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Pearman PB, Broennimann O, Aavik T, Albayrak T, Alves PC, Aravanopoulos FA, Bertola LD, Biedrzycka A, Buzan E, Cubric-Curik V, Djan M, Fedorca A, Fuentes-Pardo AP, Fussi B, Godoy JA, Gugerli F, Hoban S, Holderegger R, Hvilsom C, Iacolina L, Kalamujic Stroil B, Klinga P, Konopiński MK, Kopatz A, Laikre L, Lopes-Fernandes M, McMahon BJ, Mergeay J, Neophytou C, Pálsson S, Paz-Vinas I, Posledovich D, Primmer CR, Raeymaekers JAM, Rinkevich B, Rolečková B, Ruņģis D, Schuerz L, Segelbacher G, Kavčič Sonnenschein K, Stefanovic M, Thurfjell H, Träger S, Tsvetkov IN, Velickovic N, Vergeer P, Vernesi C, Vilà C, Westergren M, Zachos FE, Guisan A, Bruford M. Monitoring of species' genetic diversity in Europe varies greatly and overlooks potential climate change impacts. Nat Ecol Evol 2024; 8:267-281. [PMID: 38225425 PMCID: PMC10857941 DOI: 10.1038/s41559-023-02260-0] [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: 03/16/2023] [Accepted: 10/25/2023] [Indexed: 01/17/2024]
Abstract
Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species' joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union's Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity.
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Affiliation(s)
- Peter B Pearman
- Department of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country UPV/EHU, Leioa, Spain.
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain.
- BC3 Basque Center for Climate Change, Leioa, Spain.
| | - Olivier Broennimann
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, Lausanne, Switzerland
| | - Tsipe Aavik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tamer Albayrak
- Science and Art Faculty, Department of Biology, Lab of Ornithology, Burdur Mehmet Akif Ersoy University, Burdur, Turkey
| | - Paulo C Alves
- CIBIO-InBIO Laboratório Associado & Departamento de Biologia, Faculdade de Ciências do Porto, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- EBM, Estação Biológica de Mértola, Mértola, Portugal
| | - F A Aravanopoulos
- Faculty of Agriculture, Forest Science and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Elena Buzan
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Koper, Slovenia
- Faculty of Environmental Protection, Velenje, Slovenia
| | | | - Mihajla Djan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Ancuta Fedorca
- Department of Wildlife, National Institute for Research and Development in Forestry 'Marin Dracea', Brasov, Romania
- Department of Silviculture, Faculty of Silviculture and Forest Engineering, Transilvania University of Brasov, Brasov, Romania
| | - Angela P Fuentes-Pardo
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Barbara Fussi
- Bavarian Office for Forest Genetics, Teisendorf, Germany
| | - José A Godoy
- Doñana Biological Station (EBD-CSIC), Seville, Spain
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Sean Hoban
- Center for Tree Science, Morton Arboretum, Lisle, IL, USA
| | - Rolf Holderegger
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Sciences D-USYS, ETH Zürich, Zürich, Switzerland
| | | | - Laura Iacolina
- Faculty of Mathematics, Natural Sciences and Information Technologies, Department of Biodiversity, University of Primorska, Koper, Slovenia
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Belma Kalamujic Stroil
- Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Peter Klinga
- Faculty of Forestry, Technical University in Zvolen, Zvolen, Slovak Republic
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Maciej K Konopiński
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | | | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | - Margarida Lopes-Fernandes
- Centre for Research in Anthropology, Lisbon, Portugal
- Institute for Nature Conservation and Forests, Lisbon, Portugal
| | - Barry John McMahon
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
- Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
| | - Charalambos Neophytou
- Institute of Silviculture, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Forest Nature Conservation, Forest Research Institute Baden-Württemberg, Freiburg, Germany
| | - Snæbjörn Pálsson
- Department of Biology, University of Iceland, Reykjavik, Iceland
| | - Ivan Paz-Vinas
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Diana Posledovich
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | - Craig R Primmer
- Faculty of Biological & Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Barbora Rolečková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Dainis Ruņģis
- Genetic Resource Centre, Latvian State Forest Research Institute 'Silava', Salaspils, Latvia
| | - Laura Schuerz
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | | | - Milomir Stefanovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Henrik Thurfjell
- Swedish Species Information Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sabrina Träger
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Ivaylo N Tsvetkov
- Department of Forest Genetics, Physiology and Plantations, Forest Research Institute, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Nevena Velickovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Philippine Vergeer
- Plant Ecology and Nature Conservation Group, Wageningen University, Wageningen, the Netherlands
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Carles Vilà
- Doñana Biological Station (EBD-CSIC), Seville, Spain
| | | | - Frank E Zachos
- Natural History Museum Vienna, Vienna, Austria
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Antoine Guisan
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, Lausanne, Switzerland
| | - Michael Bruford
- School of Biosciences, Cardiff University, Cardiff, UK
- Department of Biochemistry, Genetics and Molecular Biology, University of Pretoria, Pretoria, South Africa
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Lopes AM, Almeida T, Diz S, Côrte-Real JV, Osório HC, Ramilo DW, Rebelo MT, da Fonseca IP, Esteves PJ, Alves PC, Santos N, Abrantes J. The potential role of scavenging flies as mechanical vectors of Lagovirus europaeus/GI.2. Virol J 2023; 20:103. [PMID: 37237382 DOI: 10.1186/s12985-023-02065-4] [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: 12/22/2022] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
The European rabbit (Oryctolagus cuniculus) populations of the Iberian Peninsula have been severely affected by the emergence of the rabbit haemorrhagic disease virus (RHDV) Lagovirus europaeus/GI.2 (RHDV2/b). Bushflies and blowflies (Muscidae and Calliphoridae families, respectively) are important RHDV vectors in Oceania, but their epidemiological role is unknown in the native range of the European rabbit. In this study, scavenging flies were collected between June 2018 and February 2019 in baited traps at one site in southern Portugal, alongside a longitudinal capture-mark-recapture study of a wild European rabbit population, aiming to provide evidence of mechanical transmission of GI.2 by flies. Fly abundance, particularly from Calliphoridae and Muscidae families, peaked in October 2018 and in February 2019. By employing molecular tools, we were able to detect the presence of GI.2 in flies belonging to the families Calliphoridae, Muscidae, Fanniidae and Drosophilidae. The positive samples were detected during an RHD outbreak and absent in samples collected when no evidence of viral circulation in the local rabbit population was found. We were able to sequence a short viral genomic fragment, confirming its identity as RHDV GI.2. The results suggest that scavenging flies may act as mechanical vectors of GI.2 in the native range of the southwestern Iberian subspecies O. cuniculus algirus. Future studies should better assess their potential in the epidemiology of RHD and as a tool for monitoring viral circulation in the field.
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Affiliation(s)
- Ana M Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Unidade Multidisciplinar de Investigação Biomédica (UMIB), Universidade do Porto, Porto, 4050-313, Portugal
| | - Tereza Almeida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Sílvia Diz
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - João V Côrte-Real
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany
| | - Hugo C Osório
- Centro de Estudos de Vectores e Doenças Infecciosas, Instituto Nacional de Saúde Doutor Ricardo Jorge, Marateca, Portugal
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - David W Ramilo
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-s-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Faculdade de Medicina Veterinária, Universidade Lusófona, Lisbon, Portugal
| | - Maria Teresa Rebelo
- CESAM - Centre for Environmental and Marine Studies, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Isabel Pereira da Fonseca
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-s-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
- CITS - Center of Investigation in Health Technologies, CESPU, 4585-116, Gandra, Portugal
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal
| | - Nuno Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal.
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Ferreira MS, Thurman TJ, Jones MR, Farelo L, Kumar AV, Mortimer SME, Demboski JR, Mills LS, Alves PC, Melo-Ferreira J, Good JM. The evolution of white-tailed jackrabbit camouflage in response to past and future seasonal climates. Science 2023; 379:1238-1242. [PMID: 36952420 DOI: 10.1126/science.ade3984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The genetic basis of adaptive traits has rarely been used to predict future vulnerability of populations to climate change. We show that light versus dark seasonal pelage in white-tailed jackrabbits (Lepus townsendii) tracks snow cover and is primarily determined by genetic variation at endothelin receptor type B (EDNRB), corin serine peptidase (CORIN), and agouti signaling protein (ASIP). Winter color variation was associated with deeply divergent alleles at these genes, reflecting selection on both ancestral and introgressed variation. Forecasted reductions in snow cover are likely to induce widespread camouflage mismatch. However, simulated populations with variation for darker winter pelage are predicted to adapt rapidly, providing a trait-based genetic framework to facilitate evolutionary rescue. These discoveries demonstrate how the genetic basis of climate change adaptation can inform conservation.
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Affiliation(s)
- Mafalda S Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Timothy J Thurman
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Alexander V Kumar
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
- US Fish and Wildlife Service, Fort Collins, CO, USA
| | | | - John R Demboski
- Zoology Department, Denver Museum of Nature & Science, Denver, CO, USA
| | - L Scott Mills
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
- Office of Research and Creative Scholarship, University of Montana, Missoula, MT, USA
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
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Carpio AJ, Queirós J, Laguna E, Jiménez-Ruiz S, Vicente J, Alves PC, Acevedo P. Understanding the impact of wild boar on the European wild rabbit and red-legged partridge populations using a diet metabarcoding approach. EUR J WILDLIFE RES 2023. [DOI: 10.1007/s10344-023-01647-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
AbstractEuropean wild rabbit (Oryctolagus cuniculus) and red-legged partridge (Alectoris rufa) are main small game species of conservation concern in Mediterranean ecosystems. To date, their presence in wild boar’s (Sus scrofa) diet and factors driving their consumption have been little investigated. A genetic metabarcoding approach was used on 80 wild boar faeces collected from four hunting estates devoted to small game hunting during two different seasons. Abundances of wild boar, rabbits and partridges were first estimated. Results showed DNA of seventeen chordate species. The highest frequency of occurrence (FO) corresponded to mammals and birds, with 77.6 and 22.3%, respectively. DNA of game species was detected in 39/71 (FO = 55.0%) samples, highlighting the presence of European wild rabbit in 27 (FO = 38.0%) and red-legged partridge in eight (FO = 11.3%). Dietary composition varied between seasons and estates, being rabbit the main responsible (explaining 35.26% and 39.45% of differences, respectively). Rabbit FO in the diet was positively related to the abundance of wild boar and rabbit density on the estate. It was greater in autumn and in estates where rabbits were hunted. Regarding red-legged partridge, a significant and positive relationship between its population density and its diet FO was observed, without significant differences between seasons or estates. Overall, our results suggest wild boar as an opportunistic species whose diet is largely determined by the relative availability of different food resources. Its ecological role concerning small game species in Mediterranean agroecosystems seems to be more related to consumption of carrion during the hunting season than to direct predation.
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Moraga-Fernández A, Sánchez-Sánchez M, Queirós J, Lopes AM, Vicente J, Pardavila X, Sereno-Cadierno J, Alves PC, de la Fuente J, Fernández de Mera IG. A study of viral pathogens in bat species in the Iberian Peninsula: identification of new coronavirus genetic variants. Int J Vet Sci Med 2022; 10:100-110. [PMID: 36407496 PMCID: PMC9639555 DOI: 10.1080/23144599.2022.2139985] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bats have long been associated with multiple pathogens, including viruses affecting humans such as henipaviruses, filoviruses, bunyaviruses and coronaviruses. The alpha and beta coronaviruses genera can infect most mammalian species. Among them, betacoronavirus SARS-CoV, MERS-CoV and SARS-CoV-2, which have caused the three major pandemics in the last two decades, have been proposed to originate in bats. In this study, 194 oral swabs from 22 bats species sampled in 19 locations of the Iberian Peninsula were analysed and characterized by three different PCR tests (coronavirus generic real-time RT-PCR, multiplex conventional PCR, and SARS-CoV-2 specific real-time RT-PCR) to detect bat coronaviruses. Screening with coronavirus generic PCR showed 102 positives out of 194 oral swabs analysed. Then, metabarcoding with multiplex PCR amplified 15 positive samples. Most of the coronaviruses detected in this study belong to alphacoronavirus (α-CoV) genus, with multiple alphacoronaviruses identified by up to five different genetic variants coexisting in the same bat. One of the positive samples identified in a Miniopterus schreibersii bat positive for the generic coronavirus PCR and the specific SARS-CoV-2 PCR was classified as betacoronavirus (-CoV) through phylogenetic analysis. These results support the rapid evolution of coronaviruses to generate new genomic potentially pathogenic variants likely through co-infection and recombination.
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Affiliation(s)
- Alberto Moraga-Fernández
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
| | - Marta Sánchez-Sánchez
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
| | - João Queirós
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Estação Biológica de Mértola (EBM), CIBIO, Praça Luís de Camões, Mértola, Portugal
| | - Ana M. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Joaquín Vicente
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
| | - Xosé Pardavila
- Sorex, Ecoloxía e Medio Ambiente S.L., Santiago de Compostela. A Coruña, Spain
| | - Jorge Sereno-Cadierno
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Estação Biológica de Mértola (EBM), CIBIO, Praça Luís de Camões, Mértola, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - José de la Fuente
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
- Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
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6
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Nilson SM, Gandolfi B, Grahn RA, Kurushima JD, Lipinski MJ, Randi E, Waly NE, Driscoll C, Murua Escobar H, Schuster RK, Maruyama S, Labarthe N, Chomel BB, Ghosh SK, Ozpinar H, Rah HC, Millán J, Mendes-de-Almeida F, Levy JK, Heitz E, Scherk MA, Alves PC, Decker JE, Lyons LA. Genetics of randomly bred cats support the cradle of cat domestication being in the Near East. Heredity (Edinb) 2022; 129:346-355. [PMID: 36319737 PMCID: PMC9708682 DOI: 10.1038/s41437-022-00568-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/04/2022] Open
Abstract
Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats' predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor's (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.
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Affiliation(s)
- Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Monika J Lipinski
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Øst, Denmark
| | - Nashwa E Waly
- Department of Animal Medicine, Faculty of Veterinary Medicine, Assuit University, 71526, Assiut, Egypt
| | | | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, 18055, Rostock, Germany
| | - Rolf K Schuster
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Soichi Maruyama
- Laboratory of Veterinary Public Health, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Norma Labarthe
- Programa de Bioética, Ética Aplicada e Saúde Coletiva, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Bruno B Chomel
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | | | - Haydar Ozpinar
- Graduate School of Health Sciences, Istanbul Gedik University, 34876, İstanbul, Turkey
| | - Hyung-Chul Rah
- Research Institute of Veterinary Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, South Korea
| | - Javier Millán
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Miguel Servet 177, 50013, Zaragoza, Spain
- Fundación ARAID, Avda. de Ranillas, 50018, Zaragoza, Spain
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Flavya Mendes-de-Almeida
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Julie K Levy
- Maddie's Shelter Medicine Program, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32608, USA
| | | | | | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Associate Lab & Faculdade de Ciências, Universidade do Porto, Campus e Vairão, 4485-661, Vila do Conde, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.
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7
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González-Barrio D, Diezma-Diaz C, Queirós J, Alves PC, Velarde R, Estruch J, Vieira-Pinto M, Álvarez-García G. Absence of anti-Besnoitia spp. specific antibodies in European wild lagomorphs from the Iberian Peninsula. Transbound Emerg Dis 2022; 69:e3447-e3454. [PMID: 36215394 DOI: 10.1111/tbed.14730] [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] [Received: 06/08/2022] [Revised: 09/20/2022] [Accepted: 10/05/2022] [Indexed: 02/04/2023]
Abstract
Besnoitia besnoiti is an apicomplexan parasite whose life cycle is not completely understood. It is assumed that this parasite might have an indirect life cycle with a carnivore as a definitive host able to shed oocysts after the ingestion of mature cysts in tissues of an infected intermediate host. Cattle and wild cervids on the Iberian Peninsula can act as intermediate hosts of B. besnoiti, and exposure to the parasite has been demonstrated in equids. In this study, we aimed to assess the presence of members of the genera Besnoitia in wild lagomorphs from the Iberian Peninsula and the potential role of these host species in the life cycle of B. besnoiti, as all the animals were sampled from 19 regions of the Iberian Peninsula where cases of bovine besnoitiosis have been previously detected. Serum samples (Oryctolagus cuniculus: n = 552; Lepus europaeus: n = 122) were first analysed by ELISA and subsequently confirmed by Western blot (WB). Specific antibodies against B. besnoiti were not found in any sampled animal by WB. In addition, lung samples from a subset of wild rabbits (n = 16) were tested by PCR and Besnoitia spp. DNA was not detected. These results suggest that Besnoitia spp. are unlikely to circulate in wild lagomorphs in the Iberian Peninsula. Thus, lagomorphs are not expected to play a key role in the biological cycle of B. besnoiti. Further studies are necessary to assess whether different micromammal species, such as rodents, can serve as natural reservoirs of Besnoitia spp. in other European regions.
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Affiliation(s)
- David González-Barrio
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, Madrid, Spain.,Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, Madrid, Spain
| | - Carlos Diezma-Diaz
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, Madrid, Spain
| | - Joao Queirós
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.,EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, Portugal.,Universidade do Porto, R. Monte-Crasto, Vairão, Portugal, Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.,EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, Portugal.,Universidade do Porto, R. Monte-Crasto, Vairão, Portugal, Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
| | - Roser Velarde
- Wildlife Ecology & Health Group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animal, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Josep Estruch
- Wildlife Ecology & Health Group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animal, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Madalena Vieira-Pinto
- Centro de Ciência Animal e Veterinária (CECAV), Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal.,Departamento de Ciências Veterinárias, Escola de Ciências Agrárias e Veterinárias, UTAD, Vila Real, Portugal
| | - Gema Álvarez-García
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, Madrid, Spain
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8
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Giska I, Pimenta J, Farelo L, Boursot P, Hackländer K, Jenny H, Reid N, Montgomery WI, Prodöhl PA, Alves PC, Melo-Ferreira J. The evolutionary pathways for local adaptation in mountain hares. Mol Ecol 2022; 31:1487-1503. [PMID: 34995383 PMCID: PMC9303332 DOI: 10.1111/mec.16338] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022]
Abstract
Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole‐genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome‐wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area‐specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP, a gene previously implicated in introgression‐driven winter coat colour variation in mountain and snowshoe hares (L. americanus), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares’ adaptive variants appear predominantly species‐specific. However, using coalescent simulations, we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our study shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post‐glacial dynamics of species.
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Affiliation(s)
- Iwona Giska
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - João Pimenta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pierre Boursot
- Institut des Sciences de l'Évolution Montpellier (ISEM), Université Montpellier, CNRS, IRD, Montpellier, France
| | - Klaus Hackländer
- Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Sciences, Vienna, Austria.,Deutsche Wildtier Stiftung (German Wildlife Foundation), Hamburg, Germany
| | - Hannes Jenny
- Department of Wildlife and Fishery Service Grison, Chur, Switzerland
| | - Neil Reid
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - W Ian Montgomery
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Paulo A Prodöhl
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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9
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Martins FMS, Feio MJ, Porto M, Filipe AF, Bonin A, Serra SRQ, Alves PC, Taberlet P, Beja P. Assessing changes in stream macroinvertebrate communities across ecological gradients using morphological versus DNA metabarcoding approaches. Sci Total Environ 2021; 797:149030. [PMID: 34311381 DOI: 10.1016/j.scitotenv.2021.149030] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that despite differences in the number and identity of taxa recorded, both approaches may retrieve comparable patterns of community change, and detect similar ecological gradients influencing such changes. We compared results obtained with morphological identification at family level of macroinvertebrates collected at 80 streams under a Water Framework Directive biomonitoring program in Portugal, with results obtained with metabarcoding from the ethanol preserving the bulk samples, using either single (COI-M19BR2, 16S-Inse01, 18S-Euka02) or multiple markers. Metabarcoding recorded less families and different communities compared to morphotaxonomy, but community sensitivities to disturbance estimated with the IASPT index were more similar across approaches. Spatial variation in local community metrics and the factors influencing such variation were significantly correlated between morphotaxonomy and metabarcoding. After reducing random noise in the dissimilarity matrices, the spatial variation in community composition was also significantly correlated across methods. A dominant gradient of community change was consistently retrieved, and all methods identified a largely similar set of anthropogenic stressors strongly influencing such gradient. Overall, results confirm our initial hypothesis, suggesting that morphotaxonomy and metabarcoding can estimate consistent spatial patterns of community variation and their main drivers. These results are encouraging for macroinvertebrate biomonitoring using metabarcoding approaches, suggesting that they can be intercalibrated with morphotaxonomic approaches to recover equivalent spatial and temporal gradients of ecological change.
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Affiliation(s)
- Filipa M S Martins
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal.
| | - Maria J Feio
- Universidade de Coimbra, MARE, Centro de Ciências do Mar e do Ambiente, Departamento de Ciência da Vida, Coimbra, Portugal
| | - Miguel Porto
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Ana F Filipe
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Aurélie Bonin
- Université Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Grenoble, France
| | - Sónia R Q Serra
- Universidade de Coimbra, MARE, Centro de Ciências do Mar e do Ambiente, Departamento de Ciência da Vida, Coimbra, Portugal
| | - Paulo C Alves
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal
| | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Grenoble, France; UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Pedro Beja
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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10
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Cardoso B, García-Bocanegra I, Acevedo P, Cáceres G, Alves PC, Gortázar C. Stepping up from wildlife disease surveillance to integrated wildlife monitoring in Europe. Res Vet Sci 2021; 144:149-156. [PMID: 34815105 DOI: 10.1016/j.rvsc.2021.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/12/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022]
Abstract
In a context of disease emergence and faced with the ever-growing evidence of the role of wildlife in the epidemiology of transmissible diseases, efforts have been made to develop wildlife disease surveillance (WDS) programs throughout Europe. Disease monitoring is ideally composed of "numerator data" (number of infected individuals) and "denominator data" (size of the target population). Too often however, information is available for only one. Hence, there is a need for developing integrated and harmonized disease and population monitoring tools for wildlife: integrated wildlife monitoring (IWM). IWM should have three components. Passive disease surveillance improves the likelihood of early detection of emerging diseases, while active surveillance and population monitoring are required to assess epidemiological dynamics, freedom of disease, and the outcome of interventions. Here, we review the characteristics of ongoing WDS in Europe, observe how pathogens have been ranked, and note a need for ranking host species, too. Then, we list the challenges for WDS and draw a roadmap for stepping up from WDS to IWM. There is a need to integrate and maintain an equilibrium between the three components of IWM, improve data collection and accessibility, and guarantee the adaptability of these schemes to each epidemiological context and temporal period. Methodological harmonization and centralization of information at a European level would increase efficiency of national programs and improve the follow-up of eventual interventions. The ideal IWM would integrate capacities from different stakeholder; allow to rapidly incorporate relevant new knowledge; and rely on stable capacities and funding.
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Affiliation(s)
- Beatriz Cardoso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; IREC, Instituto de Investigación en Recursos Cinegéticos, UCLM-CSIC-JCCM, Ronda Toledo 12, 13071 Ciudad Real, Spain; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
| | - Ignacio García-Bocanegra
- GISAZ, Grupo de Investigación en Sanidad Animal y Zoonosis, Departamento de Sanidad Animal, Universidad de Córdoba, 14014 Córdoba, Spain
| | - Pelayo Acevedo
- IREC, Instituto de Investigación en Recursos Cinegéticos, UCLM-CSIC-JCCM, Ronda Toledo 12, 13071 Ciudad Real, Spain
| | - Germán Cáceres
- Departamento de Epidemiologia, Ministerio de Agricultura, Pesca y Alimentación, 28014 Madrid, Spain
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Christian Gortázar
- IREC, Instituto de Investigación en Recursos Cinegéticos, UCLM-CSIC-JCCM, Ronda Toledo 12, 13071 Ciudad Real, Spain
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11
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Ferreira MS, Jones MR, Callahan CM, Farelo L, Tolesa Z, Suchentrunk F, Boursot P, Mills LS, Alves PC, Good JM, Melo-Ferreira J. The Legacy of Recurrent Introgression during the Radiation of Hares. Syst Biol 2021; 70:593-607. [PMID: 33263746 PMCID: PMC8048390 DOI: 10.1093/sysbio/syaa088] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 06/28/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 12/30/2022] Open
Abstract
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1-4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation. [Adaptation; ancient introgression; hybridization; Lepus; phylogenomics.].
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Affiliation(s)
- Mafalda S Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Zelalem Tolesa
- Department of Biology, Hawassa University, Hawassa, Ethiopia
| | - Franz Suchentrunk
- Department for Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Pierre Boursot
- Institut des Sciences de l’Évolution Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, France
| | - L Scott Mills
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
- Office of Research and Creative Scholarship, University of Montana, Missoula, Montana, United States of America; Jeffrey M. Good and José Melo-Ferreira shared the senior authorship
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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12
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Schai-Braun SC, Lapin K, Bernhardt KG, Alves PC, Hackländer K. Effect of landscape type, elevation, vegetation period, and taxonomic plant identification level on diet preferences of Alpine mountain hares (Lepus timidus varronis). EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-01398-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Marques JP, Seixas FA, Farelo L, Callahan CM, Good JM, Montgomery WI, Reid N, Alves PC, Boursot P, Melo-Ferreira J. An Annotated Draft Genome of the Mountain Hare (Lepus timidus). Genome Biol Evol 2020; 12:3656-3662. [PMID: 31834364 PMCID: PMC6951464 DOI: 10.1093/gbe/evz273] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2019] [Indexed: 12/25/2022] Open
Abstract
Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated 24,578 protein coding genes by combining ab-initio predictions, homology search, and transcriptome data, of which 683 were solely derived from hare-specific transcriptome data. The hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Similar estimates of heterozygosity and inferred demographic history profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. Our results validate previous reference-based strategies and suggest that the chromosome-scale hare draft genome should enable chromosome-wide analyses and genome scans on hares.
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Affiliation(s)
- João P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências do Porto, Portugal.,Institut des Sciences de l'Evolution Montpellier (ISEM), Univ Montpellier, CNRS, IRD, EPHE, France
| | - Fernando A Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências do Porto, Portugal.,Institut des Sciences de l'Evolution Montpellier (ISEM), Univ Montpellier, CNRS, IRD, EPHE, France
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | | | - Jeffrey M Good
- Division of Biological Sciences, University of Montana.,Wildlife Biology Program, University of Montana
| | - W Ian Montgomery
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, United Kingdom
| | - Neil Reid
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, United Kingdom
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências do Porto, Portugal.,Wildlife Biology Program, University of Montana
| | - Pierre Boursot
- Institut des Sciences de l'Evolution Montpellier (ISEM), Univ Montpellier, CNRS, IRD, EPHE, France
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências do Porto, Portugal
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14
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Monterroso P, Díaz-Ruiz F, Lukacs PM, Alves PC, Ferreras P. Ecological traits and the spatial structure of competitive coexistence among carnivores. Ecology 2020; 101:e03059. [PMID: 32333382 DOI: 10.1002/ecy.3059] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 02/06/2020] [Accepted: 02/25/2020] [Indexed: 11/06/2022]
Abstract
Competition is a widespread interaction among carnivores, ultimately manifested through one or more dimensions of the species' ecological niche. One of the most explicit manifestations of competitive interactions regards spatial displacement. Its interpretation under a theoretical context provides an important tool to deepen our understanding of biological systems and communities, but also for wildlife management and conservation. We used Bayesian multispecies occupancy models on camera-trapping data from multiple sites in Southwestern Europe (SWE) to investigate competitive interactions within a carnivore guild, and to evaluate how species' ecological traits are shaping coexistence patterns. Seventeen out of 26 pairwise interactions departed from a hypothesis of independent occurrence, with spatial association being twice as frequent as avoidance. Association behaviors were only detected among mesocarnivores, while avoidance mainly involved mesocarnivores avoiding the apex predator (n = 4) and mesocarnivore-only interactions (n = 2). Body mass ratios, defined as the dominant over the subordinate species body mass, revealed an important negative effect ( β ^ = - 0.38 ; C I 95 = - 0.81 t o - 0.06 ) on co-occurrence probability, and support that spatially explicit competitive interactions are mostly expressed by larger species able to dominate over smaller ones, with a threshold in body mass ratios of ~4, above which local-scale intraguild coexistence is unlikely. We found a weak relationship between pairwise trophic niche overlap and the probability of coexistence ( β ^ = - 0.19 ; C I 95 = - 0.58 t o 0.21 ), suggesting that competition for feeding resources may not be a key driver of competition, at least at the scale of our analysis. Despite local-scale avoidance, regional-scale coexistence appears to be maintained by the spatial structuring of the competitive environment. We provide evidence that SWE ecosystems consist of spatially structured competitive environments, and propose that coexistence among near-sized species is likely achieved through the interplay of "facultative" and "behavioral" character displacements. Factors influencing carnivore coexistence likely include context-dependent density and trait-mediated effects, which should be carefully considered for a sound understanding of the mechanisms regulating these communities.
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Affiliation(s)
- Pedro Monterroso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quinta 7, Vairão, 3385-661, Portugal
| | - Francisco Díaz-Ruiz
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo 12, Ciudad Real, 12071, Spain.,Departamento de Biología Animal, Facultad de Ciencias, Universidad de Málaga, Avda. Cervantes 2, Málaga, 29071, Spain
| | - Paul M Lukacs
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, W.A. Franke College of Forestry and Conservation, University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA
| | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quinta 7, Vairão, 3385-661, Portugal.,Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, W.A. Franke College of Forestry and Conservation, University of Montana, 32 Campus Drive, Missoula, Montana, 59812, USA.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Edificio FC4, Porto, 4169-007, Portugal
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo 12, Ciudad Real, 12071, Spain
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15
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Cogné B, Latypova X, Senaratne LDS, Martin L, Koboldt DC, Kellaris G, Fievet L, Le Meur G, Caldari D, Debray D, Nizon M, Frengen E, Bowne SJ, Cadena EL, Daiger SP, Bujakowska KM, Pierce EA, Gorin M, Katsanis N, Bézieau S, Petersen-Jones SM, Occelli LM, Lyons LA, Legeai-Mallet L, Sullivan LS, Davis EE, Isidor B, Buckley RM, Aberdein D, Alves PC, Barsh GS, Bellone RR, Bergström TF, Boyko AR, Brockman JA, Casal ML, Castelhano MG, Distl O, Dodman NH, Ellinwood NM, Fogle JE, Forman OP, Garrick DJ, Ginns EI, Häggström J, Harvey RJ, Hasegawa D, Haase B, Helps CR, Hernandez I, Hytönen MK, Kaukonen M, Kaelin CB, Kosho T, Leclerc E, Lear TL, Leeb T, Li RH, Lohi H, Longeri M, Magnuson MA, Malik R, Mane SP, Munday JS, Murphy WJ, Pedersen NC, Rothschild MF, Rusbridge C, Shapiro B, Stern JA, Swanson WF, Terio KA, Todhunter RJ, Warren WC, Wilcox EA, Wildschutte JH, Yu Y. Mutations in the Kinesin-2 Motor KIF3B Cause an Autosomal-Dominant Ciliopathy. Am J Hum Genet 2020; 106:893-904. [PMID: 32386558 DOI: 10.1016/j.ajhg.2020.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/02/2020] [Indexed: 11/26/2022] Open
Abstract
Kinesin-2 enables ciliary assembly and maintenance as an anterograde intraflagellar transport (IFT) motor. Molecular motor activity is driven by a heterotrimeric complex comprised of KIF3A and KIF3B or KIF3C plus one non-motor subunit, KIFAP3. Using exome sequencing, we identified heterozygous KIF3B variants in two unrelated families with hallmark ciliopathy phenotypes. In the first family, the proband presents with hepatic fibrosis, retinitis pigmentosa, and postaxial polydactyly; he harbors a de novo c.748G>C (p.Glu250Gln) variant affecting the kinesin motor domain encoded by KIF3B. The second family is a six-generation pedigree affected predominantly by retinitis pigmentosa. Affected individuals carry a heterozygous c.1568T>C (p.Leu523Pro) KIF3B variant segregating in an autosomal-dominant pattern. We observed a significant increase in primary cilia length in vitro in the context of either of the two mutations while variant KIF3B proteins retained stability indistinguishable from wild type. Furthermore, we tested the effects of KIF3B mutant mRNA expression in the developing zebrafish retina. In the presence of either missense variant, rhodopsin was sequestered to the photoreceptor rod inner segment layer with a concomitant increase in photoreceptor cilia length. Notably, impaired rhodopsin trafficking is also characteristic of recessive KIF3B models as exemplified by an early-onset, autosomal-recessive, progressive retinal degeneration in Bengal cats; we identified a c.1000G>A (p.Ala334Thr) KIF3B variant by genome-wide association study and whole-genome sequencing. Together, our genetic, cell-based, and in vivo modeling data delineate an autosomal-dominant syndromic retinal ciliopathy in humans and suggest that multiple KIF3B pathomechanisms can impair kinesin-driven ciliary transport in the photoreceptor.
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16
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von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020. [PMID: 31925943 DOI: 10.1111/1755-0998.13136.applying] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
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Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
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17
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Ferreira MS, Alves PC, Callahan CM, Giska I, Farelo L, Jenny H, Mills LS, Hackländer K, Good JM, Melo‐Ferreira J. Transcriptomic regulation of seasonal coat color change in hares. Ecol Evol 2020; 10:1180-1192. [PMID: 32076506 PMCID: PMC7029059 DOI: 10.1002/ece3.5956] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 12/27/2022] Open
Abstract
Color molts from summer brown to winter white coats have evolved in several species to maintain camouflage year-round in environments with seasonal snow. Despite the eco-evolutionary relevance of this key phenological adaptation, its molecular regulation has only recently begun to be addressed. Here, we analyze skin transcription changes during the autumn molt of the mountain hare (Lepus timidus) and integrate the results with an established model of gene regulation across the spring molt of the closely related snowshoe hare (L. americanus). We quantified differences in gene expression among three stages of molt progression-"brown" (early molt), "intermediate," and "white" (late molt). We found 632 differentially expressed genes, with a major pulse of expression early in the molt, followed by a milder one in late molt. The functional makeup of differentially expressed genes anchored the sampled molt stages to the developmental timeline of the hair growth cycle, associating anagen to early molt and the transition to catagen to late molt. The progression of color change was characterized by differential expression of genes involved in pigmentation, circadian, and behavioral regulation. We found significant overlap between differentially expressed genes across the seasonal molts of mountain and snowshoe hares, particularly at molt onset, suggesting conservatism of gene regulation across species and seasons. However, some discrepancies suggest seasonal differences in melanocyte differentiation and the integration of nutritional cues. Our established regulatory model of seasonal coat color molt provides an important mechanistic context to study the functional architecture and evolution of this crucial seasonal adaptation.
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Affiliation(s)
- Mafalda S. Ferreira
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
| | - Paulo C. Alves
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
- Wildlife Biology ProgramUniversity of MontanaMissoulaMTUSA
| | | | - Iwona Giska
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
| | - Liliana Farelo
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
| | - Hannes Jenny
- Amt für Jagd und Fischerei GraubündenChurSwitzerland
| | - L. Scott Mills
- Wildlife Biology ProgramUniversity of MontanaMissoulaMTUSA
- Office of Research and Creative ScholarshipUniversity of MontanaMissoulaMTUSA
| | - Klaus Hackländer
- Institute of Wildlife Biology and Game ManagementBOKU—University of Natural Resources and Life SciencesViennaAustria
| | - Jeffrey M. Good
- Wildlife Biology ProgramUniversity of MontanaMissoulaMTUSA
- Division of Biological SciencesUniversity of MontanaMissoulaMTUSA
| | - José Melo‐Ferreira
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
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18
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von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020; 20. [PMID: 31925943 DOI: 10.1111/1755-0998.13136] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 09/05/2018] [Revised: 12/24/2019] [Accepted: 01/05/2020] [Indexed: 01/16/2023]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
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Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
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19
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Tiesmeyer A, Ramos L, Manuel Lucas J, Steyer K, Alves PC, Astaras C, Brix M, Cragnolini M, Domokos C, Hegyeli Z, Janssen R, Kitchener AC, Lambinet C, Mestdagh X, Migli D, Monterroso P, Mulder JL, Schockert V, Youlatos D, Pfenninger M, Nowak C. Range-wide patterns of human-mediated hybridisation in European wildcats. CONSERV GENET 2020. [DOI: 10.1007/s10592-019-01247-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
AbstractHybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat (Felis silvestris) has been shown to hybridise with domestic cats (Felis catus). Previously suggested spatially divergent introgression levels have not been confirmed on a European scale due to significant differences in the applied methods to assess hybridisation of the European wildcat. We analysed 926 Felis spp. samples from 13 European countries, using a set of 86 selected ancestry-informative SNPs, 14 microsatellites, and ten mitochondrial and Y-chromosome markers to study regional hybridisation and introgression patterns and population differentiation. We detected 51 hybrids (four F1 and 47 F2 or backcrosses) and 521 pure wildcats throughout Europe. The abundance of hybrids varied considerably among studied populations. All samples from Scotland were identified as F2 hybrids or backcrosses, supporting previous findings that the genetic integrity of that wildcat population has been seriously compromised. In other European populations, low to moderate levels of hybridisation were found, with the lowest levels being in Central and Southeast Europe. The occurrence of distinct maternal and paternal markers between wildcat and domestic cat suggests that there were no severe hybridisation episodes in the past. The overall low (< 1%) prevalence of F1 hybrids suggests a low risk of hybridisation for the long-term genetic integrity of the wildcat in most of Europe. However, regionally elevated introgression rates confirm that hybridisation poses a potential threat. We propose regional in-depth monitoring of hybridisation rates to identify factors driving hybridisation so as to develop effective strategies for conservation.
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20
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Fletcher NK, Acevedo P, Herman JS, Paupério J, Alves PC, Searle JB. Glacial cycles drive rapid divergence of cryptic field vole species. Ecol Evol 2019; 9:14101-14113. [PMID: 31938506 PMCID: PMC6953675 DOI: 10.1002/ece3.5846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 11/07/2022] Open
Abstract
Understanding the factors that contribute to the generation of reproductively isolated forms is a fundamental goal of evolutionary biology. Cryptic species are an especially interesting challenge to study in this context since they lack obvious morphological differentiation that provides clues to adaptive divergence that may drive reproductive isolation. Geographical isolation in refugial areas during glacial cycling is known to be important for generating genetically divergent populations, but its role in the origination of new species is still not fully understood and likely to be situation dependent. We combine analysis of 35,434 single-nucleotide polymorphisms (SNPs) with environmental niche modeling (ENM) to investigate genomic and ecological divergence in three cryptic species formerly classified as the field vole (Microtus agrestis). The SNPs demonstrate high genomic divergence (pairwise F ST values of 0.45-0.72) and little evidence of gene flow among the three field vole cryptic species, and we argue that genetic drift may have been a particularly important mechanism for divergence in the group. The ENM reveals three areas as potential glacial refugia for the cryptic species and differing climatic niches, although with spatial overlap between species pairs. This evidence underscores the role that glacial cycling has in promoting genetic differentiation and reproductive isolation by subdivision into disjunct distributions at glacial maxima in areas relatively close to ice sheets. Future investigation of the intrinsic barriers to gene flow between the field vole cryptic species is required to fully assess the mechanisms that contribute to reproductive isolation. In addition, the Portuguese field vole (M. rozianus) shows a high inbreeding coefficient and a restricted climatic niche, and warrants investigation into its conservation status.
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Affiliation(s)
| | - Pelayo Acevedo
- Instituto de Investigación en Recursos Cinegéticos, IREC (UCLM‐CSIC‐JCCM)Ciudad RealSpain
| | - Jeremy S. Herman
- Department of Natural SciencesNational Museums ScotlandEdinburghUK
| | - Joana Paupério
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto, Campus de VairãoVairãoPortugal
| | - Paulo C. Alves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto, Campus de VairãoVairãoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoPortoPortugal
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto, Campus de VairãoVairãoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoPortoPortugal
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21
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Martins FMS, Galhardo M, Filipe AF, Teixeira A, Pinheiro P, Paupério J, Alves PC, Beja P. Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring. Mol Ecol Resour 2019; 19:863-876. [PMID: 30901128 PMCID: PMC6850371 DOI: 10.1111/1755-0998.13012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 01/07/2023]
Abstract
DNA metabarcoding can contribute to improving cost-effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time-consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column-based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic-based enzymatic protocol (BEAD), and a 313-bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7-14 than 1-7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoring.
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Affiliation(s)
- Filipa M. S. Martins
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Mafalda Galhardo
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Ana F. Filipe
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Amílcar Teixeira
- CIMO‐ESA‐IPB, Centro de Investigação de MontanhaInstituto Politécnico de BragançaBragançaPortugal
| | | | - Joana Paupério
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Paulo C. Alves
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- Wildlife Biology ProgramUniversity of MontanaMissoulaMontana
| | - Pedro Beja
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
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22
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Schai-Braun SC, Posautz A, Alves PC, Hackländer K. Gastrointestinal parasite infestation in the alpine mountain hare ( Lepus timidus varronis): Are abiotic environmental factors such as elevation, temperature and precipitation affecting prevalence of parasite species? Int J Parasitol Parasites Wildl 2019; 9:202-208. [PMID: 31193935 PMCID: PMC6545328 DOI: 10.1016/j.ijppaw.2019.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 01/23/2023]
Abstract
Information concerning factors regulating Alpine mountain hare (Lepus timidus varronis) populations such as host-parasite interactions is missing as only a few parasitological surveys exist of this subspecies. Parasites are not only dependent on their host but also on suitable environmental conditions for infestation. Abiotic environmental factors have an important regulating role on parasites in mammals. It is estimated that the elevation range of parasites is likely to shift in response to alternate host movement and changes in climate. Here we assess the parasitic infestation in the Alpine mountain hare by analysing the parasites in faeces and comparing the parasite infestation at different elevation ranges and at varied weather conditions for two years in the Austrian Alps. Almost half of the faecal samples were free of parasites (46.2%, n = 52). Most frequent was the infection by Coccidia (46.2%), whereas stomach intestine strongylids, Trichuris spp, and Cestoda were only found in 9.6% of all faeces. Hence, only Coccidia may be prevalent enough to regulate Alpine mountain hare populations in the Austrian Alps. Elevation had a significant positive effect on the infection of animals by Trichuris spp, whereas temperature had a significant negative effect on the infection by any parasite traceable in faeces and, when looking at the parasite groups individually, on Coccidia. Almost half of the Alpine mountain hare faecal samples were free of parasites. Coccidia was more frequent in our hare faeces than in other examined populations. Stomach intestine strongylids and Cestoda were only found in 9.6% of our samples. Only Coccidia may be prevalent enough to regulate this hare population. Temperature had a significant negative effect on the incidence of any parasite in the faecal samples.
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Affiliation(s)
- Stéphanie C Schai-Braun
- Institute of Wildlife Biology and Game Management, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria
| | - Annika Posautz
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Vienna, Austria
| | - Paulo C Alves
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Klaus Hackländer
- Institute of Wildlife Biology and Game Management, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria
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23
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Queirós J, Acevedo P, Santos JPV, Barasona J, Beltran-Beck B, González-Barrio D, Armenteros JA, Diez-Delgado I, Boadella M, Fernandéz de Mera I, Ruiz-Fons JF, Vicente J, de la Fuente J, Gortázar C, Searle JB, Alves PC. Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonization history. PLoS One 2019; 14:e0210282. [PMID: 30620758 PMCID: PMC6324796 DOI: 10.1371/journal.pone.0210282] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 08/10/2018] [Accepted: 12/19/2018] [Indexed: 01/31/2023] Open
Abstract
The red deer (Cervus elaphus) is a widespread wild ungulate in Europe that has suffered strong anthropogenic impacts over their distribution during the last centuries, but also at the present time, due its economic importance as a game species. Here we focus on the evolutionary history of the red deer in Iberia, one of the three main southern refugial areas for temperate species in Europe, and addressed the hypothesis of a cryptic refugia at higher latitudes during the Last Glacial Maximum (LGM). A total of 911 individuals were sampled, genotyped for 34 microsatellites specifically developed for red deer and sequenced for a fragment of 670 bp of the mitochondrial (mtDNA) D-loop. The results were combined with published mtDNA sequences, and integrated with species distribution models and historical European paleo-distribution data, in order to further examine the alternative glacial refugial models and the influence of cryptic refugia on European postglacial colonization history. Clear genetic differentiation between Iberian and European contemporary populations was observed at nuclear and mtDNA levels, despite the mtDNA haplotypes central to the phylogenetic network are present across western Europe (including Iberia) suggesting a panmictic population in the past. Species distribution models, fossil records and genetic data support a timing of divergence between Iberian and European populations that overlap with the LGM. A notable population structure was also found within the Iberian Peninsula, although several populations displayed high levels of admixture as a consequence of recent red deer translocations. Five D-loop sub-lineages were found in Iberia that belong to the Western European mtDNA lineage, while there were four main clusters based on analysis of nuclear markers. Regarding glacial refugial models, our findings provide detailed support for the hypothesis that red deer may have persisted in cryptic northern refugia in western Europe during the LGM, most likely in southern France, southern Ireland, or in a region between them (continental shelf), and these regions were the source of individuals during the European re-colonization. This evidence heightens the importance of conserving the high mitochondrial and nuclear diversity currently observed in Iberian populations.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- * E-mail:
| | - Pelayo Acevedo
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - João P. V. Santos
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Departamento de Biologia & CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Jose Barasona
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Beatriz Beltran-Beck
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - David González-Barrio
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose A. Armenteros
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Iratxe Diez-Delgado
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Mariana Boadella
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- SABIOtec. Ed. Polivalente UCLM, Ciudad Real, Spain
| | - Isabel Fernandéz de Mera
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose F. Ruiz-Fons
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Joaquin Vicente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States of America
| | - Christian Gortázar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jeremy B. Searle
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Paulo C. Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, United States of America
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24
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Monterroso P, Godinho R, Oliveira T, Ferreras P, Kelly MJ, Morin DJ, Waits LP, Alves PC, Mills LS. Feeding ecological knowledge: the underutilised power of faecal
DNA
approaches for carnivore diet analysis. Mamm Rev 2018. [DOI: 10.1111/mam.12144] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pedro Monterroso
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
| | - Raquel Godinho
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Teresa Oliveira
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM) Ronda de Toledo 12 Ciudad Real 13071 Spain
| | - Marcella J. Kelly
- Department of Fish and Wildlife ConservationVirginia Tech 146 Cheatham Hall Blacksburg VA 24061‐0321 USA
| | - Dana J. Morin
- Cooperative Wildlife Research LaboratorySouthern Illinois University 251 Lincoln Drive Carbondale IL 62901 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS 1136 Moscow ID 83844‐1136 USA
| | - Paulo C. Alves
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
| | - L. Scott Mills
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
- Office of Research and Creative ScholarshipUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
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25
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Queirós J, Villar M, Hernández-Jarguín A, López V, Fernández de Mera I, Vicente J, Alves PC, Gortazar C, Fuente JDL. A metaproteomics approach reveals changes in mandibular lymph node microbiota of wild boar naturally exposed to an increasing trend of Mycobacterium tuberculosis complex infection. Tuberculosis (Edinb) 2018; 114:103-112. [PMID: 30711148 DOI: 10.1016/j.tube.2018.12.003] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/14/2018] [Accepted: 12/16/2018] [Indexed: 12/19/2022]
Abstract
Constraints in the characterization of microbiota community that circulates in the host have limited the extent of co-infection studies in natural populations. In this study, we used a metaproteomics approach to characterize the mandibular lymph nodes microbiota of wild boar (Sus scrofa) naturally exposed to an increasing trend of Mycobacterium tuberculosis complex (MTC) infection. Our results showed a reduction in microbiota diversity and changes in the composition, structure and functionality of the microbiota community associated with an increase in tuberculosis prevalence, from 45% in 2002/06 to 83% in 2009/12. These temporal changes were accompanied by an increase in the relative abundance of Babesia, Theileria and Pestivirus genera and a decrease in the Ascogregarina and Chlorella. A positive association was also evidenced between the prevalence of tuberculosis and the presence of microbial proteins responsible for carbohydrate transport and metabolism. Our findings suggest MTC-host-microbiota interactions at the population level, which may occur in order to ensure sufficient metabolic resources for MTC survival, growth and transmission. We strongly recommend the use of metaproteomics when studying microbiota communities in wildlife populations, for which traditional diagnostic techniques are limited and in which new organisms with a pathogenic potential for domestic animals and humans may appear.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus de Vairão, R. Monte-Crasto, 4485-661, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s⁄n, 4169-007, Porto, Portugal; SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Margarita Villar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Angélica Hernández-Jarguín
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Vladimir López
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Isabel Fernández de Mera
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Joaquín Vicente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Paulo C Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus de Vairão, R. Monte-Crasto, 4485-661, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s⁄n, 4169-007, Porto, Portugal; Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA.
| | - Christian Gortazar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain; Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
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26
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Barbosa S, Mestre F, White TA, Paupério J, Alves PC, Searle JB. Integrative approaches to guide conservation decisions: Using genomics to define conservation units and functional corridors. Mol Ecol 2018; 27:3452-3465. [PMID: 30030869 DOI: 10.1111/mec.14806] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [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: 03/27/2017] [Revised: 07/01/2018] [Accepted: 07/05/2018] [Indexed: 01/13/2023]
Abstract
Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary change for long-term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of evolutionary factors. Existing genetic diversity needs to be thoroughly evaluated and spatially mapped to define conservation units (CUs) in an evolutionary context, and we address that here. We also propose a multidisciplinary approach to determine corridors and functional connectivity between CUs by including genetic diversity in the modelling while controlling for isolation by distance and phylogeographic history. We evaluate our approach on a Near Threatened Iberian endemic rodent by analysing genotyping-by-sequencing (GBS) genomic data from 107 Cabrera voles (Microtus cabrerae), screening the entire species distribution to define categories of CUs and their connectivity: We defined six management units (MUs) which can be grouped into four evolutionarily significant units (ESUs) and three (putatively) adaptive units (AUs). We demonstrate that the three different categories of CU can be objectively defined using genomic data, and their characteristics and connectivity can inform conservation decision-making. In particular, we show that connectivity of the Cabrera vole is very limited in eastern Iberia and that the pre-Pyrenean and part of the Betic geographic nuclei contribute the most to the species genetic diversity. We argue that a multidisciplinary framework for CU definition is essential and that this framework needs a strong evolutionary basis.
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Affiliation(s)
- Soraia Barbosa
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Frederico Mestre
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade de Évora/InBIO Laboratório Associado, Évora, Portugal
| | - Thomas A White
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Joana Paupério
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal
| | - Paulo C Alves
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Jeremy B Searle
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
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27
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Mills LS, Bragina EV, Kumar AV, Zimova M, Lafferty DJR, Feltner J, Davis BM, Hackländer K, Alves PC, Good JM, Melo-Ferreira J, Dietz A, Abramov AV, Lopatina N, Fay K. Winter color polymorphisms identify global hot spots for evolutionary rescue from climate change. Science 2018; 359:1033-1036. [DOI: 10.1126/science.aan8097] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 01/02/2018] [Indexed: 12/13/2022]
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28
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Rafati N, Blanco-Aguiar JA, Rubin CJ, Sayyab S, Sabatino SJ, Afonso S, Feng C, Alves PC, Villafuerte R, Ferrand N, Andersson L, Carneiro M. A genomic map of clinal variation across the European rabbit hybrid zone. Mol Ecol 2018; 27:1457-1478. [PMID: 29359877 DOI: 10.1111/mec.14494] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 10/03/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 01/02/2023]
Abstract
Speciation is a process proceeding from weak to complete reproductive isolation. In this continuum, naturally hybridizing taxa provide a promising avenue for revealing the genetic changes associated with the incipient stages of speciation. To identify such changes between two subspecies of rabbits that display partial reproductive isolation, we studied patterns of allele frequency change across their hybrid zone using whole-genome sequencing. To connect levels and patterns of genetic differentiation with phenotypic manifestations of subfertility in hybrid rabbits, we further investigated patterns of gene expression in testis. Geographic cline analysis revealed 253 regions characterized by steep changes in allele frequency across their natural region of contact. This catalog of regions is likely to be enriched for loci implicated in reproductive barriers and yielded several insights into the evolution of hybrid dysfunction in rabbits: (i) incomplete reproductive isolation is likely governed by the effects of many loci, (ii) protein-protein interaction analysis suggest that genes within these loci interact more than expected by chance, (iii) regulatory variation is likely the primary driver of incompatibilities, and (iv) large chromosomal rearrangements appear not to be a major mechanism underlying incompatibilities or promoting isolation in the face of gene flow. We detected extensive misregulation of gene expression in testis of hybrid males, but not a statistical overrepresentation of differentially expressed genes in candidate regions. Our results also did not support an X chromosome-wide disruption of expression as observed in mice and cats, suggesting variation in the mechanistic basis of hybrid male reduced fertility among mammals.
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Affiliation(s)
- Nima Rafati
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - José A Blanco-Aguiar
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Instituto de Investigacion en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Carl J Rubin
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shumaila Sayyab
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Stephen J Sabatino
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Chungang Feng
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | | | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland, South Africa
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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29
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Marques JP, Ferreira MS, Farelo L, Callahan CM, Hackländer K, Jenny H, Montgomery WI, Reid N, Good JM, Alves PC, Melo-Ferreira J. Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares. Sci Data 2017; 4:170178. [PMID: 29206218 PMCID: PMC5716010 DOI: 10.1038/sdata.2017.178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 10/13/2017] [Indexed: 11/14/2022] Open
Abstract
We report the first mountain hare (Lepus timidus) transcriptome, produced by de novo assembly of RNA-sequencing reads. Data were obtained from eight specimens sampled in two localities, Alps and Ireland. The mountain hare tends to be replaced by the invading European hare (Lepus europaeus) in their numerous contact zones where the species hybridize, which affects their gene pool to a yet unquantified degree. We characterize and annotate the mountain hare transcriptome, detect polymorphism in the two analysed populations and use previously published data on the European hare (three specimens, representing the European lineage of the species) to identify 4 672 putative diagnostic sites between the species. A subset of 85 random independent SNPs was successfully validated using PCR and Sanger sequencing. These valuable genomic resources can be used to design tools to assess population status and monitor hybridization between species.
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Affiliation(s)
- João P. Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências do Porto, Porto 4169-007, Portugal
| | - Mafalda S. Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências do Porto, Porto 4169-007, Portugal
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
| | - Colin M. Callahan
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Klaus Hackländer
- Institute of Wildlife Biology and Game Management, BOKU-University of Natural Resources and Life Sciences, Vienna 1180, Austria
| | - Hannes Jenny
- Amt für Jagd und Fischerei Graubünden, Chur 7001, Switzerland
| | - W. Ian Montgomery
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5BN, UK
- School of Biological Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Neil Reid
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5BN, UK
- School of Biological Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências do Porto, Porto 4169-007, Portugal
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências do Porto, Porto 4169-007, Portugal
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30
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Lopes AM, Silvério D, Magalhães MJ, Areal H, Alves PC, Esteves PJ, Abrantes J. Characterization of old RHDV strains by complete genome sequencing identifies a novel genetic group. Sci Rep 2017; 7:13599. [PMID: 29051566 PMCID: PMC5648873 DOI: 10.1038/s41598-017-13902-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 10/13/2016] [Accepted: 04/04/2017] [Indexed: 11/11/2022] Open
Abstract
Rabbit hemorrhagic disease (RHD) is a veterinary disease that affects the European rabbit and has a significant economic and ecological negative impact. In Portugal, rabbit hemorrhagic disease virus (RHDV) was reported in 1989 and still causes enzootic outbreaks. Several recombination events have been detected in RHDV strains, including in the first reported outbreak. Here we describe the occurrence of recombination in RHDV strains recovered from rabbit and Iberian hare samples collected in the mid-1990s in Portugal. Characterization of full genomic sequences revealed the existence of a single recombination breakpoint at the boundary of the non-structural and the structural encoding regions, further supporting the importance of this region as a recombination hotspot in lagoviruses. Phylogenetic analysis showed that in the structural region, the recombinant strains were similar to pathogenic G1 strains, but in the non-structural region they formed a new group that diverged ~13% from known strains. No further reports of such group exist, but this recombination event was also detected in an Iberian hare that was associated with the earliest species jump in RHDV. Our results highlight the importance of the characterization of full genomes to disclose RHDV evolution and show that lagoviruses’ diversity has been significantly undersampled.
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Affiliation(s)
- Ana M Lopes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Diogo Silvério
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Maria J Magalhães
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Helena Areal
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Paulo C Alves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, 59812, Montana, USA
| | - Pedro J Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
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31
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Ferreira MS, Alves PC, Callahan CM, Marques JP, Mills LS, Good JM, Melo‐Ferreira J. The transcriptional landscape of seasonal coat colour moult in the snowshoe hare. Mol Ecol 2017; 26:4173-4185. [DOI: 10.1111/mec.14177] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 05/03/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Mafalda S. Ferreira
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
| | - Paulo C. Alves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
- Wildlife Biology Program University of Montana Missoula MT USA
| | - Colin M. Callahan
- Division of Biological Sciences University of Montana Missoula MT USA
| | - João P. Marques
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
| | - L. Scott Mills
- Wildlife Biology Program University of Montana Missoula MT USA
- Department of Forestry and Environmental Resources Fisheries, Wildlife and Conservation Biology Program North Carolina State University Raleigh NC USA
| | - Jeffrey M. Good
- Division of Biological Sciences University of Montana Missoula MT USA
| | - José Melo‐Ferreira
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
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32
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Affiliation(s)
- Carl-Gustaf Thulin
- Department of Wildlife, Fish, and Environmental Studies; Swedish University of Agricultural Sciences; Umeå 901 83 Sweden
| | - Paulo C. Alves
- CIBIO-InBIO; Faculdade de Ciências da Universidade do Porto; Campus de Vairão Vairão 4485-661 Portugal
| | - Mihajla Djan
- Department of Biology and Ecology, Faculty of Sciences; University of Novi Sad; Novi Sad 21000 Serbia
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences; University of Bologna; Bologna 40127 Italy
| | - David Peacock
- Biosecurity SA; GPO Box 1671 Adelaide 5001 Australia
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33
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Lopes AM, Magalhães MJ, Alves PC, Esteves PJ, Abrantes J. An update on the rabbit hemorrhagic disease virus (RHDV) strains circulating in Portugal in the 1990s: earliest detection of G3-G5 and G6. Arch Virol 2017; 162:2061-2065. [PMID: 28299483 DOI: 10.1007/s00705-017-3318-0] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/22/2017] [Indexed: 01/23/2023]
Abstract
Rabbit hemorrhagic disease virus (RHDV) causes devastating effects on European rabbit (Oryctolagus cuniculus) populations in the Iberian Peninsula. According to the information available, only genogroup 1 strains were circulating in Iberian wild rabbits until 2011; the antigenic variant G6 has been sporadically detected in rabbitries since 2007. Here, we show for the first time that G3-G5 strains were already present in mainland Portugal in 1998 and that G6 has been circulating since at least 1999. Moreover, we report a G3-G5 strain from the Azores collected in 1998, which is the likely ancestor of Azorean G3-G5like strains. These observations improve the current knowledge on RHDV epidemiology in the Iberian Peninsula and the Azores.
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Affiliation(s)
- Ana M Lopes
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
| | - Maria J Magalhães
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Paulo C Alves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Pedro J Esteves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Joana Abrantes
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
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34
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Monterroso P, Garrote G, Serronha A, Santos E, Delibes-Mateos M, Abrantes J, Perez de Ayala R, Silvestre F, Carvalho J, Vasco I, Lopes AM, Maio E, Magalhães MJ, Mills LS, Esteves PJ, Simón MÁ, Alves PC. Disease-mediated bottom-up regulation: An emergent virus affects a keystone prey, and alters the dynamics of trophic webs. Sci Rep 2016; 6:36072. [PMID: 27796353 PMCID: PMC5086860 DOI: 10.1038/srep36072] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/10/2016] [Indexed: 11/19/2022] Open
Abstract
Emergent diseases may alter the structure and functioning of ecosystems by creating new biotic interactions and modifying existing ones, producing cascading processes along trophic webs. Recently, a new variant of the rabbit haemorrhagic disease virus (RHDV2 or RHDVb) arguably caused widespread declines in a keystone prey in Mediterranean ecosystems - the European rabbit (Oryctolagus cuniculus). We quantitatively assess the impact of RHDV2 on natural rabbit populations and in two endangered apex predator populations: the Iberian lynx (Lynx pardinus) and the Spanish Imperial eagle (Aquila adalberti). We found 60–70% declines in rabbit populations, followed by decreases of 65.7% in Iberian lynx and 45.5% in Spanish Imperial eagle fecundities. A revision of the web of trophic interactions among rabbits and their dependent predators suggests that RHDV2 acts as a keystone species, and may steer Mediterranean ecosystems to management-dependent alternative states, dominated by simplified mesopredator communities. This model system stresses the importance of diseases as functional players in the dynamics of trophic webs.
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Affiliation(s)
- Pedro Monterroso
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Germán Garrote
- Agencia de Medio Ambiente y Agua de Andalucía, C/Johan G. Gutenberg. 1, 41092, Seville, Spain
| | - Ana Serronha
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Emídio Santos
- Instituto da Conservação da Natureza e das Florestas, Av. da República, 161050-191, Lisbon, Portugal
| | - Miguel Delibes-Mateos
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,IESA-CSIC, Instituto de Estudios Sociales Avanzados, Plz Campo Santo de los Mártires. 7, 14004 Córdoba, Spain
| | - Joana Abrantes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | | | - Fernando Silvestre
- Fundación CBD-Habitat, C/ Gustavo Fernández Balbuena 2, Entreplanta, Oficina A, 28002, Madrid, Spain
| | - João Carvalho
- ANPC, Associação Nacional Proprietários Rurais, Gestão Cinegética e Biodiversidade, R. Mestre Lima de Freitas, 1-5°, 1549-012, Lisbon, Portugal
| | - Inês Vasco
- Instituto da Conservação da Natureza e das Florestas, Av. da República, 161050-191, Lisbon, Portugal
| | - Ana M Lopes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Elisa Maio
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Maria J Magalhães
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - L Scott Mills
- Wildlife Biology Program, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Pedro J Esteves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Miguel Ángel Simón
- Consejería de Medio Ambiente de la Junta de Andalucía, C/ Doctor Eduardo García-Triviño López 15, 23071 Jaén, Spain
| | - Paulo C Alves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
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35
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Queirós J, Vicente J, Alves PC, de la Fuente J, Gortazar C. Tuberculosis, genetic diversity and fitness in the red deer, Cervus elaphus. Infect Genet Evol 2016; 43:203-12. [PMID: 27245150 DOI: 10.1016/j.meegid.2016.05.031] [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] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 05/20/2016] [Accepted: 05/22/2016] [Indexed: 12/16/2022]
Abstract
Understanding how genetic diversity, infections and fitness interact in wild populations is a major challenge in ecology and management. These interactions were addressed through heterozygosity-fitness correlation analyses, by assessing the genetic diversity, tuberculosis (TB) and body size in adult red deer. Heterozygosity-fitness correlation models provided a better understanding of the link between genetic diversity and TB at individual and population levels. A single local effect was found for Ceh45 locus at individual level, enhancing the importance of its close functional genes in determining TB presence. At population level, the ability of the red deer to control TB progression correlated positively with population genetic diversity, indicating that inbred populations might represent more risk of deer TB severity. Statistical models also gained insights into the dynamics of multi-host interaction in natural environments. TB prevalence in neighbouring wild boar populations was positively associated with deer TB at both individual and population levels. Additionally, TB presence correlated positively with red deer body size, for which "general and local effect" hypotheses were found. Although body size might be correlated with age, an indirect genetic effect on TB presence could be implied. This study provides new insights towards understanding host-pathogen interactions in wild populations and their relation to fitness traits.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, R. Monte-Crasto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s⁄n, 4169-007 Porto, Portugal; SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain.
| | - Joaquín Vicente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
| | - Paulo C Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, R. Monte-Crasto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s⁄n, 4169-007 Porto, Portugal; Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA
| | - José de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain; Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Christian Gortazar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
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36
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Monterroso P, Rebelo P, Alves PC, Ferreras P. Niche partitioning at the edge of the range: a multidimensional analysis with sympatric martens. J Mammal 2016. [DOI: 10.1093/jmammal/gyw016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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Fontanesi L, Di Palma F, Flicek P, Smith AT, Thulin CG, Alves PC. LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order. J Hered 2016; 107:295-308. [PMID: 26921276 DOI: 10.1093/jhered/esw010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 09/20/2015] [Accepted: 02/02/2016] [Indexed: 01/07/2023] Open
Abstract
The order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important economically and scientifically as major human food resources, valued game species, pests of agricultural significance, model laboratory animals, and key elements in food webs. A quarter of the lagomorph species are listed as threatened. They are native to all continents except Antarctica, and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range of environmental conditions. The order has notable taxonomic problems presenting significant difficulties for defining a species due to broad phenotypic variation, overlap of morphological characteristics, and relatively recent speciation events. At present, only the genomes of 2 species, the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been sequenced and assembled. Starting from a paucity of genome information, the main scientific aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of the European COST Action "A Collaborative European Network on Rabbit Genome Biology-RGB-Net" and the World Lagomorph Society (WLS), is to provide an international framework for the sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration.
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Affiliation(s)
- Luca Fontanesi
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves).
| | - Federica Di Palma
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves)
| | - Paul Flicek
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves)
| | - Andrew T Smith
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves)
| | - Carl-Gustaf Thulin
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves)
| | - Paulo C Alves
- From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves).
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Gargan LM, Cornette R, Yearsley JM, Montgomery WI, Paupério J, Alves PC, Butler F, Pascal M, Tresset A, Herrel A, Lusby J, Tosh DG, Searle JB, McDevitt AD. Molecular and morphological insights into the origin of the invasive greater white-toothed shrew (Crocidura russula) in Ireland. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1056-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Mattucci F, Oliveira R, Lyons LA, Alves PC, Randi E. European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation? Ecol Evol 2015; 6:3-22. [PMID: 26811770 PMCID: PMC4716505 DOI: 10.1002/ece3.1815] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [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: 09/23/2015] [Revised: 10/14/2015] [Accepted: 10/14/2015] [Indexed: 02/03/2023] Open
Abstract
Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over‐hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random‐bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well‐differentiated clusters (average ФST = 0.159, rst = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild‐living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average ФST = 0.103, rst = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north‐eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene–early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free‐ranging domestic cats along corridor edges should be carefully monitored.
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Affiliation(s)
- Federica Mattucci
- Laboratorio di Genetica Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) 40064 Ozzano dell'Emilia Bologna Italy
| | - Rita Oliveira
- InBio - Laboratório Associado Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO) Universidade do Porto Campus de Vairão 4485-661 Vairão Portugal; Departamento de Biologia Faculdade de Ciências da Universidade do Porto 4099-002 Porto Portugal
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery College of Veterinary Medicine University of Missouri-Columbia Columbia 65211 Missouri USA
| | - Paulo C Alves
- InBio - Laboratório Associado Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO) Universidade do Porto Campus de Vairão 4485-661 Vairão Portugal; Departamento de Biologia Faculdade de Ciências da Universidade do Porto 4099-002 Porto Portugal; Wildlife Biology Program Department of Ecosystem and Conservation Sciences University of Montana Missoula 59812 Montana USA
| | - Ettore Randi
- Laboratorio di Genetica Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) 40064 Ozzano dell'Emilia BolognaItaly; Department 18/Section of Environmental Engineering Aalborg University 9000 Aalborg Denmark
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40
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Oliveira R, Randi E, Mattucci F, Kurushima JD, Lyons LA, Alves PC. Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris). Heredity (Edinb) 2015; 115:195-205. [PMID: 26103945 DOI: 10.1038/hdy.2015.25] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 12/13/2014] [Accepted: 02/03/2015] [Indexed: 01/16/2023] Open
Abstract
Endemic gene pools have been severely endangered by human-mediated hybridization, which is posing new challenges in the conservation of several vertebrate species. The endangered European wildcat is an example of this problem, as several natural populations are suffering introgression of genes from the domestic cat. The implementation of molecular methods for detecting hybridization is crucial for supporting appropriate conservation programs on the wildcat. In this study, genetic variation at 158 single-nucleotide polymorphisms (SNPs) was analyzed in 139 domestic cats, 130 putative European wildcats and 5 captive-bred hybrids (N=274). These SNPs were variable both in wild (HE=0.107) and domestic cats (HE=0.340). Although we did not find any SNP that was private in any population, 22 SNPs were monomorphic in wildcats and pairwise FCT values revealed marked differences between domestic and wildcats, with the most divergent 35 loci providing an average FCT>0.74. The power of all the loci to accurately identify admixture events and discriminate the different hybrid categories was evaluated. Results from simulated and real genotypes show that the 158 SNPs provide successful estimates of admixture, with 100% hybrid individuals (two to three generations in the past) being correctly identified in STRUCTURE and over 92% using the NEWHYBRIDS' algorithm. None of the unclassified cats were wrongly allocated to another hybrid class. Thirty-five SNPs, showing the highest FCT values, provided the most parsimonious panel for robust inferences of parental and first generations of admixed ancestries. This approach may be used to further reconstruct the evolution of wildcat populations and, hopefully, to develop sound conservation guidelines for its legal protection in Europe.
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Affiliation(s)
- R Oliveira
- 1] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO-Laboratório Associado, Vairão, Portugal [2] Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - E Randi
- 1] Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, Italy [2] Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - F Mattucci
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, Italy
| | - J D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - L A Lyons
- 1] Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA [2] Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, MI, USA
| | - P C Alves
- 1] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO-Laboratório Associado, Vairão, Portugal [2] Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal [3] Wildlife Biology Program, University of Montana, Missoula, MT, USA
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Ferreira CC, Castro F, Piorno V, Barrio IC, Delibes-Mateos M, Rouco C, Mínguez LE, Aparicio F, Blanco-Aguiar JA, Ramírez E, Iriarte C, Ríos-Saldaña CA, Cañadilla J, Arias de Reyna L, Ferreras P, Alves PC, Villafuerte R. Biometrical analysis reveals major differences between the two subspecies of the European rabbit. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12556] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Catarina Campos Ferreira
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
- InBio Laboratório Associado; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Department of Biology; Trent University; Peterborough ON K9J 7B8 Canada
| | - Francisca Castro
- Instituto de Estudios Sociales Avanzados (IESA-CSIC); Campo Santo de los Mártires 14004 Córdoba Spain
- Dpto. Zoología; Universidad de Córdoba; Campus de Rabanales 14071 Córdoba Spain
| | - Vicente Piorno
- Parque Nacional de las Islas Atlánticas de Galicia; Calle Oliva, 3 36202 Vigo Spain
| | - Isabel Catalán Barrio
- Department of Biological Sciences; University of Alberta; Biological Sciences Building CW-405 Edmonton AB T6G2E9 Canada
- Pyrenean Institute of Ecology (CSIC); Avda. Nuestra Señora de la Victoria 22700 Jaca Spain
| | - Miguel Delibes-Mateos
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
- InBio Laboratório Associado; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Instituto de Estudios Sociales Avanzados (IESA-CSIC); Campo Santo de los Mártires 14004 Córdoba Spain
| | - Carlos Rouco
- Landcare Research; PO Box 1930 9054 Dunedin New Zealand
| | - Luis E. Mínguez
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Fernando Aparicio
- Instituto de Estudios Sociales Avanzados (IESA-CSIC); Campo Santo de los Mártires 14004 Córdoba Spain
- Dpto. Zoología; Universidad de Córdoba; Campus de Rabanales 14071 Córdoba Spain
| | - José A. Blanco-Aguiar
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
- InBio Laboratório Associado; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Esther Ramírez
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Candelaria Iriarte
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Carlos A. Ríos-Saldaña
- BioCórima A. C.; Blvd. Dr. Jesús Valdés Sánchez km 10 Col. Presa de las Casas Arteaga Coahuila 25350 México
| | - Jesús Cañadilla
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Luis Arias de Reyna
- Dpto. Zoología; Universidad de Córdoba; Campus de Rabanales 14071 Córdoba Spain
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM); Ronda de Toledo, s/n 13071 Ciudad Real Spain
| | - Paulo C. Alves
- InBio Laboratório Associado; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre, s/n Edifício FC4 4169-007 Porto Portugal
- Wildlife Biology Program; College of Forestry and Conservation; University of Montana; Missoula MT USA
| | - Rafael Villafuerte
- Instituto de Estudios Sociales Avanzados (IESA-CSIC); Campo Santo de los Mártires 14004 Córdoba Spain
- Dpto. Zoología; Universidad de Córdoba; Campus de Rabanales 14071 Córdoba Spain
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Carneiro M, Piorno V, Rubin CJ, Alves JM, Ferrand N, Alves PC, Andersson L. Candidate genes underlying heritable differences in reproductive seasonality between wild and domestic rabbits. Anim Genet 2015; 46:418-25. [PMID: 25999142 DOI: 10.1111/age.12299] [Citation(s) in RCA: 13] [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] [Accepted: 03/21/2015] [Indexed: 01/03/2023]
Abstract
Reproductive seasonality is a trait that often differs between domestic animals and their wild ancestors, with domestic animals showing prolonged or even continuous breeding seasons. However, the genetic basis underlying this trait is still poorly understood for most species, and because environmental factors and resource availability are known to play an important role in determining breeding seasons, it is also not clear in most cases to what extent this phenotypic shift is determined by the more lenient captive conditions or by genetic factors. Here, using animals resulting from an initial cross between wild and domestic rabbits followed by two consecutive backcrosses (BC1 and BC2) to wild rabbits, we evaluated the yearly distribution of births for the different generations. Similar to domestic rabbits, F1 animals could be bred all year round but BC1 and BC2 animals showed a progressive and significant reduction in the span of the breeding season, providing experimental evidence that reduced seasonal breeding in domestic rabbits has a clear genetic component and is not a simple by-product of rearing conditions. We then took advantage of a recently published genome-wide scan of selection in the domesticated lineage and searched for candidate genes potentially associated with this phenotypic shift. Candidate genes located within regions targeted by selection include well-known examples of genes controlling clock functions (CRY1 and NR3C1) and reproduction (PRLR).
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Affiliation(s)
- Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Vicente Piorno
- Parque Nacional de las Islas Atlánticas de Galicia, Calle Oliva 3, 36202, Vigo, Spain
| | - Carl-Johan Rubin
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Joel M Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Department of Genetics, University of Cambridge, CB2 3EH, Cambridge, UK
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s⁄n, 4169-007, Porto, Portugal
| | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s⁄n, 4169-007, Porto, Portugal
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, USA
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43
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Pinheiro A, Woof JM, Almeida T, Abrantes J, Alves PC, Gortázar C, Esteves PJ. Leporid immunoglobulin G shows evidence of strong selective pressure on the hinge and CH3 domains. Open Biol 2015; 4:140088. [PMID: 25185680 PMCID: PMC4185434 DOI: 10.1098/rsob.140088] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Immunoglobulin G (IgG) is the predominant serum immunoglobulin and has the longest serum half-life of all the antibody classes. The European rabbit IgG has been of significant importance in immunological research, and is therefore well characterized. However, the IgG of other leporids has been disregarded. To evaluate the evolution of this gene in leporids, we sequenced the complete IGHG for six other genera: Bunolagus, Brachylagus, Lepus, Pentalagus, Romerolagus and Sylvilagus. The newly sequenced leporid IGHG gene has an organization and structure similar to that of the European rabbit IgG. A gradient in leporid IgG constant domain diversity was observed, with the CH1 being the most conserved and the CH3 the most variable domain. Positive selection was found to be acting on all constant domains, but with a greater incidence in the CH3 domain, where a cluster of three positively selected sites was identified. In the hinge region, only three polymorphic positions were observed. The same hinge length was observed for all leporids. Unlike the variation observed for the European rabbit, all 11 Lepus species studied share exactly the same hinge motif, suggesting its maintenance as a result of an advantageous structure or conformation.
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Affiliation(s)
- Ana Pinheiro
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal SaBio IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real 13071, Spain
| | - Jenny M Woof
- Division of Cancer Research, Medical Research Institute, University of Dundee Medical School, Ninewells Hospital, Dundee DD1 9SY, UK
| | - Tereza Almeida
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Joana Abrantes
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Paulo C Alves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA
| | - Christian Gortázar
- SaBio IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real 13071, Spain
| | - Pedro J Esteves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
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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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Grahn RA, Alhaddad H, Alves PC, Randi E, Waly NE, Lyons LA. Feline mitochondrial DNA sampling for forensic analysis: when enough is enough! Forensic Sci Int Genet 2014; 16:52-57. [PMID: 25531059 DOI: 10.1016/j.fsigen.2014.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 05/21/2014] [Revised: 10/28/2014] [Accepted: 11/22/2014] [Indexed: 10/24/2022]
Abstract
Pet hair has a demonstrated value in resolving legal issues. Cat hair is chronically shed and it is difficult to leave a home with cats without some level of secondary transfer. The power of cat hair as an evidentiary resource may be underused because representative genetic databases are not available for exclusionary purposes. Mitochondrial control region databases are highly valuable for hair analyses and have been developed for the cat. In a representative worldwide data set, 83% of domestic cat mitotypes belong to one of twelve major types. Of the remaining 17%, 7.5% are unique within the published 1394 sample database. The current research evaluates the sample size necessary to establish a representative population for forensic comparison of the mitochondrial control region for the domestic cat. For most worldwide populations, randomly sampling 50 unrelated local individuals will achieve saturation at 95%. The 99% saturation is achieved by randomly sampling 60-170 cats, depending on the numbers of mitotypes available in the population at large. Likely due to the recent domestication of the cat and minimal localized population substructure, fewer cats are needed to meet mitochondria DNA control region database practical saturation than for humans or dogs. Coupled with the available worldwide feline control region database of nearly 1400 cats, minimal local sampling will be required to establish an appropriate comparative representative database and achieve significant exclusionary power.
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Affiliation(s)
- Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616, USA.
| | - Hasan Alhaddad
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616, USA
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos and Departamento de Biologia da Faculdade de Ciências do Porto, Universidade do Porto, Portugal
| | - Ettore Randi
- Laboratorio di Genetica, ISPRA, Istituto Superiore per la Protezione e la Ricerca Ambientale, Via Cà Fornacetta 9, 40064 Ozzano dell'Emilia, BO, Italy; Department 18/Section of Environmental Engineering, Aalborg University, Sohngårdsholmsvej 57, 9000 Aalborg, Denmark
| | - Nashwa E Waly
- Department of Animal Medicine, Faculty of Veterinary Medicine, Assiut University, 71526 Assiut, Egypt
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616, USA
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Queirós J, Godinho R, Lopes S, Gortazar C, de la Fuente J, Alves PC. Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications. Mol Ecol Resour 2014; 15:747-60. [PMID: 25403329 DOI: 10.1111/1755-0998.12349] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [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: 11/29/2013] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 11/27/2022]
Abstract
Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.
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Affiliation(s)
- J Queirós
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - R Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - S Lopes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - C Gortazar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - J de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - P C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
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Melo-Ferreira J, Seixas FA, Cheng E, Mills LS, Alves PC. The hidden history of the snowshoe hare,Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation. Mol Ecol 2014; 23:4617-30. [DOI: 10.1111/mec.12886] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 01/09/2023]
Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Fernando A. Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; 4099-002 Porto Portugal
| | - Ellen Cheng
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
- Ugyen Wangchuck Institute for Conservation and Environment; Lamai Goempa Bumthang Bhutan
| | - L. Scott Mills
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
- Fisheries, Wildlife and Conservation Biology Program; North Carolina State University; Raleigh NC 27695-7617 USA
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO - Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento Biologia; Faculdade de Ciências da Universidade do Porto; 4099-002 Porto Portugal
- Wildlife Biology; University of Montana; 32 Campus Drive Missoula MT 59812 USA
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48
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Cheng E, Hodges KE, Melo-Ferreira J, Alves PC, Mills LS. Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare. Mol Ecol 2014; 23:2929-42. [PMID: 24814937 DOI: 10.1111/mec.12790] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 05/23/2013] [Revised: 05/05/2014] [Accepted: 05/05/2014] [Indexed: 11/27/2022]
Abstract
With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of the microsatellite data suggests initial subdivision in two groups, Boreal and southwestern. The southwestern group further splits into Greater Pacific Northwest and U.S. Rockies. The genealogical information retrieved from mtDNA is congruent with the three highly differentiated and divergent groups of snowshoe hares. These groups can correspond with evolutionarily significant units that might have evolved in separate refugia south and east of the Pleistocene ice sheets. Genetic diversity was highest at mid-latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mtDNA and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mtDNA lineage were more closely related to black-tailed jackrabbits (Lepus californicus) than to other snowshoe hares, which may result from secondary introgression or shared ancestral polymorphism. Given the genetic distinctiveness of southern populations and minimal gene flow with their northern neighbours, fragmentation and loss of southern boreal habitats could mean loss of many unique alleles and reduced evolutionary potential.
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Affiliation(s)
- Ellen Cheng
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
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Abrantes J, Lopes AM, Dalton KP, Melo P, Correia JJ, Ramada M, Alves PC, Parra F, Esteves PJ. New variant of rabbit hemorrhagic disease virus, Portugal, 2012-2013. Emerg Infect Dis 2014; 19:1900-2. [PMID: 24206671 PMCID: PMC3837648 DOI: 10.3201/eid1911.130908] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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50
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Cheng E, Hodges KE, Melo-Ferreira J, Alves PC, Mills LS. Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare. Mol Ecol 2014; 23:2929-2942. [PMID: 24814937 DOI: 10.1111/med.12790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 05/05/2014] [Accepted: 05/05/2014] [Indexed: 05/26/2023]
Abstract
With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of the microsatellite data suggests initial subdivision in two groups, Boreal and southwestern. The southwestern group further splits into Greater Pacific Northwest and U.S. Rockies. The genealogical information retrieved from mtDNA is congruent with the three highly differentiated and divergent groups of snowshoe hares. These groups can correspond with evolutionarily significant units that might have evolved in separate refugia south and east of the Pleistocene ice sheets. Genetic diversity was highest at mid-latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mtDNA and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mtDNA lineage were more closely related to black-tailed jackrabbits (Lepus californicus) than to other snowshoe hares, which may result from secondary introgression or shared ancestral polymorphism. Given the genetic distinctiveness of southern populations and minimal gene flow with their northern neighbours, fragmentation and loss of southern boreal habitats could mean loss of many unique alleles and reduced evolutionary potential.
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Affiliation(s)
- Ellen Cheng
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
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