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Pérez AA, Tobin A, Stechly JV, Ferrante JA, Hunter ME. A minimally invasive, field-applicable CRISPR/Cas biosensor to aid in the detection of Pseudogymnoascus destructans, the causative fungal agent of white-nose syndrome in bats. Mol Ecol Resour 2024; 24:e13902. [PMID: 38069533 DOI: 10.1111/1755-0998.13902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 10/30/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023]
Abstract
The accessibility to CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) genetic tools has given rise to applications beyond site-directed genome editing for the detection of DNA and RNA. These tools include precise diagnostic detection of human disease pathogens, such as SARS-CoV-2 and Zika virus. Despite the technology being rapid and cost-effective, the use of CRISPR/Cas tools in the surveillance of the causative agents of wildlife diseases has not been prominent. This study presents the development of a minimally invasive, field-applicable and user-friendly CRISPR/Cas-based biosensor for the detection of Pseudogymnoascus destructans (Pd), the causative fungal agent of white-nose syndrome (WNS), an infectious disease that has killed more than five million bats in North America since its discovery in 2006. The biosensor assay combines a recombinase polymerase amplification (RPA) step followed by CRISPR/Cas12a nuclease cleavage to detect Pd DNA from bat dermal swab and guano samples. The biosensor had similar detection results when compared to quantitative PCR in distinguishing Pd-positive versus negative field samples. Although bat dermal swabs could be analysed with the biosensor without nucleic acid extraction, DNA extraction was needed when screening guano samples to overcome inhibitors. This assay can be applied to help with more rapid delineation of Pd-positive sites in the field to inform management decisions. With further optimization, this technology has broad translation potential to wildlife disease-associated pathogen detection and monitoring applications.
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Affiliation(s)
- Adam A Pérez
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, USA
| | - Abigail Tobin
- Washington Department of Fish and Wildlife, Olympia, Washington, USA
| | - John V Stechly
- Cherokee Nation System Solutions, Contractor to the U.S. Geological Survey, Gainesville, Florida, USA
| | - Jason A Ferrante
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, USA
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, USA
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2
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Gonzalez A, Vihervaara P, Balvanera P, Bates AE, Bayraktarov E, Bellingham PJ, Bruder A, Campbell J, Catchen MD, Cavender-Bares J, Chase J, Coops N, Costello MJ, Czúcz B, Delavaud A, Dornelas M, Dubois G, Duffy EJ, Eggermont H, Fernandez M, Fernandez N, Ferrier S, Geller GN, Gill M, Gravel D, Guerra CA, Guralnick R, Harfoot M, Hirsch T, Hoban S, Hughes AC, Hugo W, Hunter ME, Isbell F, Jetz W, Juergens N, Kissling WD, Krug CB, Kullberg P, Le Bras Y, Leung B, Londoño-Murcia MC, Lord JM, Loreau M, Luers A, Ma K, MacDonald AJ, Maes J, McGeoch M, Mihoub JB, Millette KL, Molnar Z, Montes E, Mori AS, Muller-Karger FE, Muraoka H, Nakaoka M, Navarro L, Newbold T, Niamir A, Obura D, O'Connor M, Paganini M, Pelletier D, Pereira H, Poisot T, Pollock LJ, Purvis A, Radulovici A, Rocchini D, Roeoesli C, Schaepman M, Schaepman-Strub G, Schmeller DS, Schmiedel U, Schneider FD, Shakya MM, Skidmore A, Skowno AL, Takeuchi Y, Tuanmu MN, Turak E, Turner W, Urban MC, Urbina-Cardona N, Valbuena R, Van de Putte A, van Havre B, Wingate VR, Wright E, Torrelio CZ. Author Correction: A global biodiversity observing system to unite monitoring and guide action. Nat Ecol Evol 2023; 7:2173. [PMID: 37985899 DOI: 10.1038/s41559-023-02263-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Affiliation(s)
- Andrew Gonzalez
- Department of Biology, Group on Earth Observations Biodiversity Observation Network, McGill University, Montreal, Quebec, Canada.
| | | | - Patricia Balvanera
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Amanda E Bates
- Biology Department, University of Victoria, Victoria, British Columbia, Canada
| | - Elisa Bayraktarov
- EcoCommons Australia, Research, Specialised and Data Foundations, Griffith University, Nathan, Queensland, Australia
| | | | - Andreas Bruder
- Institute of Microbiology, University of Applied Sciences and Arts of Southern Switzerland, Mendrisio, Switzerland
| | - Jillian Campbell
- Secretariat of the Convention on Biological Diversity, Montreal, Quebec, Canada
| | - Michael D Catchen
- Department of Biology, Group on Earth Observations Biodiversity Observation Network, McGill University, Montreal, Quebec, Canada
| | | | - Jonathan Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle, Germany
- Department of Computer Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Nicholas Coops
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark J Costello
- Faculty of Biosciences and Aquaculture, Nord Universitet, Bodø, Norway
| | - Bálint Czúcz
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | | | - Maria Dornelas
- Centre for Biological Diversity, University of St Andrews, St Andrews, UK
- Guia Marine Lab, MARE, Faculdade de Ciências da Universidade de Lisboa, Cascais, Portugal
| | - Grégoire Dubois
- Knowledge Centre for Biodiversity, Joint Research Centre of the European Commission, Ispra, Italy
| | - Emmett J Duffy
- Tennenbaum Marine Observatories Network and MarineGEO program, Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - Hilde Eggermont
- Belgian Science Policy Office, Belgian Biodiversity Platform/Biodiversa+, Brussels, Belgium
| | - Miguel Fernandez
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Nestor Fernandez
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle, Germany
- Department of Computer Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Simon Ferrier
- CSIRO Environment, Canberra, Australian Capital Territory, Australia
| | - Gary N Geller
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Dominique Gravel
- Département de biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle, Germany
- Department of Biology, University of Leipzig, Leipzig, Germany
| | - Robert Guralnick
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | | | - Tim Hirsch
- Global Biodiversity Information Facility, Copenhagen, Denmark
| | - Sean Hoban
- The Center for Tree Science, The Morton Arboretum, Lisle, IL, USA
| | - Alice C Hughes
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | | | - Margaret E Hunter
- US Geological Survey, Wetland & Aquatic Research Center, Sirenia Project, Gainesville, FL, USA
| | - Forest Isbell
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Center for Biodiversity and Global Change, Yale University, New Haven, CT, USA
| | - Norbert Juergens
- Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Cornelia B Krug
- bioDISCOVERY, Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Peter Kullberg
- Finnish Environment Institute (SYKE), Nature Solutions Unit, Helsinki, Finland
| | - Yvan Le Bras
- Pôle national de données de biodiversité, PatriNat, Muséum National d'Histoire Naturelle, Station Marine de Concarneau, Concarneau, France
| | - Brian Leung
- Department of Biology, Group on Earth Observations Biodiversity Observation Network, McGill University, Montreal, Quebec, Canada
| | | | - Jean-Michel Lord
- The Group on Earth Observations Biodiversity Observation Network (GEO BON), Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Michel Loreau
- Theoretical and Experimental Ecology Station, CNRS, Moulis, France
| | | | - Keping Ma
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Anna J MacDonald
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | | | - Melodie McGeoch
- Securing Antarctica's Environmental Future, Department of Environment and Genetics, La Trobe University, Melbourne, Victoria, Australia
| | - Jean Baptiste Mihoub
- Centre d'Écologie et des Sciences de la Conservation (CESCO), Muséum National d'Histoire Naturelle, Sorbonne Université, Centre National de la Recherche Scientifique, CP 135, Paris, France
| | - Katie L Millette
- The Group on Earth Observations Biodiversity Observation Network (GEO BON), Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Zsolt Molnar
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
| | - Enrique Montes
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA
| | - Akira S Mori
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | | | - Hiroyuki Muraoka
- River Basin Research Center, Gifu University, Gifu, Japan
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masahiro Nakaoka
- Akkeshi Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | | | - Tim Newbold
- Centre for Biodiversity and Environment Research, University College London, London, UK
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt, Germany
| | | | - Mary O'Connor
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Henrique Pereira
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle, Germany
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Timothée Poisot
- Département de Sciences Biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - Laura J Pollock
- Department of Biology, Group on Earth Observations Biodiversity Observation Network, McGill University, Montreal, Quebec, Canada
| | - Andy Purvis
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Adriana Radulovici
- The Group on Earth Observations Biodiversity Observation Network (GEO BON), Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Duccio Rocchini
- Department of Biological, Geological, and Environmental Science, Università di Bologna, Bologna, Italy
| | - Claudia Roeoesli
- Remote Sensing Laboratories, Department of Geography, University of Zurich, Zurich, Switzerland
| | - Michael Schaepman
- Remote Sensing Laboratories, Department of Geography, University of Zurich, Zurich, Switzerland
| | - Gabriela Schaepman-Strub
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Dirk S Schmeller
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, INPT, UPS, CNRS, Toulouse, France
| | - Ute Schmiedel
- Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Fabian D Schneider
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Andrew Skidmore
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Enschede, The Netherlands
| | - Andrew L Skowno
- South African National Biodiversity Institute, Kirstenbosch National Botanical Gardens, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Yayioi Takeuchi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Mao-Ning Tuanmu
- Thematic Center for Systematics and Biodiversity Informatics, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Eren Turak
- NSW Department of Environment and Planning, Parramatta, New South Wales, Australia
| | - Woody Turner
- Earth Science Division, NASA Headquarters, Washington, DC, USA
| | - Mark C Urban
- Center of Biological Risk and Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Nicolás Urbina-Cardona
- Facultad de Estudios Ambientales y Rurales, Departamento de Ecología y Territorio, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Ruben Valbuena
- Division of Remote Sensing of Forests, Department of Forest Resource Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | - Anton Van de Putte
- Royal Belgian Institute for Naturalsciences, Brussels, Belgium
- Université Libre de Bruxelles, Brussels, Belgium
| | | | | | - Elaine Wright
- NZ Department of Conservation, Christchurch, New Zealand
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3
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Gonzalez A, Vihervaara P, Balvanera P, Bates AE, Bayraktarov E, Bellingham PJ, Bruder A, Campbell J, Catchen MD, Cavender-Bares J, Chase J, Coops N, Costello MJ, Czúcz B, Delavaud A, Dornelas M, Dubois G, Duffy EJ, Eggermont H, Fernandez M, Fernandez N, Ferrier S, Geller GN, Gill M, Gravel D, Guerra CA, Guralnick R, Harfoot M, Hirsch T, Hoban S, Hughes AC, Hugo W, Hunter ME, Isbell F, Jetz W, Juergens N, Kissling WD, Krug CB, Kullberg P, Le Bras Y, Leung B, Londoño-Murcia MC, Lord JM, Loreau M, Luers A, Ma K, MacDonald AJ, Maes J, McGeoch M, Mihoub JB, Millette KL, Molnar Z, Montes E, Mori AS, Muller-Karger FE, Muraoka H, Nakaoka M, Navarro L, Newbold T, Niamir A, Obura D, O'Connor M, Paganini M, Pelletier D, Pereira H, Poisot T, Pollock LJ, Purvis A, Radulovici A, Rocchini D, Roeoesli C, Schaepman M, Schaepman-Strub G, Schmeller DS, Schmiedel U, Schneider FD, Shakya MM, Skidmore A, Skowno AL, Takeuchi Y, Tuanmu MN, Turak E, Turner W, Urban MC, Urbina-Cardona N, Valbuena R, Van de Putte A, van Havre B, Wingate VR, Wright E, Torrelio CZ. A global biodiversity observing system to unite monitoring and guide action. Nat Ecol Evol 2023; 7:1947-1952. [PMID: 37620553 DOI: 10.1038/s41559-023-02171-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Affiliation(s)
- Andrew Gonzalez
- Department of Biology, Group on Earth Observations Biodiversity Observation Network, McGill University, Montreal, Quebec, Canada.
| | | | - Patricia Balvanera
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Amanda E Bates
- Biology Department, University of Victoria, Victoria, British Columbia, Canada
| | - Elisa Bayraktarov
- EcoCommons Australia, Research, Specialised and Data Foundations, Griffith University, Nathan, Queensland, Australia
| | | | - Andreas Bruder
- Institute of Microbiology, University of Applied Sciences and Arts of Southern Switzerland, Mendrisio, Switzerland
| | - Jillian Campbell
- Secretariat of the Convention on Biological Diversity, Montreal, Quebec, Canada
| | - Michael D Catchen
- Department of Biology, Group on Earth Observations Biodiversity Observation Network, McGill University, Montreal, Quebec, Canada
| | | | - Jonathan Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle, Germany
- Department of Computer Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Nicholas Coops
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark J Costello
- Faculty of Biosciences and Aquaculture, Nord Universitet, Bodø, Norway
| | - Bálint Czúcz
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | | | - Maria Dornelas
- Centre for Biological Diversity, University of St Andrews, St Andrews, UK
- Guia Marine Lab, MARE, Faculdade de Ciências da Universidade de Lisboa, Cascais, Portugal
| | - Grégoire Dubois
- Knowledge Centre for Biodiversity, Joint Research Centre of the European Commission, Ispra, Italy
| | - Emmett J Duffy
- Tennenbaum Marine Observatories Network and MarineGEO program, Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - Hilde Eggermont
- Belgian Science Policy Office, Belgian Biodiversity Platform/Biodiversa+, Brussels, Belgium
| | - Miguel Fernandez
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Nestor Fernandez
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle, Germany
- Department of Computer Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Simon Ferrier
- CSIRO Environment, Canberra, Australian Capital Territory, Australia
| | - Gary N Geller
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Dominique Gravel
- Département de biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle, Germany
- Department of Biology, University of Leipzig, Leipzig, Germany
| | - Robert Guralnick
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | | | - Tim Hirsch
- Global Biodiversity Information Facility, Copenhagen, Denmark
| | - Sean Hoban
- The Center for Tree Science, The Morton Arboretum, Lisle, IL, USA
| | - Alice C Hughes
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | | | - Margaret E Hunter
- US Geological Survey, Wetland & Aquatic Research Center, Sirenia Project, Gainesville, FL, USA
| | - Forest Isbell
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Center for Biodiversity and Global Change, Yale University, New Haven, CT, USA
| | - Norbert Juergens
- Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Cornelia B Krug
- bioDISCOVERY, Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Peter Kullberg
- Finnish Environment Institute (SYKE), Nature Solutions Unit, Helsinki, Finland
| | - Yvan Le Bras
- Pôle national de données de biodiversité, PatriNat, Muséum National d'Histoire Naturelle, Station Marine de Concarneau, Concarneau, France
| | - Brian Leung
- Department of Biology, Group on Earth Observations Biodiversity Observation Network, McGill University, Montreal, Quebec, Canada
| | | | - Jean-Michel Lord
- The Group on Earth Observations Biodiversity Observation Network (GEO BON), Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Michel Loreau
- Theoretical and Experimental Ecology Station, CNRS, Moulis, France
| | | | - Keping Ma
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Anna J MacDonald
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | | | - Melodie McGeoch
- Securing Antarctica's Environmental Future, Department of Environment and Genetics, La Trobe University, Melbourne, Victoria, Australia
| | - Jean Baptiste Mihoub
- Centre d'Écologie et des Sciences de la Conservation (CESCO), Muséum National d'Histoire Naturelle, Sorbonne Université, Centre National de la Recherche Scientifique, CP 135, Paris, France
| | - Katie L Millette
- The Group on Earth Observations Biodiversity Observation Network (GEO BON), Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Zsolt Molnar
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
| | - Enrique Montes
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA
| | - Akira S Mori
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | | | - Hiroyuki Muraoka
- River Basin Research Center, Gifu University, Gifu, Japan
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masahiro Nakaoka
- Akkeshi Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | | | - Tim Newbold
- Centre for Biodiversity and Environment Research, University College London, London, UK
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt, Germany
| | | | - Mary O'Connor
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Henrique Pereira
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle, Germany
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Timothée Poisot
- Département de Sciences Biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - Laura J Pollock
- Department of Biology, Group on Earth Observations Biodiversity Observation Network, McGill University, Montreal, Quebec, Canada
| | - Andy Purvis
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Adriana Radulovici
- The Group on Earth Observations Biodiversity Observation Network (GEO BON), Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Duccio Rocchini
- Department of Biological, Geological, and Environmental Science, Università di Bologna, Bologna, Italy
| | - Claudia Roeoesli
- Remote Sensing Laboratories, Department of Geography, University of Zurich, Zurich, Switzerland
| | - Michael Schaepman
- Remote Sensing Laboratories, Department of Geography, University of Zurich, Zurich, Switzerland
| | - Gabriela Schaepman-Strub
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Dirk S Schmeller
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, INPT, UPS, CNRS, Toulouse, France
| | - Ute Schmiedel
- Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Fabian D Schneider
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Andrew Skidmore
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Enschede, The Netherlands
| | - Andrew L Skowno
- South African National Biodiversity Institute, Kirstenbosch National Botanical Gardens, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Yayioi Takeuchi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Mao-Ning Tuanmu
- Thematic Center for Systematics and Biodiversity Informatics, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Eren Turak
- NSW Department of Environment and Planning, Parramatta, New South Wales, Australia
| | - Woody Turner
- Earth Science Division, NASA Headquarters, Washington, DC, USA
| | - Mark C Urban
- Center of Biological Risk and Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Nicolás Urbina-Cardona
- Facultad de Estudios Ambientales y Rurales, Departamento de Ecología y Territorio, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Ruben Valbuena
- Division of Remote Sensing of Forests, Department of Forest Resource Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | - Anton Van de Putte
- Royal Belgian Institute for Naturalsciences, Brussels, Belgium
- Université Libre de Bruxelles, Brussels, Belgium
| | | | | | - Elaine Wright
- NZ Department of Conservation, Christchurch, New Zealand
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4
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Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MR, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. bioRxiv 2023:2023.07.25.550582. [PMID: 37546854 PMCID: PMC10402094 DOI: 10.1101/2023.07.25.550582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.
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Affiliation(s)
- Francisco J. Pardo-Palacios
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- These authors contributed equally to this work
| | - Dingjie Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Fairlie Reese
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- These authors contributed equally to this work
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- These authors contributed equally to this work
| | - Jane E. Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Maite De María
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Matthew S. Adams
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Gabriela Balderrama-Gutierrez
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Amit K. Behera
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Jose M. Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Flomics Biotech, Dr Aiguader 88, Barcelona 08003, Spain
- These authors contributed equally to this work
| | - Cindy E. Liang
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Haoran Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Marcus Jerryd Meade
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- These authors contributed equally to this work
| | - David A. Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Andrey D. Prjibelski
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- These authors contributed equally to this work
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Hamed Bostan
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Ashley M. Brooks
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Muhammed Hasan Çelik
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ying Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei R,M. Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Jonathan Göke
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Saber Hafezqorani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Joseph Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian Liang Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Matthias Lienhard
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alla Mikheenko
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Dennis Mulligan
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Matthew E. Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andre D. Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alison D. Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Changqing Wang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Brandon Y. Wong
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | | | - Luis Ferrández-Peral
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA
| | | | | | | | | | | | | | - Jorge Mestre-Tomás
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Jonathan M. Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nedka G. Panayotova
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | | | - Eric Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Enrique Sapena
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Melissa Laird Smith
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hazuki Takahashi
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
| | | | - Piero Carninci
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
- Human Technopole, Milano, Italy
| | - Nancy D. Denslow
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, Department of Physiological Sciences,, University of Florida, Gainesville, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Hagen U. Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA
| | - Barbara J. Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- Center for Public Health Genomics
- UVA Cancer Center, University of Virginia, Charlottesville, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Angela N. Brooks
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
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5
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Ooi V, McMichael L, Hunter ME, Takoukam Kamla A, Lanyon JM. A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong. PLoS One 2023; 18:e0278792. [PMID: 37285349 DOI: 10.1371/journal.pone.0278792] [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] [Received: 11/22/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new 'High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol' (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.
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Affiliation(s)
- Vicky Ooi
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Lee McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Sirenia Project, Gainesville, Florida, United States of America
| | - Aristide Takoukam Kamla
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- African Marine Mammal Conservation Organization, Dizangue, Littoral, Cameroon
| | - Janet M Lanyon
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
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6
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Sepulveda AJ, Dumoulin CE, Blanchette DL, McPhedran J, Holme C, Whalen N, Hunter ME, Merkes CM, Richter CA, Neilson ME, Daniel WM, Jones DN, Smith DR. When are environmental DNA early detections of invasive species actionable? J Environ Manage 2023; 343:118216. [PMID: 37247541 DOI: 10.1016/j.jenvman.2023.118216] [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] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/19/2023] [Accepted: 05/19/2023] [Indexed: 05/31/2023]
Abstract
Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an early detection rapid response program because positive eDNA detections are not always indicative of an eventual infestation. We used a structured decision making (SDM) framework to evaluate appropriate response actions to hypothetical eDNA early detections of an introduced aquatic plant in Sebago Lake (Maine, USA). The results were juxtaposed to a recent study that used a similar SDM approach to evaluate response actions to hypothetical eDNA early detections of introduced mussels in Jordanelle Reservoir (Utah, USA). We found that eDNA early detections were not actionable in Sebago Lake because the plant's invasion potential was spatially constrained and the current management activities provided acceptable levels of mitigation. In Jordanelle Reservoir, eDNA detections were actionable due to high invasion potential and analyses supported management actions to contain the invasion. The divergent outcomes of the two case studies are related to the unique attributes of the habitats and species, highlighting the utility of the SDM approach when considering an eDNA monitoring program. We use these two case studies to present a general SDM framework and a set of heuristics that can be efficiently applied to eDNA early detection rapid response scenarios and other instances associated with indeterminant eDNA detections, especially when there is an imperative to make decisions as quickly as possible.
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Affiliation(s)
- Adam J Sepulveda
- U.S. Geological Survey Northern Rocky Mountain Science Center, Bozeman, MT, 59715, USA.
| | - Christine E Dumoulin
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown, WV, 25430, USA
| | | | - John McPhedran
- Maine Department of Environmental Protection, Augusta, ME, 04333, USA
| | - Colin Holme
- Lakes Environmental Association, Bridgton, ME, 04009, USA
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA
| | - Christopher M Merkes
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, WI, 54603, USA
| | - Catherine A Richter
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, 65201, USA
| | - Matthew E Neilson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA
| | - Wesley M Daniel
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA
| | - Devin N Jones
- U.S. Geological Survey Northern Rocky Mountain Science Center, Bozeman, MT, 59715, USA
| | - David R Smith
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown, WV, 25430, USA
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7
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Graham AM, Jamison JM, Bustos M, Cournoyer C, Michaels A, Presnell JS, Richter R, Crocker DE, Fustukjian A, Hunter ME, Rea LD, Marsillach J, Furlong CE, Meyer WK, Clark NL. Reduction of Paraoxonase Expression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization. Mol Biol Evol 2023; 40:msad104. [PMID: 37146172 PMCID: PMC10202596 DOI: 10.1093/molbev/msad104] [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: 11/14/2022] [Revised: 03/27/2023] [Accepted: 04/17/2023] [Indexed: 05/07/2023] Open
Abstract
Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages-Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.
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Affiliation(s)
- Allie M Graham
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Jerrica M Jamison
- Department of Biological Sciences, University of Toronto—Scarborough, Scarborough, Ontario, Canada
| | - Marisol Bustos
- Department of Biomedical Engineering, University of Texas—San Antonio, San Antonio, TX
| | | | - Alexa Michaels
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA
- The Jackson Laboratory, Bar Harbor, ME
| | - Jason S Presnell
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Rebecca Richter
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Daniel E Crocker
- Department of Biology, Sonoma State University, Rohnert Park, CA
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL
| | - Lorrie D Rea
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska—Fairbanks, Fairbanks, AK
| | - Judit Marsillach
- Department of Environmental & Occupational Health Sciences, University of Washington School of Public Health, Seattle, WA
| | - Clement E Furlong
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA
| | - Nathan L Clark
- Department of Human Genetics, University of Utah, Salt Lake City, UT
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8
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Guzy JC, Falk BG, Smith BJ, Willson JD, Reed RN, Aumen NG, Avery ML, Bartoszek IA, Campbell E, Cherkiss MS, Claunch NM, Currylow AF, Dean T, Dixon J, Engeman R, Funck S, Gibble R, Hengstebeck KC, Humphrey JS, Hunter ME, Josimovich JM, Ketterlin J, Kirkland M, Mazzotti FJ, McCleery R, Miller MA, McCollister M, Parker MR, Pittman SE, Rochford M, Romagosa C, Roybal A, Snow RW, Spencer MM, Waddle JH, Yackel Adams AA, Hart KM. Burmese pythons in Florida: A synthesis of biology, impacts, and management tools. NB 2023. [DOI: 10.3897/neobiota.80.90439] [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] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Burmese pythons (Python molurus bivittatus) are native to southeastern Asia, however, there is an established invasive population inhabiting much of southern Florida throughout the Greater Everglades Ecosystem. Pythons have severely impacted native species and ecosystems in Florida and represent one of the most intractable invasive-species management issues across the globe. The difficulty stems from a unique combination of inaccessible habitat and the cryptic and resilient nature of pythons that thrive in the subtropical environment of southern Florida, rendering them extremely challenging to detect. Here we provide a comprehensive review and synthesis of the science relevant to managing invasive Burmese pythons. We describe existing control tools and review challenges to productive research, identifying key knowledge gaps that would improve future research and decision making for python control.
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9
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Hoban S, Bruford MW, da Silva JM, Funk WC, Frankham R, Gill MJ, Grueber CE, Heuertz M, Hunter ME, Kershaw F, Lacy RC, Lees C, Lopes-Fernandes M, MacDonald AJ, Mastretta-Yanes A, McGowan PJK, Meek MH, Mergeay J, Millette KL, Mittan-Moreau CS, Navarro LM, O'Brien D, Ogden R, Segelbacher G, Paz-Vinas I, Vernesi C, Laikre L. Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework. CONSERV GENET 2023; 24:181-191. [PMID: 36683963 PMCID: PMC9841145 DOI: 10.1007/s10592-022-01492-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/30/2022] [Indexed: 01/18/2023]
Abstract
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.
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Affiliation(s)
- Sean Hoban
- The Morton Arboretum, Center for Tree Science, Lisle, USA.,The University of Chicago, Chicago, USA
| | | | - Jessica M da Silva
- South African National Biodiversity Institute, Pretoria, South Africa.,Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Richard Frankham
- School of Natural Sciences, Macquarie University, Sydney, NSW Australia
| | - Michael J Gill
- NatureServe, Biodiversity Indicators Program, Arlington, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Francine Kershaw
- Oceans Division, Natural Resources Defense Council, NewYork, USA
| | - Robert C Lacy
- Chicago Zoological Society, Species Conservation Toolkit Initiative, Brookfield, USA
| | - Caroline Lees
- Conservation Planning Specialist Group, IUCN SSC, Auckland, New Zealand
| | | | - Anna J MacDonald
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Australia
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Mexico City, Mexico.,Consejo Nacional de Ciencia Y Tecnología (CONACYT), Mexico City, Mexico
| | - Philip J K McGowan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Mariah H Meek
- Department of Integrative Biology; Ecology, Evolution, and Behavior Program, Michigan State University, AgBio Research, Lansing, USA
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Katie L Millette
- Group on Earth Observations Biodiversity Observation Network (GEO BON), McGill University, Montreal, Canada
| | - Cinnamon S Mittan-Moreau
- Kellogg Biological Station; Ecology and Evolutionary Biology, Michigan State University, Lansing, USA
| | | | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, Midlothian, United Kingdom
| | | | - Ivan Paz-Vinas
- Department of Biology, Colorado State University, Fort Collins, USA
| | | | - Linda Laikre
- Department of Zoology, Stockholm University, Stockholm, Sweden
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10
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Meyer R, Davies N, Pitz KJ, Meyer C, Samuel R, Anderson J, Appeltans W, Barker K, Chavez FP, Duffy JE, Goodwin KD, Hudson M, Hunter ME, Karstensen J, Laney CM, Leinen M, Mabee P, Macklin JA, Muller-Karger F, Pade N, Pearlman J, Phillips L, Provoost P, Santi I, Schigel D, Schriml LM, Soccodato A, Suominen S, Thibault KM, Ung V, van de Kamp J, Wallis E, Walls R, Buttigieg PL. The founding charter of the Omic Biodiversity Observation Network (Omic BON). Gigascience 2022; 12:giad068. [PMID: 37632753 PMCID: PMC10460158 DOI: 10.1093/gigascience/giad068] [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: 06/29/2023] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023] Open
Abstract
Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.
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Affiliation(s)
- Raïssa Meyer
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
- Faculty of Geosciences, University of Bremen, Bremen 28359, Germany
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Neil Davies
- Gump South Pacific Research Station, University of California Berkeley, Moorea 98728, French Polynesia
- Berkeley Institute for Data Science, University of California, Berkeley, CA 94720, USA
| | - Kathleen J Pitz
- Science Department, Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Chris Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Robyn Samuel
- School of Ocean and Earth Science, University of Southampton, Southampton SO17 1BJ, UK
- Ocean Technology and Engineering Group, National Oceanography Center, Southampton SO14 3ZH, UK
| | - Jane Anderson
- Department of Anthropology, New York University, New York City, NY 10012, USA
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System, Oostende 8400, Begium
| | - Katharine Barker
- Global Genome Biodiversity Network Secretariat Office, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Francisco P Chavez
- Science Department, Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - J Emmett Duffy
- Tennenbaum Marine Observatories Network and MarineGEO Program, Smithsonian Environmental Research Center, Edgewater, MD 21037, USA
| | - Kelly D Goodwin
- National Oceanic & Atmospheric Administration, NOAA Ocean Exploration, La Jolla, CA 92037, USA
| | - Maui Hudson
- Te Kotahi Research Institute, University of Waikato, Hamilton 3240, New Zealand
| | - Margaret E Hunter
- Wetland and Aquatic Research Center, U.S. Geological Survey, Gainesville, FL 32653, USA
| | - Johannes Karstensen
- Department of Physical Oceanography, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24105, Germany
| | - Christine M Laney
- Science department, National Ecological Observatory Network, Boulder, CO 80301, USA
| | - Margaret Leinen
- Geosciences Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Paula Mabee
- Observatory Leadership department, National Ecological Observatory Network, Boulder, CO 80301, USA
| | - James A Macklin
- Botany and Biodiversity Informatics, Agriculture and Agri-Food Canada (AAFC), Ottawa, Ontario K1A 0C6, Canada
| | - Frank Muller-Karger
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA
| | - Nicolas Pade
- European Marine Biological Resource Centre (EMBRC-ERIC), Paris 75252, France
| | | | - Lori Phillips
- Agriculture and Agri-Food Canada (AAFC), Harrow N0R 1G0, Ontario, Canada
| | - Pieter Provoost
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System, Oostende 8400, Begium
| | - Ioulia Santi
- European Marine Biological Resource Centre (EMBRC-ERIC), Paris 75252, France
- Marine Microbiology, Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Heraklion GR71003, Greece
| | - Dmitry Schigel
- GBIF | Global Biodiversity Information Facility, Copenhagen DK-2100, Denmark
| | - Lynn M Schriml
- Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alice Soccodato
- European Marine Biological Resource Centre (EMBRC-ERIC), Paris 75252, France
| | - Saara Suominen
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System, Oostende 8400, Begium
| | - Katherine M Thibault
- Science department, National Ecological Observatory Network, Boulder, CO 80301, USA
| | | | | | | | - Ramona Walls
- Data Science department, Critical Path Institute, Tucson, AZ 85718, USA
| | - Pier Luigi Buttigieg
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
- Information, Data and Computer Center, Helmholtz Metadata Collaboration/GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24105, Germany
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11
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Alvarez-Aleman A, Hunter ME, Frazer TK, Powell JA, Alfonso EG, Austin JD. The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba. Genetica 2022; 150:327-341. [PMID: 36271978 DOI: 10.1007/s10709-022-00172-8] [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: 04/20/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
Abstract
The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population's genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. We genotyped 49 manatees at 18 microsatellite loci, a subset of 27 samples on 1703 single nucleotide polymorphisms (SNPs), and sequenced 59 manatees at the mitochondrial control region. The Cuba manatee population had low nuclear (microsatellites HE = 0.44, and SNP HE = 0.29) and mitochondrial genetic diversity (h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite FIS = 0.12, SNP FIS = 0.10). Our results suggest that the western portion of the archipelago undergoes periodic exchange of alleles based on the evidence of shared ancestry and low but significant differentiation. The southeast Guantanamo Bay region and the western portion of the archipelago were more differentiated than southwest and northwest manatees. The genetic distinctiveness observed in the southeast supports its recognition as a demographically independent unit for natural resource management regardless of whether it is due to historical isolation or isolation by distance. Estimates of the regional effective population sizes, with the microsatellite and SNP datasets, were small (all Ne < 60). Subsequent analyses using additional samples could better examine how the observed structure is masking simple isolation by distance patterns or whether ecological or biogeographic forces shape genetic patterns.
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Affiliation(s)
- Anmari Alvarez-Aleman
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA. .,Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16 # 114 Entre 1ra y 3ra Plaza, Havana, Cuba. .,Clearwater Marine Aquarium Research Institute, Clearwater Marine Aquarium, Clearwater, FL, USA.
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Thomas K Frazer
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA.,College of Marine Science, University of South Florida, 140 Seventh Avenue South, KRC 3109, St. Petersburg, FL, 33701, USA
| | - James A Powell
- Clearwater Marine Aquarium Research Institute, Clearwater Marine Aquarium, Clearwater, FL, USA
| | - Eddy Garcia Alfonso
- Refugio de Fauna Lanzanillo-Pajonal-Fragoso, Empresa Provincial para la Protección de la Flora y la Fauna, Villa Clara, Cuba
| | - James D Austin
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA.,Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
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12
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van Rees CB, Hand BK, Carter SC, Bargeron C, Cline TJ, Daniel W, Ferrante JA, Gaddis K, Hunter ME, Jarnevich CS, McGeoch MA, Morisette JT, Neilson ME, Roy HE, Rozance MA, Sepulveda A, Wallace RD, Whited D, Wilcox T, Kimball JS, Luikart G. A framework to integrate innovations in invasion science for proactive management. Biol Rev Camb Philos Soc 2022; 97:1712-1735. [PMID: 35451197 DOI: 10.1111/brv.12859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 10/07/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches has produced tools with the potential to greatly accelerate invasion research and management, innovation has far outpaced implementation and coordination. Technological and methodological syntheses are urgently needed to close the growing implementation gap and facilitate interdisciplinary collaboration and synergy among evolving disciplines. A broad review is necessary to demonstrate the utility and relevance of work in diverse fields to generate actionable science for the ongoing invasion crisis. Here, we review such advances in relevant fields including remote sensing, epidemiology, big data analytics, environmental DNA (eDNA) sampling, genomics, and others, and present a generalized framework for distilling existing and emerging data into products for proactive IAS research and management. This integrated workflow provides a pathway for scientists and practitioners in diverse disciplines to contribute to applied invasion biology in a coordinated, synergistic, and scalable manner.
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Affiliation(s)
- Charles B van Rees
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Sean C Carter
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Chuck Bargeron
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Timothy J Cline
- U.S. Geological Survey, Northern Rocky Mountain Science Center, 2327 University Way STE 2, Bozeman MT 59717 & 320 Grinnel Drive, West Glacier, MT, 59936, U.S.A
| | - Wesley Daniel
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Jason A Ferrante
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Keith Gaddis
- NASA Biological Diversity and Ecological Forecasting Programs, 300 E St. SW, Washington, DC, 20546, U.S.A
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Catherine S Jarnevich
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue Bldg C, Fort Collins, CO, 80526, U.S.A
| | - Melodie A McGeoch
- Department of Environment and Genetics, La Trobe University, Plenty Road & Kingsbury Drive, Bundoora, Victoria, 3086, Australia
| | - Jeffrey T Morisette
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Matthew E Neilson
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Helen E Roy
- UK Centre for Ecology & Hydrology, MacLean Building, Benson Lane, Crowmarsh Gifford, OX10 8BB, U.K
| | - Mary Ann Rozance
- Northwest Climate Adaptation Science Center, University of Washington, Box 355674, Seattle, WA, 98195, U.S.A
| | - Adam Sepulveda
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Rebekah D Wallace
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Diane Whited
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Taylor Wilcox
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - John S Kimball
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Gordon Luikart
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
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13
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Hoban S, Archer FI, Bertola LD, Bragg JG, Breed MF, Bruford MW, Coleman MA, Ekblom R, Funk WC, Grueber CE, Hand BK, Jaffé R, Jensen E, Johnson JS, Kershaw F, Liggins L, MacDonald AJ, Mergeay J, Miller JM, Muller-Karger F, O'Brien D, Paz-Vinas I, Potter KM, Razgour O, Vernesi C, Hunter ME. Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition. Biol Rev Camb Philos Soc 2022; 97:1511-1538. [PMID: 35415952 PMCID: PMC9545166 DOI: 10.1111/brv.12852] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/14/2022]
Abstract
Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (Ne). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.
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Affiliation(s)
- Sean Hoban
- Center for Tree Science, The Morton Arboretum, 4100 Illinois Rt 53, Lisle, IL, 60532, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, NOAA/NMFS, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Laura D Bertola
- City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, University Drive, Bedford Park, SA, 5042, Australia
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, Wales, UK
| | - Melinda A Coleman
- Department of Primary Industries, New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
| | - Robert Ekblom
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, Blekholmsterrassen 36, Stockholm, SE-106 48, Sweden
| | - W Chris Funk
- Department of Biology, Graduate Degree in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523-1878, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Carslaw Building, Sydney, NSW, 2006, Australia
| | - Brian K Hand
- Flathead Lake Biological Station, 32125 Bio Station Ln, Polson, MT, 59860, USA
| | - Rodolfo Jaffé
- Exponent, 15375 SE 30th Place, Suite 250, Bellevue, WA, 98007, USA
| | - Evelyn Jensen
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, Newcastle Upon Tyne, NE1 7RU, UK
| | - Jeremy S Johnson
- Department of Environmental Studies, Prescott College, 220 Grove Avenue, Prescott, AZ, 86303, USA
| | - Francine Kershaw
- Natural Resources Defense Council, 40 West 20th Street, New York, NY, 10011, USA
| | - Libby Liggins
- School of Natural Sciences, Massey University, Ōtehā Rohe campus, Gate 4 Albany Highway, Auckland, Aotearoa, 0745, New Zealand
| | - Anna J MacDonald
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, 9500, Geraardsbergen, Belgium.,Aquatic Ecology, Evolution and Conservation, KULeuven, Charles Deberiotstraat 32, box 2439, 3000, Leuven, Belgium
| | - Joshua M Miller
- Department of Biological Sciences, MacEwan University, 10700 104 Avenue, Edmonton, AB, T5J 4S2, Canada
| | - Frank Muller-Karger
- College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, Florida, 33701, USA
| | - David O'Brien
- NatureScot, Great Glen House, Leachkin Road, Inverness, IV3 8NW, UK
| | - Ivan Paz-Vinas
- Laboratoire Evolution et Diversité Biologique, Université de Toulouse, CNRS, IRD, UPS, UMR-5174 EDB, 118 route de Narbonne, Toulouse, 31062, France
| | - Kevin M Potter
- Department of Forestry and Environmental Resources, North Carolina State University, 3041 Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Orly Razgour
- Biosciences, University of Exeter, Streatham Campus, Hatherly Laboratories, Prince of Wales Road, Exeter, EX4 4PS, UK
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, Via E. Mach, 1, San Michele all'Adige, 38010, (TN), Italy
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
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14
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Kershaw F, Bruford MW, Funk WC, Grueber CE, Hoban S, Hunter ME, Laikre L, MacDonald AJ, Meek MH, Mittan C, O´Brien D, Ogden R, Shaw RE, Vernesi C, Segelbacher G. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Conservat Sci and Prac 2022. [DOI: 10.1111/csp2.12635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
| | | | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado USA
| | - Catherine E. Grueber
- School of Life and Environmental Sciences, The University of Sydney New South Wales Australia
| | - Sean Hoban
- The Morton Arboretum, Center for Tree Science Lisle Illinois USA
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville Florida USA
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics Stockholm University Stockholm Sweden
| | - Anna J. MacDonald
- Research School of Biology The Australian National University Canberra Acton Australia
| | - Mariah H. Meek
- Department of Integrative Biology, AgBio Research, and Ecology, Evolution, and Behavior Program Michigan State University East Lansing Michigan USA
| | - Cinnamon Mittan
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh Edinburgh UK
| | - Robyn E. Shaw
- Environmental and Conservation Sciences Murdoch University Perth Australia
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre‐Fondazione Edmund Mach San Michele all’Adige Trentino Italy
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15
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Takoukam Kamla A, Gomes DGE, Beck CA, Keith‐Diagne LW, Hunter ME, Francis‐Floyd R, Bonde RK. Diet composition of the African manatee: Spatial and temporal variation within the Sanaga River Watershed, Cameroon. Ecol Evol 2021; 11:15833-15845. [PMID: 34824793 PMCID: PMC8601922 DOI: 10.1002/ece3.8254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 11/08/2022] Open
Abstract
The present study aimed to investigate the diet of African manatees in Cameroon to better inform conservation decisions within protected areas. A large knowledge gap on diet and seasonal changes in forage availability limits the ability to develop informed local management plans for the African manatee in much of its range. This research took place in the Sanaga River Watershed, which includes two protected areas in the Littoral Region of Cameroon: the Douala-Edea National Park and the Lake Ossa Wildlife Reserve. We analyzed 113 manatee fecal samples and surveyed shoreline emergent and submerged vegetation within the Sanaga River Watershed. We used microhistological analyses to determine the relative contribution of each plant species to African manatee diets and compared across locations and across seasons (wet vs. dry season). We found that the shoreline vegetation is diverse with over 160 plant species, unevenly distributed across space and season, and dominated by emergent vegetation mostly represented by the antelope grass (Echinochloa pyramidalis). We recorded a total of 36 plant species from fecal samples with a spatial and temporal distribution mostly reflecting that of the corresponding shoreline vegetation. African manatees appear to be primarily opportunistically feeding on available vegetation across the seasons and habitat. This work documents the current, but changing, state of plant availability in the Sanaga River Watershed and reports the African manatee diet in Cameroon for the first time. This information can play a critical role in successfully managing the species and these protected areas. If we wish to protect the African manatee and the aquatic ecosystems within the Sanaga River Watershed, we must understand how forage availability changes over time, especially as its waters become nutrient enriched, eutrophic, and exposed to invasive species of plants in a changing world.
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Affiliation(s)
- Aristide Takoukam Kamla
- African Marine Mammal Conservation OrganizationEdeaCameroon
- Department of Large Animal Clinical SciencesCollege of Veterinary MedicineUniversity of FloridaGainesvilleFloridaUSA
| | - Dylan G. E. Gomes
- African Marine Mammal Conservation OrganizationEdeaCameroon
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
- Present address:
Cooperative Institute for Marine Resources StudiesHatfield Marine Science CenterOregon State UniversityNewportOregonUSA
| | - Cathy A. Beck
- U.S. Geological SurveyWetland and Aquatic Research CenterGainesvilleFloridaUSA
| | | | - Margaret E. Hunter
- U.S. Geological SurveyWetland and Aquatic Research CenterGainesvilleFloridaUSA
| | - Ruth Francis‐Floyd
- Department of Large Animal Clinical SciencesCollege of Veterinary MedicineUniversity of FloridaGainesvilleFloridaUSA
| | - Robert K. Bonde
- Clearwater Marine Aquarium Research InstituteClearwaterFloridaUSA
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16
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Ferrante JA, Smith CH, Thompson LM, Hunter ME. Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01402-w] [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: 11/30/2022]
Abstract
AbstractGenome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.
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17
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Hoban S, Bruford MW, Funk WC, Galbusera P, Griffith MP, Grueber CE, Heuertz M, Hunter ME, Hvilsom C, Stroil BK, Kershaw F, Khoury CK, Laikre L, Lopes-Fernandes M, MacDonald AJ, Mergeay J, Meek M, Mittan C, Mukassabi TA, O'Brien D, Ogden R, Palma-Silva C, Ramakrishnan U, Segelbacher G, Shaw RE, Sjögren-Gulve P, Veličković N, Vernesi C. Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible. Bioscience 2021; 71:964-976. [PMID: 34475806 PMCID: PMC8407967 DOI: 10.1093/biosci/biab054] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.
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Affiliation(s)
- Sean Hoban
- The Morton Arboretum, Center for Tree Science, Lisle, Illinois, United States
| | | | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, United States
| | - Peter Galbusera
- Royal Zoological Society of Antwerp, Centre for Research and Conservation, Antwerp, Belgium
| | | | - Catherine E Grueber
- University of Sydney's School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Myriam Heuertz
- INRAE, and the University of Bordeaux, Biogeco, Cestas, France
| | - Margaret E Hunter
- US Geological Survey's Wetland and Aquatic Research Center, Gainesville, Florida, United States
| | | | - Belma Kalamujic Stroil
- University of Sarajevo Institute for Genetic Engineering and Biotechnology, Laboratory for Molecular Genetics of Natural Resources, Sarajevo, Bosnia and Herzegovina
| | - Francine Kershaw
- Natural Resources Defense Council, New York, New York, United States
| | - Colin K Khoury
- International Center for Tropical Agriculture, Cali, Colombia
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | | | - Anna J MacDonald
- Australian National University, John Curtin School of Medical Research and Research School of Biology, Canberra, Australia
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Mariah Meek
- Michigan State University Department of Integrative Biology, AgBio Research, Ecology, Evolution, and Behavior Program, East Lansing, Michigan, United States
| | - Cinnamon Mittan
- Cornell University's Department of Ecology and Evolutionary Biology, Ithaca, New York, United States
| | - Tarek A Mukassabi
- University of Benghazi Department of Botany, Faculty of Sciences, Benghazi, Libya
| | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and with the Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Scotland, United Kingdom
| | | | - Uma Ramakrishnan
- Department of Ecology and Evolution, National Centre for Biological Sciences, Bangalore, India
| | - Gernot Segelbacher
- Chair of wildlife ecology and management, University Freiburg, Freiburg, Germany
| | - Robyn E Shaw
- Department of Environmental and Conservation Sciences, Murdoch University, Perth, Australia
| | - Per Sjögren-Gulve
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, Stockholm, Sweden
| | - Nevena Veličković
- University of Novi Sad's Faculty of Sciences, Department of Biology and Ecology, Novi Sad, Serbia
| | - Cristiano Vernesi
- Forest Ecology and Biogeochemical Fluxes Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Italy
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18
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De María M, Silva-Sanchez C, Kroll KJ, Walsh MT, Nouri MZ, Hunter ME, Ross M, Clauss TM, Denslow ND. Chronic exposure to glyphosate in Florida manatee. Environ Int 2021; 152:106493. [PMID: 33740675 DOI: 10.1016/j.envint.2021.106493] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 05/25/2023]
Abstract
Florida manatees depend on freshwater environments as a source of drinking water and as warm-water refuges. These freshwater environments are in direct contact with human activities where glyphosate-based herbicides are being used. Glyphosate is the most used herbicide worldwide and it is intensively used in Florida as a sugarcane ripener and to control invasive aquatic plants. The objective of the present study was to determine the concentration of glyphosate and its breakdown product, aminomethylphosphonic acid (AMPA), in Florida manatee plasma and assess their exposure to manatees seeking a warm-water refuge in Crystal River (west central Florida), and in South Florida. We analyzed glyphosate's and AMPA's concentrations in Florida manatee plasma (n = 105) collected during 2009-2019 using HPLC-MS/MS. We sampled eight Florida water bodies between 2019 and 2020, three times a year: before, during and after the sugarcane harvest using grab samples and molecular imprinted passive Polar Organic Chemical Integrative Samplers (MIP-POCIS). Glyphosate was present in 55.8% of the sampled Florida manatees' plasma. The concentration of glyphosate has significantly increased in Florida manatee samples from 2009 until 2019. Glyphosate and AMPA were ubiquitous in water bodies. The concentration of glyphosate and AMPA was higher in South Florida than in Crystal River, particularly before and during the sugarcane harvest when Florida manatees depend on warm water refuges. Based on our results, Florida manatees were chronically exposed to glyphosate and AMPA, during and beyond the glyphosate applications to sugarcane, possibly associated with multiple uses of glyphosate-based herbicides for other crops or to control aquatic weeds. This chronic exposure in Florida water bodies may have consequences for Florida manatees' immune and renal systems which may further be compounded by other environmental exposures such as red tide or cold stress.
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Affiliation(s)
- Maite De María
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA; Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, PO Box 100136, Gainesville, FL 32610, USA.
| | - Cecilia Silva-Sanchez
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA.
| | - Kevin J Kroll
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA.
| | - Michael T Walsh
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, PO Box 100136, Gainesville, FL 32610, USA.
| | - Mohammad-Zaman Nouri
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA.
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL 32653, United States.
| | - Monica Ross
- Clearwater Marine Aquarium, 249 Windward Passage, Clearwater, FL 33767, USA.
| | - Tonya M Clauss
- Georgia Aquarium, Atlanta, Georgia, 225 Baker Street Northwest, Atlanta, GA 30313, USA.
| | - Nancy D Denslow
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
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19
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Laikre L, Hohenlohe PA, Allendorf FW, Bertola LD, Breed MF, Bruford MW, Funk WC, Gajardo G, González-Rodríguez A, Grueber CE, Hedrick PW, Heuertz M, Hunter ME, Johannesson K, Liggins L, MacDonald AJ, Mergeay J, Moharrek F, O’Brien D, Ogden R, Orozco-terWengel P, Palma-Silva C, Pierson J, Paz-Vinas I, Russo IRM, Ryman N, Segelbacher G, Sjögren-Gulve P, Waits LP, Vernesi C, Hoban S. Correction to: Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01376-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A correction to this paper has been published: https://doi.org/10.1007/s10592-021-01376-9
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20
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Phelan R, Baumgartner B, Brand S, Brister E, Burgiel SW, Charo RA, Coche I, Cofrancesco A, Delborne JA, Edwards O, Fisher JP, Gaywood M, Gordon DR, Howald G, Hunter ME, Kareiva P, Mankad A, Marvier M, Moseby K, Newhouse AE, Novak BJ, Ohrstrom G, Olson S, Palmer MJ, Palumbi S, Patterson N, Pedrono M, Pelegri F, Rohwer Y, Ryder OA, Saah JR, Scheller RM, Seddon PJ, Shaffer HB, Shapiro B, Sweeney M, Tercek MR, Thizy D, Tilt W, Weber M, Wegrzyn RD, Whitelaw B, Winkler M, Wodak J, Zimring M, Robbins P. Intended consequences statement. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
| | | | | | - Evelyn Brister
- Rochester Institute of Technology Rochester New York USA
| | | | - R. Alta Charo
- University of Wisconsin‐Madison Madison Wisconsin USA
| | | | - Al Cofrancesco
- U.S. Army Corps of Engineers, Engineer Research and Development Center Vicksburg Mississippi USA
| | - Jason A. Delborne
- Genetic Engineering and Society Center North Carolina State University Raleigh North Carolina USA
| | - Owain Edwards
- Commonwealth Scientific and Industrial Research Organisation Floreat Western Australia Australia
| | | | | | - Doria R. Gordon
- Environmental Defense Fund Washington District of Columbia USA
| | - Gregg Howald
- Advanced Conservation Strategies Williamsburg Virginia USA
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville Florida USA
| | | | - Aditi Mankad
- Commonwealth Scientific and Industrial Research Organisation Floreat Western Australia Australia
| | - Michelle Marvier
- Department of Environmental Studies and Sciences Santa Clara University Santa Clara California USA
| | | | - Andrew E. Newhouse
- State University of New York, College of Environmental Science and Forestry Syracuse New York USA
| | | | | | - Steven Olson
- Association of Zoos and Aquariums Silver Spring Maryland USA
| | | | - Stephen Palumbi
- Hopkins Marine Station Stanford University Pacific Grove California USA
| | - Neil Patterson
- State University of New York College of Environmental Science and Forestry Center for Native Peoples & the Environment Syracuse New York USA
| | - Miguel Pedrono
- French Agricultural Research Centre for International Development (CIRAD, UMR ASTRE) Montpellier France
| | - Francisco Pelegri
- Laboratory of Genetics University of Wisconsin‐Madison Madison Wisconsin USA
| | - Yasha Rohwer
- Oregon Institute of Technology Klamath Falls Oregon USA
| | | | | | - Robert M. Scheller
- Department of Forestry and Environmental Resources North Carolina State University Raleigh North Carolina USA
| | | | - H. Bradley Shaffer
- Department of Ecology and Evolutionary Biology and La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability University of California Los Angeles California USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, and the Howard Hughes Medical Institute University of California Santa Cruz California USA
| | - Mike Sweeney
- The Nature Conservancy San Francisco California USA
| | | | | | | | | | | | - Bruce Whitelaw
- The Roslin Institute University of Edinburgh Midlothian UK
| | | | - Josh Wodak
- Institute for Culture and Society, Western Sydney University Parramatta New South Wales Australia
| | - Mark Zimring
- The Nature Conservancy San Francisco California USA
| | - Paul Robbins
- Nelson Institute for Environmental Studies University of Wisconsin‐Madison Madison Wisconsin USA
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21
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Paz-Vinas I, Jensen EL, Bertola LD, Breed MF, Hand BK, Hunter ME, Kershaw F, Leigh DM, Luikart G, Mergeay J, Miller JM, Van Rees CB, Segelbacher G, Hoban S. Macrogenetic studies must not ignore limitations of genetic markers and scale. Ecol Lett 2021; 24:1282-1284. [PMID: 33749962 DOI: 10.1111/ele.13732] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 09/18/2020] [Revised: 11/14/2020] [Accepted: 12/06/2020] [Indexed: 11/30/2022]
Abstract
Millette et al. (Ecology Letters, 2020, 23:55-67) reported no consistent worldwide anthropogenic effects on animal genetic diversity using repurposed mitochondrial DNA sequences. We reexamine data from this study, describe genetic marker and scale limitations which might lead to misinterpretations with conservation implications, and provide advice to improve future macrogenetic studies.
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Affiliation(s)
- Ivan Paz-Vinas
- Laboratoire Evolution & Diversité Biologique, Centre National pour la Recherche Scientifique, Institut de Recherche pour le Développement, Université de Toulouse, UPS, CNRS, IRD, UMR 5174, 118 route de Narbonne, Toulouse, 31062, France.,Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, UPS, CNRS, INP, UMR 5245, 118 route de Narbonne, Toulouse, 31062, France
| | - Evelyn L Jensen
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem St, New Haven, CT, 06520, USA
| | - Laura D Bertola
- City College of New York, 160 Convent Ave, New York, NY, 10031, USA
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Brian K Hand
- Flathead Lake Biological Station, 32125 Bio Station Ln, Polson, MT, 59860, USA
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st St, Gainesville, FL, 32653, USA
| | - Francine Kershaw
- Natural Resources Defense Council, 40 West 20th Street, New York, NY, 10011, USA
| | - Deborah M Leigh
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Gordon Luikart
- Flathead Lake Biological Station, 32125 Bio Station Ln, Polson, MT, 59860, USA
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, Geraardsbergen, 9500, Belgium.,Aquatic Ecology, Evolution and Conservation, KULeuven, Charles Deberiotstraat 32, box 2439, Leuven, 3000, Belgium
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Charles B Van Rees
- Flathead Lake Biological Station, 32125 Bio Station Ln, Polson, MT, 59860, USA
| | - Gernot Segelbacher
- Chair of Wildlife Ecology and Management, University Freiburg, Tennenbacher Str. 4, Freiburg, D-79106, Germany
| | - Sean Hoban
- Center for Tree Science, The Morton Arboretum, 4100 Illinois Rt 53, Lisle, 60532, USA
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22
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Lazensky R, Hunter ME, Moraga Amador D, Al-Khedery B, Yu F, Walsh C, Gitzendanner MA, Tripp K, Walsh MT, Denslow ND. Investigating the gene expression profiles of rehabilitated Florida manatees (Trichechus manatus latirostris) following red tide exposure. PLoS One 2020; 15:e0234150. [PMID: 32614830 PMCID: PMC7331979 DOI: 10.1371/journal.pone.0234150] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/19/2020] [Indexed: 01/14/2023] Open
Abstract
To investigate a Florida manatee (Trichechus manatus latirostris) mortality event following a red tide bloom in Southwest Florida, an RNA sequencing experiment was conducted. Gene expression changes in white blood cells were assessed in manatees rescued from a red tide affected area (n = 4) and a control group (n = 7) using RNA sequencing. The genes with the largest fold changes were compared between the two groups to identify molecular pathways related to cellular and disease processes. In total, 591 genes (false discovery rate <0.05) were differentially expressed in the red tide group. Of these, 158 were upregulated and 433 were downregulated. This suggests major changes in white blood cell composition following an exposure to red tide. The most highly upregulated gene, Osteoclast associated 2C immunoglobulin-like receptor (OSCAR), was upregulated 12-fold. This gene is involved in initiating the immune response and maintaining a role in adaptive and innate immunity. The most highly downregulated gene, Piccolo presynaptic cytomatrix protein (PCLO), was downregulated by a factor of 977-fold. This gene is associated with cognitive functioning and neurotransmitter release. Downregulation of this gene in other studies was associated with neuronal loss and neuron synapse dysfunction. Among the cellular pathways that were most affected, immune response, including inflammation, wounds and injuries, cell proliferation, and apoptosis were the most predominant. The pathway with the most differentially expressed genes was the immune response pathway with 98 genes involved, many of them downregulated. Assessing the changes in gene expression associated with red tide exposure enhances our understanding of manatee immune response to the red tide toxins and will aid in the development of red tide biomarkers.
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Affiliation(s)
- Rebecca Lazensky
- Department of Physiological Sciences and Center for Environmental & Human Toxicology, University of Florida, Gainesville, Florida, United States of America
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Margaret E. Hunter
- Wetland and Aquatic Research Center, U. S. Geological Survey, Sirenia Project, Gainesville, Florida, United States of America
| | - David Moraga Amador
- Interdisciplinary Center for Biotechnology Research, Gainesville, Florida, United States of America
| | - Basima Al-Khedery
- Interdisciplinary Center for Biotechnology Research, Gainesville, Florida, United States of America
| | - Fahong Yu
- Interdisciplinary Center for Biotechnology Research, Gainesville, Florida, United States of America
| | - Cathy Walsh
- Mote Marine Laboratory, Sarasota, Florida, United States of America
| | - Matthew A. Gitzendanner
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Katie Tripp
- Save the Manatee Club, Maitland, Florida, United States of America
| | - Michael T. Walsh
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (NDD); (MTW)
| | - Nancy D. Denslow
- Department of Physiological Sciences and Center for Environmental & Human Toxicology, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (NDD); (MTW)
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23
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Orzechowski SCM, Frederick PC, Dorazio RM, Hunter ME. Environmental DNA sampling reveals high occupancy rates of invasive Burmese pythons at wading bird breeding aggregations in the central Everglades. PLoS One 2019; 14:e0213943. [PMID: 30970028 PMCID: PMC6457569 DOI: 10.1371/journal.pone.0213943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/04/2019] [Indexed: 11/18/2022] Open
Abstract
The Burmese python (Python bivittatus) is now established as a breeding population throughout south Florida, USA. However, the extent of the invasion, and the ecological impacts of this novel apex predator on animal communities are incompletely known, in large part because Burmese pythons (hereafter “pythons”) are extremely cryptic and there has been no efficient way to detect them. Pythons are recently confirmed nest predators of long-legged wading bird breeding colonies (orders Ciconiiformes and Pelecaniformes). Pythons can consume large quantities of prey and may not be recognized as predators by wading birds, therefore they could be a particular threat to colonies. To quantify python occupancy rates at tree islands where wading birds breed, we utilized environmental DNA (eDNA) analysis—a genetic tool which detects shed DNA in water samples and provides high detection probabilities. We fitted multi-scale Bayesian occupancy models to test the prediction that pythons occupy islands with wading bird colonies at higher rates compared to representative control islands containing no breeding birds. Our results suggest that pythons are widely distributed across the central Everglades in proximity to active wading bird colonies. In support of our prediction that pythons are attracted to colonies, site-level python eDNA occupancy rates were higher at wading bird colonies (ψ = 0.88, 95% credible interval [0.59–1.00]) than at the control islands (ψ = 0.42 [0.16–0.80]) in April through June (n = 15 colony-control pairs). We found our water temperature proxy (time of day) to be informative of detection probability, in accordance with other studies demonstrating an effect of temperature on eDNA degradation in occupied samples. Individual sample concentrations ranged from 0.26 to 38.29 copies/μL and we generally detected higher concentrations of python eDNA in colony sites. Continued monitoring of wading bird colonies is warranted to determine the effect pythons are having on populations and investigate putative management activities.
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Affiliation(s)
- Sophia C. M. Orzechowski
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Peter C. Frederick
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America
| | - Robert M. Dorazio
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, United States of America
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, United States of America
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24
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Card DC, Perry BW, Adams RH, Schield DR, Young AS, Andrew AL, Jezkova T, Pasquesi GI, Hales NR, Walsh MR, Rochford MR, Mazzotti FJ, Hart KM, Hunter ME, Castoe TA. Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons. Mol Ecol 2018; 27:4744-4757. [DOI: 10.1111/mec.14885] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Daren C. Card
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Blair W. Perry
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Richard H. Adams
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Drew R. Schield
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Acacia S. Young
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Audra L. Andrew
- Department of Biology The University of Texas at Arlington Arlington Texas
| | | | | | - Nicole R. Hales
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Matthew R. Walsh
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Michael R. Rochford
- Fort Lauderdale Research & Education Center University of Florida Fort Lauderdale Florida
| | - Frank J. Mazzotti
- Fort Lauderdale Research & Education Center University of Florida Fort Lauderdale Florida
| | - Kristen M. Hart
- U. S. Geological Survey Wetland and Aquatic Research Center Davie Florida
| | - Margaret E. Hunter
- U. S. Geological Survey Wetland and Aquatic Research Center Gainesville Florida
| | - Todd A. Castoe
- Department of Biology The University of Texas at Arlington Arlington Texas
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25
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Hunter ME, Johnson NA, Smith BJ, Davis MC, Butterfield JSS, Snow RW, Hart KM. Cytonuclear discordance in the Florida Everglades invasive Burmese python ( Python bivittatus) population reveals possible hybridization with the Indian python ( P. molurus). Ecol Evol 2018; 8:9034-9047. [PMID: 30271564 PMCID: PMC6157680 DOI: 10.1002/ece3.4423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 06/08/2018] [Accepted: 06/22/2018] [Indexed: 12/04/2022] Open
Abstract
The invasive Burmese python (Python bivittatus) has been reproducing in the Florida Everglades since the 1980s. These giant constrictor snakes have caused a precipitous decline in small mammal populations in southern Florida following escapes or releases from the commercial pet trade. To better understand the invasion pathway and genetic composition of the population, two mitochondrial (mtDNA) loci across 1,398 base pairs were sequenced on 426 snakes and 22 microsatellites were assessed on 389 snakes. Concatenated mtDNA sequences produced six haplotypes with an average nucleotide and haplotype diversity of π = 0.002 and h = 0.097, respectively. Samples collected in Florida from morphologically identified P. bivittatus snakes were similar to published cytochrome oxidase 1 and cytochrome b sequences from both P. bivittatus and Python molurus and were highly divergent (genetic distances of 5.4% and 4.3%, respectively). The average number of microsatellite alleles and expected heterozygosity were N A = 5.50 and H E = 0.60, respectively. Nuclear Bayesian assignment tests supported two genetically distinct groups and an admixed group, not geographically differentiated. The effective population size (N E = 315.1) was lower than expected for a population this large, but reflected the low genetic diversity overall. The patterns of genetic diversity between mtDNA and microsatellites were disparate, indicating nuclear introgression of separate mtDNA lineages corresponding to cytonuclear discordance. The introgression likely occurred prior to the invasion, but genetic information on the native range and commercial trade is needed for verification. Our finding that the Florida python population is comprised of distinct lineages suggests greater standing variation for adaptation and the potential for broader areas of suitable habitat in the invaded range.
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Affiliation(s)
- Margaret E. Hunter
- U.S. Geological SurveyWetland and Aquatic Research CenterGainesvilleFlorida
| | - Nathan A. Johnson
- U.S. Geological SurveyWetland and Aquatic Research CenterGainesvilleFlorida
| | - Brian J. Smith
- Wetland and Aquatic Research CenterCherokee Nation TechnologiesDavieFlorida
| | - Michelle C. Davis
- U.S. Geological SurveyWetland and Aquatic Research CenterGainesvilleFlorida
| | | | - Ray W. Snow
- U.S. National Park ServiceEverglades National ParkHomesteadFlorida
| | - Kristen M. Hart
- U.S. Geological SurveyWetland and Aquatic Research CenterDavieFlorida
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26
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Ferrante JA, Giles MR, Benzie E, Hunter ME. A novel technique for isolating DNA from Tempus™ blood RNA tubes after RNA isolation. BMC Res Notes 2018; 11:563. [PMID: 30081941 PMCID: PMC6080204 DOI: 10.1186/s13104-018-3671-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/01/2018] [Indexed: 11/10/2022] Open
Abstract
Objective We use Tempus blood RNA tubes (Applied Biosystems) during health assessments of American moose (Alces alces spp.) as a minimally invasive means to obtain RNA. Here we describe a novel protocol to additionally isolate high-quality DNA from the supernatant remaining after the RNA isolation methodology. Metrics used to qualify DNA quality included measuring the concentration, obtaining a DNA integrity number from a genomic DNA ScreenTape assay (Agilent), and running the isolated DNA on an agarose gel. Results Of the 23 samples analyzed, the average DNA concentration was 121 ng/µl (range 4–337 ng/µl) and a genomic DNA ScreenTape assay of seven samples indicated high DNA integrity values for 6 of the 7 samples (range 9.1–9.4 out of 10). Of the DNA sent for genotyping by sequencing, all proved to be of sufficient integrity to yield high-quality next-generation sequence results. We recommend this simple procedure to maximize the yield of both RNA and DNA from blood samples.
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Affiliation(s)
- Jason A Ferrante
- Cherokee Nation Technologies contracted to the U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA.
| | - Michelle R Giles
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Emily Benzie
- University of California-Davis, 1 Shields Ave, Davis, CA, 95616, USA
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
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27
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Breaux B, Hunter ME, Cruz-Schneider MP, Sena L, Bonde RK, Criscitiello MF. The Florida manatee (Trichechus manatus latirostris) T cell receptor loci exhibit V subgroup synteny and chain-specific evolution. Dev Comp Immunol 2018; 85:71-85. [PMID: 29649552 DOI: 10.1016/j.dci.2018.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/06/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
The Florida manatee (Trichechus manatus latirostris) has limited diversity in the immunoglobulin heavy chain. We therefore investigated the antigen receptor loci of the other arm of the adaptive immune system: the T cell receptor. Manatees are the first species from Afrotheria, a basal eutherian superorder, to have an in-depth characterization of all T cell receptor loci. By annotating the genome and expressed transcripts, we found that each chain has distinct features that correlates to their individual functions. The genomic organization also plays a role in modulating sequence conservation between species. There were extensive V subgroup synteny blocks in the TRA and TRB loci between T. m. latirostris and human. Increased genomic locus complexity correlated to increased locus synteny. We also identified evidence for a VHD pseudogene for the first time in a eutherian mammal. These findings emphasize the value of including species within this basal eutherian radiation in comparative studies.
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Affiliation(s)
- Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Margaret E Hunter
- Sirenia Project, Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | | | - Leonardo Sena
- Laboratory of Medical and Human Genetics, Federal University of Pará, Belém, Pará, Brazil.
| | - Robert K Bonde
- Sirenia Project, Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX 77843, USA.
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Hunter ME, Hoban SM, Bruford MW, Segelbacher G, Bernatchez L. Next-generation conservation genetics and biodiversity monitoring. Evol Appl 2018; 11:1029-1034. [PMID: 30026795 PMCID: PMC6050179 DOI: 10.1111/eva.12661] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
This special issue of Evolutionary Applications consists of 10 publications investigating the use of next-generation tools and techniques in population genetic analyses and biodiversity assessment. The special issue stems from a 2016 Next Generation Genetic Monitoring Workshop, hosted by the National Institute for Mathematical and Biological Synthesis (NIMBioS) in Tennessee, USA. The improved accessibility of next-generation sequencing platforms has allowed molecular ecologists to rapidly produce large amounts of data. However, with the increased availability of new genomic markers and mathematical techniques, care is needed in selecting appropriate study designs, interpreting results in light of conservation concerns, and determining appropriate management actions. This special issue identifies key attributes of successful genetic data analyses in biodiversity evaluation and suggests ways to improve analyses and their application in current population and conservation genetics research.
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Affiliation(s)
- Margaret E. Hunter
- U.S. Geological SurveyWetland and Aquatic Research CenterGainesvilleFlorida
| | | | - Michael W. Bruford
- Cardiff School of Biosciences and Sustainable Places InstituteCardiff UniversityCardiffUK
| | | | - Louis Bernatchez
- GIROQDépartement de BiologieUniversité LavalSte‐Foy, QuébecQCCanada
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Breaux BL, Hunter ME, Cruz-Schneider MP, Sena L, Bonde RK, Criscitiello MF. The Florida manatee ( Trichechus manatus latirostris) T cell receptor loci exhibit V segment locus synteny and chain-specific evolution. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.59.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Manatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent order Afrotheria. We have previously described the immunoglobulin heavy chain locus of the Florida manatee (Trichechus manatus latirostris) and found limited antigen receptor diversity in this humoral arm of the adaptive immune system. We therefore investigated the antigen receptor loci of the cellular arm: the T cell receptor. Manatees are the first species from either Afrotheria or Xenarthra, the most basal eutherian taxonomic groups, to have an in-depth characterization of all T cell receptor loci and expressed repertoires. We manually annotated the three TR loci on the T. m. latirostris genomic scaffolds using BLAST and RSSsite, and compared the segments and overall genomic organization to the human TR loci. We identified the human V segment subgroups that are conserved in T. m. latirostris and found that TRADV are most conserved, TRBV are moderately conserved, and TRGV are the least conserved. The V segment order in the TRAD and TRB loci also showed synteny between the two species. The TRAD locus had five V segment subgroup synteny blocks that showed long-range duplications in the T. m. latirostris locus. The TRB locus had three V segment subgroup synteny blocks that showed short-range duplications. The conservation of V segment sequence and order correlated to the locus complexity, emphasizing the role of genomic organization on gene evolution. We also identified evidence for a VHδ pseudogene for the first time in a eutherian mammal. These novel findings underline the value of including species within the basal radiation of eutherian evolution in comparative studies.
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Hunter ME, Meigs-Friend G, Ferrante JA, Takoukam Kamla A, Dorazio RM, Keith-Diagne L, Luna F, Lanyon JM, Reid JP. Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00880] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Breaux B, Deiss TC, Chen PL, Cruz-Schneider MP, Sena L, Hunter ME, Bonde RK, Criscitiello MF. The Florida manatee (Trichechus manatus latirostris) immunoglobulin heavy chain suggests the importance of clan III variable segments in repertoire diversity. Dev Comp Immunol 2017; 72:57-68. [PMID: 28131767 DOI: 10.1016/j.dci.2017.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 10/21/2016] [Revised: 01/23/2017] [Accepted: 01/23/2017] [Indexed: 06/06/2023]
Abstract
Manatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent Afrotheria. Manatee health and resistance to infectious disease is of great concern to conservation groups, but little is known about their immune system. To develop manatee-specific tools for monitoring health, we first must have a general knowledge of how the immunoglobulin heavy (IgH) chain locus is organized and transcriptionally expressed. Using the genomic scaffolds of the Florida manatee (Trichechus manatus latirostris), we characterized the potential IgH segmental diversity and constant region isotypic diversity and performed the first Afrotherian repertoire analysis. The Florida manatee has low V(D)J combinatorial diversity (3744 potential combinations) and few constant region isotypes. They also lack clan III V segments, which may have caused reduced VH segment numbers. However, we found productive somatic hypermutation concentrated in the complementarity determining regions. In conclusion, manatees have limited IGHV clan and combinatorial diversity. This suggests that clan III V segments are essential for maintaining IgH locus diversity.
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Affiliation(s)
- Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Patricia L Chen
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | | | - Leonardo Sena
- Laboratory of Medical and Human Genetics, Federal University of Pará, Belém, Pará, Brazil.
| | - Margaret E Hunter
- Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - Robert K Bonde
- Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX 77843, USA.
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Hunter ME, Dorazio RM, Butterfield JSS, Meigs‐Friend G, Nico LG, Ferrante JA. Detection limits of quantitative and digital
PCR
assays and their influence in presence–absence surveys of environmental
DNA. Mol Ecol Resour 2016; 17:221-229. [DOI: 10.1111/1755-0998.12619] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/31/2016] [Accepted: 09/19/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Margaret E. Hunter
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - Robert M. Dorazio
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - John S. S. Butterfield
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - Gaia Meigs‐Friend
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - Leo G. Nico
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
| | - Jason A. Ferrante
- U.S. Geological Survey Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL 32653 USA
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McCleery RA, Sovie A, Reed RN, Cunningham MW, Hunter ME, Hart KM. Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades. Proc Biol Sci 2015; 282:rspb.2015.0120. [PMID: 25788598 DOI: 10.1098/rspb.2015.0120] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To address the ongoing debate over the impact of invasive species on native terrestrial wildlife, we conducted a large-scale experiment to test the hypothesis that invasive Burmese pythons (Python molurus bivittatus) were a cause of the precipitous decline of mammals in Everglades National Park (ENP). Evidence linking pythons to mammal declines has been indirect and there are reasons to question whether pythons, or any predator, could have caused the precipitous declines seen across a range of mammalian functional groups. Experimentally manipulating marsh rabbits, we found that pythons accounted for 77% of rabbit mortalities within 11 months of their translocation to ENP and that python predation appeared to preclude the persistence of rabbit populations in ENP. On control sites, outside of the park, no rabbits were killed by pythons and 71% of attributable marsh rabbit mortalities were classified as mammal predations. Burmese pythons pose a serious threat to the faunal communities and ecological functioning of the Greater Everglades Ecosystem, which will probably spread as python populations expand their range.
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Affiliation(s)
- Robert A McCleery
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - Adia Sovie
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - Robert N Reed
- United States Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - Mark W Cunningham
- Florida Fish and Wildlife Conservation Commission, Gainesville, FL, USA
| | - Margaret E Hunter
- United States Geological Survey, Southeast Ecological Science Center, Gainesville, FL, USA
| | - Kristen M Hart
- United States Geological Survey, Southeast Ecological Science Center, Davie, FL, USA
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Abstract
Statistical methods for the analysis and design of experiments using digital PCR (dPCR) have received only limited attention and have been misused in many instances. To address this issue and to provide a more general approach to the analysis of dPCR data, we describe a class of statistical models for the analysis and design of experiments that require quantification of nucleic acids. These models are mathematically equivalent to generalized linear models of binomial responses that include a complementary, log-log link function and an offset that is dependent on the dPCR partition volume. These models are both versatile and easy to fit using conventional statistical software. Covariates can be used to specify different sources of variation in nucleic acid concentration, and a model's parameters can be used to quantify the effects of these covariates. For purposes of illustration, we analyzed dPCR data from different types of experiments, including serial dilution, evaluation of copy number variation, and quantification of gene expression. We also showed how these models can be used to help design dPCR experiments, as in selection of sample sizes needed to achieve desired levels of precision in estimates of nucleic acid concentration or to detect differences in concentration among treatments with prescribed levels of statistical power.
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Affiliation(s)
- Robert M Dorazio
- Southeast Ecological Science Center, U.S. Geological Survey , 7920 NW 71st Street, Gainesville, Florida 32653, United States
| | - Margaret E Hunter
- Southeast Ecological Science Center, U.S. Geological Survey , 7920 NW 71st Street, Gainesville, Florida 32653, United States
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Hunter ME, Oyler-McCance SJ, Dorazio RM, Fike JA, Smith BJ, Hunter CT, Reed RN, Hart KM. Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive burmese pythons. PLoS One 2015; 10:e0121655. [PMID: 25874630 PMCID: PMC4398459 DOI: 10.1371/journal.pone.0121655] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/12/2015] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.
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Affiliation(s)
- Margaret E. Hunter
- US Geological Survey, Southeast Ecological Science Center, Gainesville, Florida, United States of America
| | - Sara J. Oyler-McCance
- US Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Robert M. Dorazio
- US Geological Survey, Southeast Ecological Science Center, Gainesville, Florida, United States of America
| | - Jennifer A. Fike
- US Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Brian J. Smith
- University of Florida, Department of Wildlife Ecology and Conservation, Gainesville, Florida, United States of America
| | - Charles T. Hunter
- University of Florida, Institute of Food and Agricultural Sciences, Horticultural Sciences, Gainesville, Florida, United States of America
| | - Robert N. Reed
- US Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Kristen M. Hart
- US Geological Survey, Southeast Ecological Science Center, Davie, Florida, United States of America
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Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, Gilbert MTP, Gibbs RA. Convergent evolution of the genomes of marine mammals. Nat Genet 2015; 47:272-5. [PMID: 25621460 DOI: 10.1038/ng.3198] [Citation(s) in RCA: 262] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 12/29/2014] [Indexed: 12/13/2022]
Abstract
Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.
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Affiliation(s)
- Andrew D Foote
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. [2] Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Yue Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Gregg W C Thomas
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA
| | - Tomáš Vinař
- Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
| | - Jessica Alföldi
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Jixin Deng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Margaret E Hunter
- Sirenia Project, Southeast Ecological Science Center, US Geological Survey, Gainesville, Florida, USA
| | - Vandita Joshi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Kerstin Lindblad-Toh
- 1] Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Annalaura Mancia
- 1] Marine Biomedicine and Environmental Science Center, Medical University of South Carolina, Charleston, South Carolina, USA. [2] Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Rasmus Nielsen
- Center for Theoretical Evolutionary Genomics, University of California, Berkeley, Berkeley, California, USA
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Nagarjun Vijay
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- 1] Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. [2] Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew W Hahn
- 1] School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA. [2] Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - M Thomas P Gilbert
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
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Hunter ME, Nico LG. Genetic analysis of invasive Asian Black Carp (Mylopharyngodon piceus) in the Mississippi River Basin: evidence for multiple introductions. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0708-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Mahon AR, Jerde CL, Galaska M, Bergner JL, Chadderton WL, Lodge DM, Hunter ME, Nico LG. Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PLoS One 2013; 8:e58316. [PMID: 23472178 PMCID: PMC3589332 DOI: 10.1371/journal.pone.0058316] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/01/2013] [Indexed: 11/19/2022] Open
Abstract
In many North American rivers, populations of multiple species of non-native cyprinid fishes are present, including black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), and goldfish (Carassius auratus). All six of these species are found in the Mississippi River basin and tracking their invasion has proven difficult, particularly where abundance is low. Knowledge of the location of the invasion front is valuable to natural resource managers because future ecological and economic damages can be most effectively prevented when populations are low. To test the accuracy of environmental DNA (eDNA) as an early indicator of species occurrence and relative abundance, we applied eDNA technology to the six non-native cyprinid species putatively present in a 2.6 river mile stretch of the Chicago (IL, USA) canal system that was subsequently treated with piscicide. The proportion of water samples yielding positive detections increased with relative abundance of the six species, as indicated by the number of carcasses recovered after poisoning. New markers for black carp, grass carp, and a common carp/goldfish are reported and details of the marker testing to ensure specificity are provided.
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Affiliation(s)
- Andrew R Mahon
- Department of Biology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, Michigan, USA.
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Hunter ME, Hart KM. Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese Python-Python molurus bivittatus-Management. Int J Mol Sci 2013; 14:4793-804. [PMID: 23449030 PMCID: PMC3634432 DOI: 10.3390/ijms14034793] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/06/2013] [Accepted: 02/13/2013] [Indexed: 01/29/2023] Open
Abstract
Invasive species represent an increasing threat to native ecosystems, harming indigenous taxa through predation, habitat modification, cross-species hybridization and alteration of ecosystem processes. Additionally, high economic costs are associated with environmental damage, restoration and control measures. The Burmese python, Python molurus bivittatus, is one of the most notable invasive species in the US, due to the threat it poses to imperiled species and the Greater Everglades ecosystem. To address population structure and relatedness, next generation sequencing was used to rapidly produce species-specific microsatellite loci. The Roche 454 GS-FLX Titanium platform provided 6616 di-, tri- and tetra-nucleotide repeats in 117,516 sequences. Using stringent criteria, 24 of 26 selected tri- and tetra-nucleotide loci were polymerase chain reaction (PCR) amplified and 18 were polymorphic. An additional six cross-species loci were amplified, and the resulting 24 loci were incorporated into eight PCR multiplexes. Multi-locus genotypes yielded an average of 61% (39%–77%) heterozygosity and 3.7 (2–6) alleles per locus. Population-level studies using the developed microsatellites will track the invasion front and monitor population-suppression dynamics. Additionally, cross-species amplification was detected in the invasive Ball, P. regius, and Northern African python, P. sebae. These markers can be used to address the hybridization potential of Burmese pythons and the larger, more aggressive P. sebae.
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Affiliation(s)
- Margaret E. Hunter
- U.S. Geological Survey, Southeast Ecological Science Center, 7920 NW 71st Street, Gainesville, FL 32653, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-352-264-3484; Fax: +1-352-374-8080
| | - Kristen M. Hart
- U.S. Geological Survey, Southeast Ecological Science Center, 3205 College Avenue, Davie, FL 33314, USA; E-Mail:
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Tucker KP, Hunter ME, Bonde RK, Austin JD, Clark AM, Beck CA, McGuire PM, Oli MK. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation. J Mammal 2012. [DOI: 10.1644/12-mamm-a-048.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Hunter ME, Mignucci-Giannoni AA, Tucker KP, King TL, Bonde RK, Gray BA, McGuire PM. Puerto Rico and Florida manatees represent genetically distinct groups. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0414-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Wood SD, Hunter ME, Lescault TL. A comparison of expectations for selected physician and managed health care services between Medicare-eligible and the next Medicare-eligible generation. Am J Med Qual 1998; 13:111-20. [PMID: 9735473 DOI: 10.1177/106286069801300302] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The year 1998 marks the beginning of a major turning point in the composition of the Medicare-eligible population, making the next few years a significant watershed for those concerned with the provision of health care to seniors. For approximately the next 12 years, those seniors entering the Medicare-eligible health care market, the so-called Swing generation, will have different characteristics and expectations from those generations that precede or follow it. Through standard survey methods, this study explores and compares the differences in selected health services expectations between the current generation of Medicare-eligible seniors and the next Medicare-eligible generation. Significant differences were found between the two groups on variables related to wait time, medical preparedness, communication, and expectations of managed care coverage. The authors discuss the implications of the findings for health care service providers and managed care organizations.
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Affiliation(s)
- S D Wood
- Arizona State University, Scottsdale 85251, USA
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Abstract
OBJECTIVE The study evaluated the effects of using the principles of total quality management (TQM) to reduce aggressive incidents in the dining rooms at a state forensic hospital. METHODS A ten-member, multidisciplinary team, which included a patient representative and a private-sector mentor, used the TQM FADE method (focus, analyze, develop, and execute) to address the problem. The team analyzed violent mealtime incidents, reviewed mealtime policies and procedures, and conducted a patient survey. Five recommendations were made: substitute plastic utensils for silverware, play music selected by the hospital's music therapists, allow patients at the highest privilege levels to leave the dining room after eating, open the main courtyard and gym during meals, and train food service workers in therapeutic communication. RESULTS One year after implementation of the recommendations, aggressive incidents in the dining rooms were reduced by 40 percent, assaults using silverware were eliminated, and a total of 70 nursing staff hours a day were saved by eliminating silverware control procedures in the dining rooms. The milieu in the dining rooms has been improved by the addition of music and more flexible procedures. CONCLUSIONS TQM techniques can be effectively applied in public-sector institutions to analyze and solve problems such as mealtime violence.
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Affiliation(s)
- M E Hunter
- Atascadero State Hospital, California 93423, USA
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Abstract
1. Violence toward healthcare workers, particularly psychiatric nursing staff, has only recently been identified as a workplace health hazard. An occupational health perspective underscores the need for proactive monitoring and heightens incentives for prevention through the introduction of external regulation. 2. Nursing staff injury rates from violence alone are higher than injuries seen in industries traditionally considered high risk such as mining, lumber, and heavy construction. Nursing employment categories at particular risk include psychiatric technicians, male staff, and on-unit supervisory personnel. 3. It is exceedingly difficult to accurately measure the extent of violence in a given facility and injury rates are known to underestimate the actual number of violent events that occur. Nursing staff, labor organizations, and managers must work toward more reliable monitoring and risk prevention programs.
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Affiliation(s)
- C C Love
- Atascadero State Hospital, California 93423-7001, USA
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Abstract
OBJECTIVE The purpose of this study was to describe types of weapons and weapon use patterns among inpatients at a state forensic hospital to assist staff in evaluating the weapon-screening program. METHODS Data for a five-year period were drawn from special incident reports, hospital police crime reports, and supervisory logs to document weapon use in a 973-bed, all-male maximum security forensic hospital. Weapons were categorized as weapons of opportunity (objects available at the site of the attack) and manufactured or contraband weapons. Repeat use of weapons by a patient was documented. RESULTS Weapon use was relatively rare. During the five-year period less than 3 percent of inpatients used weapons, and less than 3 percent of violent incidents involved weapon use. Available objects were used in most attacks. Only 17 patients were responsible for a fourth of all weapons assaults, and these patients repeatedly used the same types of available objects, particularly furniture. Staff and patients were targeted equally in the weapon assaults. CONCLUSIONS Weapon-screening programs may prevent weapon carrying but not weapon use. Detailed histories of weapon use should be part of each patient's assessment and should be made known to staff.
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Affiliation(s)
- M E Hunter
- Atascadero State Hospital, California 93423
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Hunter ME. Could it be another disorder? Can Fam Physician 1993; 39:1726. [PMID: 8374357 PMCID: PMC2379808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Hunter ME. Dissociative disorders: need for Vancouver unit. CMAJ 1989; 141:874-5. [PMID: 2804840 PMCID: PMC1451432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Hunter ME. The irritable bowel syndrome. CMAJ 1988; 139:15. [PMID: 3383036 PMCID: PMC1267976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Hunter ME. All passengers breathe in the air. Can Fam Physician 1986; 32:241. [PMID: 21267250 PMCID: PMC2328117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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