94. [PMID: 27981608 DOI: 10.1002/zoo.21342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/14/2016] [Accepted: 11/28/2016] [Indexed: 11/12/2022]
Abstract
Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hideyuki Ito
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Kyoto City Zoo, Kyoto, Japan
| | - Rob Ogden
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
| | | | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba, Japan
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35
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Adenyo C, Ogden R, Kayang B, Onuma M, Nakajima N, Inoue-Murayama M. Genome-wide DNA markers to support genetic management for domestication and commercial production in a large rodent, the Ghanaian grasscutter (Thryonomys swinderianus). Anim Genet 2016; 48:113-115. [PMID: 27436241 DOI: 10.1111/age.12478] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2016] [Indexed: 11/28/2022]
Abstract
Domestication and commercial production of the grasscutter, Thryonomys swinderianus, a large rodent, represents an important opportunity to secure sustainable animal protein for local communities in West Africa. To support production, DNA markers are required for population diversity assessment, pedigree analysis and marker-assisted selection. This study reports the application of double-digest RAD sequencing to simultaneously discover and genotype SNP markers in 24 wild and recently domesticated grasscutters. An initial panel of 1209 SNP loci was characterised from a total of more than 21 000 candidate loci containing single SNPs. This genome-wide resource represents the first application of its type to commercial production of a large rodent for food and advances the use of agricultural genomics in Ghana.
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Affiliation(s)
- C Adenyo
- Livestock and Poultry Research Centre, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - R Ogden
- Wildlife Research Center of Kyoto University, 2-24 Tanaka-Sekiden-cho, Kyoto, 606-8203, Japan
| | - B Kayang
- Department of Animal Science, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - M Onuma
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-City, Ibaraki, 305-8506, Japan
| | - N Nakajima
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-City, Ibaraki, 305-8506, Japan
| | - M Inoue-Murayama
- Wildlife Research Center of Kyoto University, 2-24 Tanaka-Sekiden-cho, Kyoto, 606-8203, Japan
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36
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Ogden R, Linacre A. Wildlife forensic science: A review of genetic geographic origin assignment. Forensic Sci Int Genet 2015; 18:152-9. [DOI: 10.1016/j.fsigen.2015.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/12/2015] [Accepted: 02/24/2015] [Indexed: 10/23/2022]
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Shafer AB, Wolf JB, Alves PC, Bergström L, Bruford MW, Brännström I, Colling G, Dalén L, De Meester L, Ekblom R, Fawcett KD, Fior S, Hajibabaei M, Hill JA, Hoezel AR, Höglund J, Jensen EL, Krause J, Kristensen TN, Krützen M, McKay JK, Norman AJ, Ogden R, Österling EM, Ouborg NJ, Piccolo J, Popović D, Primmer CR, Reed FA, Roumet M, Salmona J, Schenekar T, Schwartz MK, Segelbacher G, Senn H, Thaulow J, Valtonen M, Veale A, Vergeer P, Vijay N, Vilà C, Weissensteiner M, Wennerström L, Wheat CW, Zieliński P. Genomics and the challenging translation into conservation practice. Trends Ecol Evol 2015; 30:78-87. [DOI: 10.1016/j.tree.2014.11.009] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
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Zouganelis GD, Ogden R, Nahar N, Runfola V, Bonab M, Ardalan A, Radford D, Barnett R, Larson G, Hildred A, Jones M, Scarlett G. An old dog and new tricks: Genetic analysis of a Tudor dog recovered from the Mary Rose wreck. Forensic Sci Int 2014; 245:51-7. [DOI: 10.1016/j.forsciint.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/23/2014] [Accepted: 10/04/2014] [Indexed: 11/25/2022]
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Summers KM, Ogden R, Clements DN, French AT, Gow AG, Powell R, Corcoran B, Mellanby RJ, Schoeman JP. Limited genetic divergence between dog breeds from geographically isolated countries. Vet Rec 2014; 175:562. [PMID: 25331973 PMCID: PMC4283627 DOI: 10.1136/vr.102739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- K M Summers
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - R Ogden
- WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - D N Clements
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - A T French
- Small Animal Hospital, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - A G Gow
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - R Powell
- Powell Torrance Diagnostic Services, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - B Corcoran
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - R J Mellanby
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - J P Schoeman
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, Republic of South Africa
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41
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Senn H, Banfield L, Wacher T, Newby J, Rabeil T, Kaden J, Kitchener AC, Abaigar T, Silva TL, Maunder M, Ogden R. Splitting or lumping? A conservation dilemma exemplified by the critically endangered dama gazelle (Nanger dama). PLoS One 2014; 9:e98693. [PMID: 24956104 PMCID: PMC4067283 DOI: 10.1371/journal.pone.0098693] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 05/02/2014] [Indexed: 01/07/2023] Open
Abstract
Managers of threatened species often face the dilemma of whether to keep populations separate to conserve local adaptations and minimize the risk of outbreeding, or whether to manage populations jointly to reduce loss of genetic diversity and minimise inbreeding. In this study we examine genetic relatedness and diversity in three of the five last remaining wild populations of dama gazelle and a number of captive populations, using mtDNA control region and cytochrome b data. Despite the sampled populations belonging to the three putative subspecies, which are delineated according to phenotypes and geographical location, we find limited evidence for phylogeographical structure within the data and no genetic support for the putative subspecies. In the light of these data we discuss the relevance of inbreeding depression, outbreeding depression, adaptive variation, genetic drift, and phenotypic variation to the conservation of the dama gazelle and make some recommendations for its future conservation management. The genetic data suggest that the best conservation approach is to view the dama gazelle as a single species without subspecific divisions.
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Affiliation(s)
- Helen Senn
- WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| | - Lisa Banfield
- Conservation Department, Al Ain Zoo, Al Ain, Abu Dhabi, United Arab Emirates
| | - Tim Wacher
- Conservation Programmes, Zoologicial Society of London, Regents Park, London, United Kingdom
| | - John Newby
- Sahara Conservation Fund, L'Isle, Switzerland
| | | | - Jennifer Kaden
- WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh, United Kingdom
- Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh, United Kingdom
| | - Teresa Abaigar
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas (CSIC), Almería, Spain
| | - Teresa Luísa Silva
- CIBIO/InBIO, Centro de Investigção em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas (CSIC), Almería, Spain
- Departamento de Biologia da, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Mike Maunder
- College of Arts and Sciences, Florida International University, Miami, Florida, United States of America
| | - Rob Ogden
- WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
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Senn H, Ogden R, Frosch C, Syrůčková A, Campbell-Palmer R, Munclinger P, Durka W, Kraus RHS, Saveljev AP, Nowak C, Stubbe A, Stubbe M, Michaux J, Lavrov V, Samiya R, Ulevicius A, Rosell F. Nuclear and mitochondrial genetic structure in the Eurasian beaver (Castor fiber) - implications for future reintroductions. Evol Appl 2014; 7:645-62. [PMID: 25067948 PMCID: PMC4105916 DOI: 10.1111/eva.12162] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 12/16/2013] [Accepted: 04/01/2014] [Indexed: 12/24/2022] Open
Abstract
Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conducting postrelease monitoring. In this study, we use a panel of 306 SNP (single nucleotide polymorphism) markers and 487-489 base pairs of mitochondrial DNA control region sequence data to examine 321 individuals from possible source populations of the Eurasian beaver for a reintroduction to Scotland. We use this information to reassess the phylogenetic history of the Eurasian beavers, to examine the genetic legacy of past reintroductions on the Eurasian landmass and to assess the future power of the genetic markers to conduct ongoing monitoring via parentage analysis and individual identification. We demonstrate the capacity of medium density genetic data (hundreds of SNPs) to provide information suitable for applied conservation and discuss the difficulty of balancing the need for high genetic diversity against phylogenetic best fit when choosing source population(s) for reintroduction.
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Affiliation(s)
- Helen Senn
- WildGenes Laboratory, Royal Zoological Society of Scotland Edinburgh, UK
| | - Rob Ogden
- WildGenes Laboratory, Royal Zoological Society of Scotland Edinburgh, UK
| | - Christiane Frosch
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt Gelnhausen, Germany
| | - Alena Syrůčková
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
| | | | - Pavel Munclinger
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
| | - Walter Durka
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ Halle, Germany
| | - Robert H S Kraus
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt Gelnhausen, Germany
| | - Alexander P Saveljev
- Russian Research Institute of Game Management and Fur Farming, Russian Academy of Sciences Kirov, Russia
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt Gelnhausen, Germany
| | - Annegret Stubbe
- Martin-Luther-Universität Halle-Wittenberg Institut für Biologie Bereich Zoologie/Molekulare Ökologie Hoher Weg 4 Halle/Saale, Germany
| | - Michael Stubbe
- Martin-Luther-Universität Halle-Wittenberg Institut für Biologie Domplatz 4 Halle/Saale, Germany
| | - Johan Michaux
- Conservation Genetics Unit, Institute of Botany (Bat. 22), University of Liège (Sart Tilman) Liège, Belgium
| | | | - Ravchig Samiya
- Department of Zoology, School of Biology and Biotechnology, National University of Mongolia Ulaanbaatar, Mongolia
| | - Alius Ulevicius
- Faculty of Natural Sciences, Vilnius University Vilnius, Lithuania
| | - Frank Rosell
- Telemark University College, Department of Environmental Sciences Telemark, Norway
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Milano I, Babbucci M, Cariani A, Atanassova M, Bekkevold D, Carvalho GR, Espiñeira M, Fiorentino F, Garofalo G, Geffen AJ, Hansen JH, Helyar SJ, Nielsen EE, Ogden R, Patarnello T, Stagioni M, Tinti F, Bargelloni L. Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius). Mol Ecol 2013; 23:118-35. [DOI: 10.1111/mec.12568] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 01/27/2023]
Affiliation(s)
- Ilaria Milano
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science-Agripolis-Viale dell'Università 16; I-35020 Legnaro Padova Italy
| | - Alessia Cariani
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Miroslava Atanassova
- Living Resources, Aquaculture and Management of their Traceability Division of ANFACO-CECOPESCA; Ctra. Colegio Universitario 16; 36.310 Vigo Spain
| | - Dorte Bekkevold
- National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 DK-8600 Silkeborg Denmark
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory; School of Biological Sciences; Bangor University; Environment Centre Wales; Bangor UK
| | - Montserrat Espiñeira
- Living Resources, Aquaculture and Management of their Traceability Division of ANFACO-CECOPESCA; Ctra. Colegio Universitario 16; 36.310 Vigo Spain
| | - Fabio Fiorentino
- National Research Council (CNR)-Institute for Coastal Marine Environment (IAMC); Via L. Vaccara 61 91026 Mazara del Vallo Trapani Italy
| | - Germana Garofalo
- National Research Council (CNR)-Institute for Coastal Marine Environment (IAMC); Via L. Vaccara 61 91026 Mazara del Vallo Trapani Italy
| | - Audrey J. Geffen
- Department of Biology; University of Bergen; P.O. Box 7803, N-5020 Bergen Norway
| | - Jakob. H. Hansen
- Living Resources, Aquaculture and Management of their Traceability Division of ANFACO-CECOPESCA; Ctra. Colegio Universitario 16; 36.310 Vigo Spain
| | - Sarah J. Helyar
- Food Safety, Environment & Genetics; Matís ohf, Vínlandsleið 12; 113 Reykjavík Iceland
| | - Einar E. Nielsen
- National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 DK-8600 Silkeborg Denmark
| | - Rob Ogden
- TRACE Wildlife Forensics Network; Royal Zoological Society of Scotland; Edinburgh EH12 6TS UK
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science-Agripolis-Viale dell'Università 16; I-35020 Legnaro Padova Italy
| | - Marco Stagioni
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Fausto Tinti
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science-Agripolis-Viale dell'Università 16; I-35020 Legnaro Padova Italy
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Shephard JM, Ogden R, Tryjanowski P, Olsson O, Galbusera P. Is population structure in the European white stork determined by flyway permeability rather than translocation history? Ecol Evol 2013; 3:4881-95. [PMID: 24455123 PMCID: PMC3892355 DOI: 10.1002/ece3.845] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 09/04/2013] [Accepted: 09/19/2013] [Indexed: 11/26/2022] Open
Abstract
European white stork are long considered to diverge to eastern and western migration pools as a result of independent overwintering flyways. In relatively recent times, the western and northern distribution has been subject to dramatic population declines and country-specific extirpations. A number of independent reintroduction programs were started in the mid 1950s to bring storks back to historical ranges. Founder individuals were sourced opportunistically from the Eastern and Western European distributions and Algeria, leading to significant artificial mixing between eastern and western flyways. Here we use mitochondrial and microsatellite DNA to test the contention that prior to translocation, eastern and western flyways were genetically distinct. The data show a surprising lack of structure at any spatial or temporal scale suggesting that even though birds were moved between flyways, there is evidence of natural mixing prior to the onset of translocation activities. Overall a high retention of genetic diversity, high Nef, and an apparent absence of recent genetic bottleneck associated with early 20th century declines suggest that the species is well equipped to respond to future environmental pressures.
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Affiliation(s)
- Jill M Shephard
- Centre for Research and Conservation - Royal Zoological Society of Antwerp Koningen Astridplein 26, 2018, Antwerp, Belgium ; School of Veterinary and Life Sciences, Murdoch University Murdoch, Western Australia, 6150, Australia
| | - Rob Ogden
- Royal Zoological Society of Scotland, Edinburgh Zoo 134 Corstorphine Road, Edinburgh, EH12 6TS, UK
| | - Piotr Tryjanowski
- Institute of Zoology, Poznan University of Life Sciences Wojska Polskiego 71 C, 60-625, Poznań, Poland
| | - Ola Olsson
- Department of Ecology, Animal Ecology, Lund University SE-223 62, Lund, Sweden
| | - Peter Galbusera
- Centre for Research and Conservation - Royal Zoological Society of Antwerp Koningen Astridplein 26, 2018, Antwerp, Belgium
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46
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Hoffman JI, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs. PLoS One 2013; 8:e68365. [PMID: 23874599 PMCID: PMC3712990 DOI: 10.1371/journal.pone.0068365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 05/28/2013] [Indexed: 01/17/2023] Open
Abstract
High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome.
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Affiliation(s)
- Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, North Rhine-Westphalia, Germany
- * E-mail:
| | - Michael A. S. Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Rob McEwing
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| | - Jaume Forcada
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Rob Ogden
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
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47
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Nielsen EE, Cariani A, Mac Aoidh E, Maes GE, Milano I, Ogden R, Taylor M, Hemmer-Hansen J, Babbucci M, Bargelloni L, Bekkevold D, Diopere E, Grenfell L, Helyar S, Limborg MT, Martinsohn JT, McEwing R, Panitz F, Patarnello T, Tinti F, Van Houdt JKJ, Volckaert FAM, Waples RS, Carvalho GR. Erratum: Corrigendum: Gene-associated markers provide tools for tackling illegal fishing and false eco-certification. Nat Commun 2013. [DOI: 10.1038/ncomms2975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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48
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Wilkinson S, Lu ZH, Megens HJ, Archibald AL, Haley C, Jackson IJ, Groenen MAM, Crooijmans RPMA, Ogden R, Wiener P. Signatures of diversifying selection in European pig breeds. PLoS Genet 2013; 9:e1003453. [PMID: 23637623 PMCID: PMC3636142 DOI: 10.1371/journal.pgen.1003453] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [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: 01/17/2013] [Accepted: 02/25/2013] [Indexed: 01/14/2023] Open
Abstract
Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition. The domestic pig, an important source of protein worldwide, was domesticated from the ancestral wild boar in multiple locations throughout the world. In Europe, local types were developed following domestication, but phenotypically distinct breeds only arose in the eighteenth century with the advent of systematic breeding. Recently developed molecular tools for pigs (as well as other livestock species) now allow a genetic characterisation of breed histories, including identification of regions of the genome that have been under selection in the establishment of breeds. We have applied these tools to identify genomic regions associated with breed development in a set of commercial and traditional pig breeds. We found strong evidence of genetic differentiation between breeds near genes associated with traits that are used to define breed standards, such as ear morphology and coat colour, as well as in regions of the genome that are associated with pork production traits. It is well documented that crosses with Asian pigs have been used to modify European breeds. We have found evidence of genetic influence from Asian pigs in European breeds, again in regions of the genome associated with breed standard characteristics, including ear shape and coat colour, as well as production traits.
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Affiliation(s)
- Samantha Wilkinson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Zen H. Lu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen UR, Wageningen, The Netherlands
| | - Alan L. Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Chris Haley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J. Jackson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Rob Ogden
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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Hemmer-Hansen J, Nielsen EE, Therkildsen NO, Taylor MI, Ogden R, Geffen AJ, Bekkevold D, Helyar S, Pampoulie C, Johansen T, Carvalho GR. A genomic island linked to ecotype divergence in Atlantic cod. Mol Ecol 2013; 22:2653-67. [DOI: 10.1111/mec.12284] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 01/20/2013] [Accepted: 01/31/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Jakob Hemmer-Hansen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | - Einar E. Nielsen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | - Nina O. Therkildsen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | - Martin I. Taylor
- School of Biological Sciences; University of East Anglia; Norwich NR4 7TJ UK
| | - Rob Ogden
- TRACE Wildlife Forensics Network; Royal Zoological Society of Scotland; Edinburgh EH12 6TS UK
| | - Audrey J. Geffen
- Department of Biology; University of Bergen; PB 7803 Bergen N-5020 Norway
| | - Dorte Bekkevold
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | | | | | - Torild Johansen
- Institute of Marine Research Tromsø; PO Box 6404 Tromsø N-9294 Norway
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory; School of Biological Sciences; Environment Centre Wales; Bangor University; Bangor Gwynedd LL57 2UW UK
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50
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Ogden R, Gharbi K, Mugue N, Martinsohn J, Senn H, Davey JW, Pourkazemi M, McEwing R, Eland C, Vidotto M, Sergeev A, Congiu L. Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing. Mol Ecol 2013; 22:3112-23. [PMID: 23473098 DOI: 10.1111/mec.12234] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 12/30/2022]
Affiliation(s)
- R. Ogden
- TRACE Wildlife Forensics Network; RZSS; Edinburgh EH12 6TS UK
| | - K. Gharbi
- The GenePool; School of Biological Sciences; The University of Edinburgh; Edinburgh UK
| | - N. Mugue
- Russian Institute for Fisheries and Oceanography (VNIRO); Moscow 107140 Russia
| | - J. Martinsohn
- Joint Research Centre of the European Commission; Maritime Affairs Unit; Institute for the Protection and Security of the Citizen; Via Fermi TP 051 Ispra VA 21027 Italy
| | - H. Senn
- WildGenes Laboratory; Royal Zoological Society of Scotland; Edinburgh EH12 6TS UK
| | - J. W. Davey
- Institute of Evolutionary Biology; School of Biological Sciences; University of Edinburgh; West Mains Road Edinburgh EH9 3JT UK
| | - M. Pourkazemi
- Sturgeon International Research Institute; PO Box 41635-3464 Rasht Iran
| | - R. McEwing
- TRACE Wildlife Forensics Network; RZSS; Edinburgh EH12 6TS UK
| | - C. Eland
- The GenePool; School of Biological Sciences; The University of Edinburgh; Edinburgh UK
| | - M. Vidotto
- Department of Biology; University of Padova; Via U. Bassi 58/b 35121 Padova Italy
| | - A. Sergeev
- Russian Institute for Fisheries and Oceanography (VNIRO); Moscow 107140 Russia
| | - L. Congiu
- Department of Biology; University of Padova; Via U. Bassi 58/b 35121 Padova Italy
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