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Sheard JK, Adriaens T, Bowler DE, Büermann A, Callaghan CT, Camprasse ECM, Chowdhury S, Engel T, Finch EA, von Gönner J, Hsing PY, Mikula P, Rachel Oh RY, Peters B, Phartyal SS, Pocock MJO, Wäldchen J, Bonn A. Emerging technologies in citizen science and potential for insect monitoring. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230106. [PMID: 38705194 PMCID: PMC11070260 DOI: 10.1098/rstb.2023.0106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
Emerging technologies are increasingly employed in environmental citizen science projects. This integration offers benefits and opportunities for scientists and participants alike. Citizen science can support large-scale, long-term monitoring of species occurrences, behaviour and interactions. At the same time, technologies can foster participant engagement, regardless of pre-existing taxonomic expertise or experience, and permit new types of data to be collected. Yet, technologies may also create challenges by potentially increasing financial costs, necessitating technological expertise or demanding training of participants. Technology could also reduce people's direct involvement and engagement with nature. In this perspective, we discuss how current technologies have spurred an increase in citizen science projects and how the implementation of emerging technologies in citizen science may enhance scientific impact and public engagement. We show how technology can act as (i) a facilitator of current citizen science and monitoring efforts, (ii) an enabler of new research opportunities, and (iii) a transformer of science, policy and public participation, but could also become (iv) an inhibitor of participation, equity and scientific rigour. Technology is developing fast and promises to provide many exciting opportunities for citizen science and insect monitoring, but while we seize these opportunities, we must remain vigilant against potential risks. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Julie Koch Sheard
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Tim Adriaens
- Research Institute for Nature and Forest (INBO), Havenlaan 88 bus 73, 1000 Brussels, Belgium
| | - Diana E. Bowler
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Andrea Büermann
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Corey T. Callaghan
- Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, FL 33314, USA
| | - Elodie C. M. Camprasse
- School of Life and Environmental Sciences, Deakin University, Melbourne Burwood Campus, 221 Burwood Highway, Burwood, Victoria 3125, Australia
| | - Shawan Chowdhury
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Thore Engel
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Elizabeth A. Finch
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Julia von Gönner
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Pen-Yuan Hsing
- Faculty of Life Sciences, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK
| | - Peter Mikula
- TUM School of Life Sciences, Ecoclimatology, Technical University of Munich, Hans-Carl-von-Carlowitz-Platz 2, 85354 Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstraße 2a, 85748 Garching, Germany
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic
| | - Rui Ying Rachel Oh
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Birte Peters
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Shyam S. Phartyal
- School of Ecology and Environment Studies, Nalanda University, Rajgir 803116, India
| | | | - Jana Wäldchen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| | - Aletta Bonn
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
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Li Y, Devenish C, Tosa MI, Luo M, Bell DM, Lesmeister DB, Greenfield P, Pichler M, Levi T, Yu DW. Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230123. [PMID: 38705177 PMCID: PMC11070265 DOI: 10.1098/rstb.2023.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/31/2024] [Indexed: 05/07/2024] Open
Abstract
Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km2 temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Yuanheng Li
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Faculty of Biology, University of Duisburg-Essen, Essen 45141, Germany
| | - Christian Devenish
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Marie I. Tosa
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Mingjie Luo
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, People’s Republic of China
| | - David M. Bell
- Pacific Northwest Research Station, U.S. Department of Agriculture Forest Service, Corvallis, OR 97331, USA
| | - Damon B. Lesmeister
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
- Pacific Northwest Research Station, U.S. Department of Agriculture Forest Service, Corvallis, OR 97331, USA
| | - Paul Greenfield
- CSIRO Energy, Lindfield, New South Wales, Australia
- School of Biological Sciences, Macquarie University, Sydney, Australia
| | | | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Douglas W. Yu
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan 650223, People’s Republic of China
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3
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Bell KL, Campos M, Hoffmann BD, Encinas-Viso F, Hunter GC, Webber BL. Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171810. [PMID: 38513869 DOI: 10.1016/j.scitotenv.2024.171810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.
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Affiliation(s)
- Karen L Bell
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Mariana Campos
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Francisco Encinas-Viso
- CSIRO Centre of Australian National Biodiversity Research, Black Mountain, Australian Capital Territory 2601, Australia
| | - Gavin C Hunter
- CSIRO Health & Biosecurity, Black Mountain, Australian Capital Territory 2601, Australia
| | - Bruce L Webber
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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Newton JP, Nevill P, Bateman PW, Campbell MA, Allentoft ME. Spider webs capture environmental DNA from terrestrial vertebrates. iScience 2024; 27:108904. [PMID: 38533454 PMCID: PMC10964257 DOI: 10.1016/j.isci.2024.108904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 03/28/2024] Open
Abstract
Environmental DNA holds significant promise as a non-invasive tool for tracking terrestrial biodiversity. However, in non-homogenous terrestrial environments, the continual exploration of new substrates is crucial. Here we test the hypothesis that spider webs can act as passive biofilters, capturing eDNA from vertebrates present in the local environment. Using a metabarcoding approach, we detected vertebrate eDNA from all analyzed spider webs (N = 49). Spider webs obtained from an Australian woodland locality yielded vertebrate eDNA from 32 different species, including native mammals and birds. In contrast, webs from Perth Zoo, less than 50 km away, yielded eDNA from 61 different vertebrates and produced a highly distinct species composition, largely reflecting exotic species hosted in the zoo. We show that higher animal biomass and proximity to animal enclosures increased eDNA detection probability in the zoo. Our results indicate a tremendous potential for using spider webs as a cost-effective means to monitor terrestrial vertebrates.
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Affiliation(s)
- Joshua P. Newton
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Philip W. Bateman
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Matthew A. Campbell
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Morten E. Allentoft
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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5
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Dyson K, Nicolau AP, Tenneson K, Francesconi W, Daniels A, Andrich G, Caldas B, Castaño S, de Campos N, Dilger J, Guidotti V, Jaques I, McCullough IM, McDevitt AD, Molina L, Nekorchuk DM, Newberry T, Pereira CL, Perez J, Richards-Dimitrie T, Rivera O, Rodriguez B, Sales N, Tello J, Wespestad C, Zutta B, Saah D. Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon. PLoS One 2024; 19:e0289437. [PMID: 38354171 PMCID: PMC10866516 DOI: 10.1371/journal.pone.0289437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/01/2023] [Indexed: 02/16/2024] Open
Abstract
Monitoring is essential to ensure that environmental goals are being achieved, including those of sustainable agriculture. Growing interest in environmental monitoring provides an opportunity to improve monitoring practices. Approaches that directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing and the site-specific community composition from environmental DNA (eDNA) can provide timely, relevant results for parties interested in the success of sustainable agricultural practices. To ensure that the measured impacts are due to the environmental projects and not exogenous factors, sites where projects have been implemented should be benchmarked against counterfactuals (no project) and control (natural habitat) sites. Results can then be used to calculate diverse sets of indicators customized to monitor different projects. Here, we report on our experience developing and applying one such approach to assess the impact of shaded cocoa projects implemented by the Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA) near São Félix do Xingu, in Pará, Brazil. We used the Continuous Degradation Detection (CODED) and LandTrendr algorithms to create a remote sensing-based assessment of forest disturbance and regeneration, estimate carbon sequestration, and changes in essential habitats. We coupled these remote sensing methods with eDNA analyses using arthropod-targeted primers by collecting soil samples from intervention and counterfactual pasture field sites and a control secondary forest. We used a custom set of indicators from the pilot application of a coupled monitoring framework called TerraBio. Our results suggest that, due to IMAFLORA's shaded cocoa projects, over 400 acres were restored in the intervention area and the community composition of arthropods in shaded cocoa is closer to second-growth forests than that of pastures. In reviewing the coupled approach, we found multiple aspects worked well, and we conclude by presenting multiple lessons learned.
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Affiliation(s)
- Karen Dyson
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Andréa P. Nicolau
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Karis Tenneson
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Wendy Francesconi
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Amy Daniels
- United States Agency for International Development (USAID), Washington, DC, United States of America
| | - Giulia Andrich
- Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA), Piracicaba, Brazil
| | - Bernardo Caldas
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Silvia Castaño
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Nathanael de Campos
- Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA), Piracicaba, Brazil
| | - John Dilger
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Vinicius Guidotti
- Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA), Piracicaba, Brazil
| | - Iara Jaques
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Ian M. McCullough
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | | | - Luis Molina
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Dawn M. Nekorchuk
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Tom Newberry
- University of Salford, Salford, Manchester, United Kingdom
| | | | - Jorge Perez
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | | | - Ovidio Rivera
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Beatriz Rodriguez
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Naiara Sales
- University of Salford, Salford, Manchester, United Kingdom
| | - Jhon Tello
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Crystal Wespestad
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Brian Zutta
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - David Saah
- University of San Francisco, San Francisco, California, United States of America
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6
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Saranholi BH, Rodriguez-Castro KG, Carvalho CS, Chahad-Ehlers S, Gestich CC, Andrade SCS, Freitas PD, Galetti PM. Comparing iDNA from mosquitoes and flies to survey mammals in a semi-controlled Neotropical area. Mol Ecol Resour 2023; 23:1790-1799. [PMID: 37535317 DOI: 10.1111/1755-0998.13851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 06/10/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023]
Abstract
Ingested-derived DNA (iDNA) from insects represents a powerful tool for assessing vertebrate diversity because insects are easy to sample, have a diverse diet and are widely distributed. Because of these advantages, the use of iDNA for detecting mammals has gained increasing attention. Here we aimed to compare the effectiveness of mosquitoes and flies to detect mammals with a small sampling effort in a semi-controlled area, a zoo that houses native and non-native species. We compared mosquitoes and flies regarding the number of mammal species detected, the amount of mammal sequence reads recovered, and the flight distance range for detecting mammals. We also verified if the combination of two mini-barcodes (12SrRNA and 16SrRNA) would perform better than either mini-barcode alone to inform local mammal biodiversity from iDNA. To capture mosquitoes and flies, we distributed insect traps in eight sampling points during 5 days. We identified 43 Operational Taxonomic Units from 10 orders, from the iDNA of 17 mosquitoes and 46 flies. There was no difference in the number of species recovered per individual insect between mosquitoes and flies, but the number of flies captured was higher, resulting in more mammal species recovered by flies. Eight species were recorded exclusively by mosquitoes and 20 by flies, suggesting that using both samplers would allow a more comprehensive screening of the biodiversity. The maximum distance recorded was 337 m for flies and 289 m for mosquitoes, but the average range distance did not differ between insect groups. Our assay proved to be efficient for mammal detection, considering the high number of species detected with a reduced sampling effort.
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Affiliation(s)
- Bruno H Saranholi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Karen G Rodriguez-Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Facultad Ciencias Básicas e Ingeniería, Universidad de los Llanos, Villavicencio, Colombia
| | - Carolina S Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Instituto Tecnológico Vale, Belém, Brazil
| | - Samira Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Carla C Gestich
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Sónia C S Andrade
- Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia D Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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7
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Zhang S, Zhao J, Yao M. Urban landscape-level biodiversity assessments of aquatic and terrestrial vertebrates by environmental DNA metabarcoding. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 340:117971. [PMID: 37119629 DOI: 10.1016/j.jenvman.2023.117971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 05/12/2023]
Abstract
Globally, expansive urbanization profoundly alters natural habitats and the associated biota. Monitoring biodiversity in cities can provide essential information for conservation management, but the complexity of urban landscapes poses serious challenges to conventional observational and capture-based surveys. Here we assessed pan-vertebrate biodiversity, including both aquatic and terrestrial taxa, using environmental DNA (eDNA) sampled from 109 water sites across Beijing, China. Using eDNA metabarcoding with a single primer set (Tele02), we detected 126 vertebrate species, including 73 fish, 39 birds, 11 mammals, and 3 reptiles belonging to 91 genera, 46 families, and 22 orders. The probability of detection from eDNA varied substantially among species and was related to their lifestyle, as shown by the greater detectability of fish compared to that of terrestrial and arboreal (birds and mammals) groups, as well as the greater detectability of water birds compared to that of forest birds (Wilcoxon rank-sum test p = 0.007). Furthermore, the eDNA detection probabilities across all vertebrates (Wilcoxon rank-sum test p = 0.009), as well as for birds (p < 0.001), were higher at lentic sites in comparison with lotic sites. Also, the detected biodiversity was positively correlated with lentic waterbody size for fish (Spearman p = 0.012), but not for other groups. Our results demonstrate the capacity of eDNA metabarcoding to efficiently surveil diverse vertebrate communities across an extensive spatial scale in heterogenous urban landscapes. With further methodological development and optimization, the eDNA approach has great potential for non-invasive, efficient, economic, and timely assessments of biodiversity responses to urbanization, thus guiding city ecosystem conservation management.
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Affiliation(s)
- Shan Zhang
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing, 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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8
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Reji Chacko M, Altermatt F, Fopp F, Guisan A, Keggin T, Lyet A, Rey PL, Richards E, Valentini A, Waldock C, Pellissier L. Catchment-based sampling of river eDNA integrates terrestrial and aquatic biodiversity of alpine landscapes. Oecologia 2023; 202:699-713. [PMID: 37558733 PMCID: PMC10475001 DOI: 10.1007/s00442-023-05428-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 07/22/2023] [Indexed: 08/11/2023]
Abstract
Monitoring of terrestrial and aquatic species assemblages at large spatial scales based on environmental DNA (eDNA) has the potential to enable evidence-based environmental policymaking. The spatial coverage of eDNA-based studies varies substantially, and the ability of eDNA metabarcoding to capture regional biodiversity remains to be assessed; thus, questions about best practices in the sampling design of entire landscapes remain open. We tested the extent to which eDNA sampling can capture the diversity of a region with highly heterogeneous habitat patches across a wide elevation gradient for five days through multiple hydrological catchments of the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at five sites per catchment for a total volume of 1800 L. Using an eDNA metabarcoding approach focusing on vertebrates and plants, we detected 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 families across ten catchments. For mammals, fishes, amphibians and plants, the detected taxa covered some of the most common species in the region according to long-term records while including a few more rare taxa. We found marked turnover among samples from distinct elevational classes indicating that the biological signal in alpine rivers remains relatively localised and is not aggregated downstream. Accordingly, species compositions differed between catchments and correlated with catchment-level forest and grassland cover. Biomonitoring schemes based on capturing eDNA across rivers within biologically integrated catchments may pave the way toward a spatially comprehensive estimation of biodiversity.
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Affiliation(s)
- Merin Reji Chacko
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland.
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Fabian Fopp
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Geopolis, Lausanne, Switzerland
| | - Thomas Keggin
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Arnaud Lyet
- World Wildlife Fund, Wildlife Conservation Team, Washington, DC, USA
| | - Pierre-Louis Rey
- Institute of Earth Surface Dynamics, University of Lausanne, Geopolis, Lausanne, Switzerland
| | - Eilísh Richards
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | | | - Conor Waldock
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Loïc Pellissier
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
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9
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Vinitpornsawan S, Fuller TK. A Camera-Trap Survey of Mammals in Thung Yai Naresuan (East) Wildlife Sanctuary in Western Thailand. Animals (Basel) 2023; 13:ani13081286. [PMID: 37106849 PMCID: PMC10135077 DOI: 10.3390/ani13081286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The Thung Yai Naresuan (East) Wildlife Sanctuary (TYNE), in the core area of the Western Forest Complex of Thailand, harbors a diverse assemblage of wildlife, and the region has become globally significant for mammal conservation. From April 2010 to January 2012, 106 camera traps were set, and, in 1817 trap-nights, registered 1821 independent records of 32 mammal species. Of the 17 IUCN-listed (from Near Threatened to Critically Endangered) mammal species recorded, 5 species listed as endangered or critically endangered included the Asiatic elephant (Elephas maximus), tiger (Panthera tigris), Malayan tapir (Tapirus indicus), dhole (Cuon alpinus), and Sunda pangolin (Manis javanica). The northern red muntjac (Muntiacus vaginalis), large Indian civet (Viverra zibetha), Malayan porcupine (Hystrix brachyuran), and sambar deer (Cervus unicolor) were the most frequently recorded species (10-22 photos/100 trap-nights), representing 62% of all independent records, while the golden jackal (Canis aureus), clouded leopard (Neofelis nebulosa), marbled cat (Pardofelis marmorata), and Sunda pangolin were the least photographed (<0.1/100 trap-nights). Species accumulation curves indicated that the number of camera trap locations needed to record 90% of taxa recorded varied from 26 sites for herbivores to 67 sites for all mammals. TYNE holds a rich community of mammals, but some differences in photo-rates from an adjacent sanctuary and comparisons with other research on local mammals suggest that some species are rare and some are missed because of the limitations of our technique. We also conclude that the management and conservation plan, which involves the exclusion of human activities from some protected areas and strict protection efforts in the sanctuaries, is still suitable for providing key habitats for endangered wildlife populations, and that augmented and regular survey efforts will help in this endeavor.
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Affiliation(s)
- Supagit Vinitpornsawan
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA
- Wildlife Conservation Office, National Parks, Wildlife and Plant Conservation Department, Bangkok 10900, Thailand
| | - Todd K Fuller
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA
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10
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Croose E, Hanniffy R, Harrington A, Põdra M, Gómez A, Bolton PL, Lavin JV, Browett SS, Pinedo J, Lacanal D, Galdos I, Ugarte J, Torre A, Wright P, MacPherson J, McDevitt AD, Carter SP, Harrington LA. Mink on the brink: comparing survey methods for detecting a critically endangered carnivore, the European mink Mustela lutreola. EUR J WILDLIFE RES 2023. [DOI: 10.1007/s10344-023-01657-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
AbstractMonitoring rare and elusive species is critical in guiding appropriate conservation management measures. Mammalian carnivores are challenging to monitor directly, due to their generally nocturnal and solitary lifestyle, and relatively large home ranges. The European mink Mustela lutreola is a critically endangered, small, semi-aquatic carnivore and is one of the most threatened mammal species in Europe. In northern Spain, the European mink population is monitored regionally using different methods and approaches, making assessment of national population status difficult. There is an urgent need to 1) assess the efficacy of survey methods and 2) identify a standard monitoring methodology that can be deployed rapidly and inexpensively over large areas of the mink’s range. We deployed four methods—camera trapping, hair tubes, live trapping, and environmental DNA (eDNA) from water samples—to compare the probability of detecting European mink when present at 25 sampling sites within five 10 × 10 km2, and the economic cost and time required for each method. All four methods successfully detected European mink but the probability of detection varied by method. Camera trapping and hair tubes had the highest probability of detection; however, eDNA and live trapping detected mink in one 10 × 10 km2 where the latter two methods did not. For future European mink monitoring programs, we recommend a combination of at least two methods and suggest that camera traps or hair tubes are combined with live trapping or eDNA (depending on the scale and aims of the study), to gather critical information on distribution, occupancy and conservation status.
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11
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Allen MC, Kwait R, Vastano A, Kisurin A, Zoccolo I, Jaffe BD, Angle JC, Maslo B, Lockwood JL. Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals. Sci Rep 2023; 13:180. [PMID: 36604526 PMCID: PMC9814459 DOI: 10.1038/s41598-023-27512-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Environmental DNA (eDNA) approaches to monitoring biodiversity in terrestrial environments have largely focused on sampling water bodies, potentially limiting the geographic and taxonomic scope of eDNA investigations. We assessed the performance of two strictly terrestrial eDNA sampling approaches to detect arboreal mammals, a guild with many threatened and poorly studied taxa worldwide, within two central New Jersey (USA) woodlands. We evaluated species detected with metabarcoding using two eDNA collection methods (tree bark vs. soil sampling), and compared the performance of two detection methods (qPCR vs. metabarcoding) within a single species. Our survey, which included 94 sampling events at 21 trees, detected 16 species of mammals, representing over 60% of the diversity expected in the area. More DNA was found for the 8 arboreal versus 8 non-arboreal species detected (mean: 2466 vs. 289 reads/sample). Soil samples revealed a generally similar composition, but a lower diversity, of mammal species. Detection rates for big brown bat were 3.4 × higher for qPCR over metabarcoding, illustrating the enhanced sensitivity of single-species approaches. Our results suggest that sampling eDNA from on and around trees could serve as a useful new monitoring tool for cryptic arboreal mammal communities globally.
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Affiliation(s)
- Michael C. Allen
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Robert Kwait
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Anthony Vastano
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Alex Kisurin
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Isabelle Zoccolo
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | | | - Jordan C. Angle
- grid.421234.20000 0004 1112 1641ExxonMobil Upstream Research Company, Spring, TX USA
| | - Brooke Maslo
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Julie L. Lockwood
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
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12
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Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
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13
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Proctor MF, Garshelis DL, Thatte P, Steinmetz R, Crudge B, McLellan BN, McShea WJ, Ngoprasert D, Nawaz MA, Te Wong S, Sharma S, Fuller AK, Dharaiya N, Pigeon KE, Fredriksson G, Wang D, Li S, Hwang MH. Review of field methods for monitoring Asian bears. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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14
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Farrell JA, Whitmore L, Mashkour N, Rollinson Ramia DR, Thomas RS, Eastman CB, Burkhalter B, Yetsko K, Mott C, Wood L, Zirkelbach B, Meers L, Kleinsasser P, Stock S, Libert E, Herren R, Eastman S, Crowder W, Bovery C, Anderson D, Godfrey D, Condron N, Duffy DJ. Detection and population genomics of sea turtle species via non-invasive environmental DNA analysis of nesting beach sand tracks and oceanic water. Mol Ecol Resour 2022; 22:2471-2493. [PMID: 35377560 DOI: 10.1111/1755-0998.13617] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/12/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022]
Abstract
Elusive aquatic wildlife, such as endangered sea turtles, are difficult to monitor and conserve. As novel molecular and genetic technologies develop, it is possible to adapt and optimize them for wildlife conservation. One such technology is environmental (e)DNA - the detection of DNA shed from organisms into their surrounding environments. We developed species-specific green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtle probe-based qPCR assays, which can detect and quantify sea turtle eDNA in controlled (captive tank water and sand samples) and free ranging (oceanic water samples and nesting beach sand) settings. eDNA detection complemented traditional in-water sea turtle monitoring by enabling detection even when turtles were not visually observed. Furthermore, we report that high throughput shotgun sequencing of eDNA sand samples enabled sea turtle population genetic studies and pathogen monitoring, demonstrating that non-invasive eDNA techniques are viable and efficient alternatives to biological sampling (e.g. biopsies and blood draws). Genetic information was obtained from sand many hours after nesting events, without having to observe or interact with the target individual. This greatly reduces the sampling stress experienced by nesting mothers and emerging hatchlings, and avoids sacrificing viable eggs for genetic analysis. The detection of pathogens from sand indicates significant potential for increased wildlife disease monitoring capacity and viral variant surveillance. Together, these results demonstrate the potential of eDNA approaches to ultimately help understand and conserve threatened species such as sea turtles.
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Affiliation(s)
- Jessica A Farrell
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Liam Whitmore
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Narges Mashkour
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Devon R Rollinson Ramia
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Rachel S Thomas
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Catherine B Eastman
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Brooke Burkhalter
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Kelsey Yetsko
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, Florida International University, Miami, FL, 33181, USA
| | - Cody Mott
- Inwater Research Group Inc, Jensen Beach, FL, 34957, USA
| | - Larry Wood
- Florida Hawksbill Project, National Save The Sea Turtle Foundation, Ft. Lauderdale, FL, 33308, USA
| | - Bette Zirkelbach
- The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Lucas Meers
- Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - Pat Kleinsasser
- Crescent Beach Turtle Patrol, Crescent Beach, FL, 32080, USA
| | - Sharon Stock
- Flagler Turtle Patrol, Marineland Beach, FL, 32080, USA
| | | | | | - Scott Eastman
- Florida Department of Environmental Protection, St Augustine, FL, 32080, USA
| | | | | | | | - David Godfrey
- The Sea Turtle Conservancy, Gainesville, FL, 32609, USA
| | - Nancy Condron
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - David J Duffy
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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15
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Clare EL, Economou CK, Bennett FJ, Dyer CE, Adams K, McRobie B, Drinkwater R, Littlefair JE. Measuring biodiversity from DNA in the air. Curr Biol 2021; 32:693-700.e5. [PMID: 34995488 DOI: 10.1016/j.cub.2021.11.064] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/05/2021] [Accepted: 11/26/2021] [Indexed: 12/22/2022]
Abstract
The crisis of declining biodiversity1 exceeds our current ability to monitor changes in ecosystems. Rapid terrestrial biomonitoring approaches are essential to quantify the causes and consequences of global change. Environmental DNA2 has revolutionized aquatic ecology,3 permitting population monitoring4 and remote diversity assessments matching or outperforming conventional methods of community sampling.3-5 Despite this model, similar methods have not been widely adopted in terrestrial ecosystems. Here, we demonstrate that DNA from terrestrial animals can be filtered, amplified, and then sequenced from air samples collected in natural settings representing a powerful tool for terrestrial ecology. We collected air samples at a zoological park, where spatially confined non-native species allowed us to track DNA sources. We show that DNA can be collected from air and used to identify species and their ecological interactions. Air samples contained DNA from 25 species of mammals and birds, including 17 known terrestrial resident zoo species. We also identified food items from air sampled in enclosures and detected taxa native to the local area, including the Eurasian hedgehog, endangered in the United Kingdom. Our data demonstrate that airborne eDNA concentrates around recently inhabited areas but disperses away from sources, suggesting an ecology to airborne eDNA and the potential for sampling at a distance. Our findings demonstrate the profound potential of air as a source of DNA for global terrestrial biomonitoring.
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Affiliation(s)
- Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
| | - Chloe K Economou
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Frances J Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Caitlin E Dyer
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | | | - Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Joanne E Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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16
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Broadhurst HA, Gregory LM, Bleakley EK, Perkins JC, Lavin JV, Bolton P, Browett SS, Howe CV, Singleton N, Tansley D, Sales NG, McDevitt AD. Mapping differences in mammalian distributions and diversity using environmental DNA from rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149724. [PMID: 34467903 DOI: 10.1016/j.scitotenv.2021.149724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Finding more efficient ways to monitor and estimate the diversity of mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. Here, we first focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding two rivers in southeastern England. Community diversity and composition was then assessed based on species richness and β-diversity, with differences between communities partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling. eDNA metabarcoding detected 25 wild mammal species from five orders, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorphs) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers. eDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.
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Affiliation(s)
- Holly A Broadhurst
- School of Science, Engineering and Environment, University of Salford, UK
| | - Luke M Gregory
- School of Science, Engineering and Environment, University of Salford, UK
| | - Emma K Bleakley
- School of Science, Engineering and Environment, University of Salford, UK
| | - Joseph C Perkins
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jenna V Lavin
- School of Science, Engineering and Environment, University of Salford, UK
| | - Polly Bolton
- School of Science, Engineering and Environment, University of Salford, UK
| | - Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, UK; School of Science and Computing, Waterford Institute of Technology, Waterford, Ireland
| | - Claire V Howe
- Natural England, Horizon House, Deanery Road, Bristol, UK
| | - Natalie Singleton
- Essex Wildlife Trust, Abbotts Hall Farm, Great Wigborough, Colchester, UK
| | - Darren Tansley
- Essex Wildlife Trust, Abbotts Hall Farm, Great Wigborough, Colchester, UK
| | | | - Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, UK.
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17
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Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information. Sci Rep 2021; 11:24241. [PMID: 34930992 PMCID: PMC8688430 DOI: 10.1038/s41598-021-03733-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 11/09/2022] Open
Abstract
Both aquatic and terrestrial biodiversity information can be detected in riverine water environmental DNA (eDNA). However, the effectiveness of using riverine water eDNA to simultaneously monitor the riverine and terrestrial biodiversity information remains unidentified. Here, we proposed that the monitoring effectiveness could be approximated by the transportation effectiveness of land-to-river and upstream-to-downstream biodiversity information flows and described by three new indicators. Subsequently, we conducted a case study in a watershed on the Qinghai-Tibet Plateau. The results demonstrated that there was higher monitoring effectiveness on summer or autumn rainy days than in other seasons and weather conditions. The monitoring of the bacterial biodiversity information was more efficient than the monitoring of the eukaryotic biodiversity information. On summer rainy days, 43-76% of species information in riparian sites could be detected in adjacent riverine water eDNA samples, 92-99% of species information in riverine sites could be detected in a 1-km downstream eDNA sample, and half of dead bioinformation (the bioinformation labeling the biological material that lacked life activity and fertility) could be monitored 4-6 km downstream for eukaryotes and 13-19 km downstream for bacteria. The current study provided reference method and data for future monitoring projects design and for future monitoring results evaluation.
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18
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Carvalho CS, de Oliveira ME, Rodriguez-Castro KG, Saranholi BH, Galetti PM. Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance. Mol Ecol Resour 2021; 22:1262-1273. [PMID: 34724330 DOI: 10.1111/1755-0998.13543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 10/20/2022]
Abstract
Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been increasingly recognized as powerful tools for biodiversity assessment and conservation management. However, eDNA/iDNA efficiency for vertebrate diversity assessment remains uncertain, and comparisons to conventional methods are still rare. Through a meta-analysis of previously published vertebrate diversity surveys, we compared the efficiency of eDNA/iDNA against conventional methods across several types of samplers, vertebrate groups, and locations (tropical vs. temperate zones). We also assess eDNA/iDNA efficiency to estimate relative abundance or biomass over different molecular methods (qPCR and metabarcoding) and type of experiment (in the laboratory or in the field). We showed that for water sampler, fish as a target species, and studies achieved in temperate zones, eDNA presents lower risk of not detecting a species or a site with a target species than conventional methods. These results show that eDNA is an efficient tool to assess fish diversity. Moreover, eDNA data presents positive correlation with fish abundance or biomass. However, such correlation was higher in laboratory experiments than in the field. For the other samplers, vertebrate groups, and in tropical zones we were not able to draw general conclusion, highlighting the urgency of conducting more comparative studies.
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Affiliation(s)
- Carolina S Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Instituto Tecnológico Vale, Belém, PA, Brazil
| | | | - Karen Giselle Rodriguez-Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Facultad de Ciencias Básicas e Ingeniería, Universidad de los Llanos, Villavicencio, Colombia
| | - Bruno H Saranholi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Department of Life Sciences, Imperial College London, London, UK
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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19
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Molecular diversity of Uzbekistan's fishes assessed with DNA barcoding. Sci Rep 2021; 11:16894. [PMID: 34413445 PMCID: PMC8376971 DOI: 10.1038/s41598-021-96487-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/31/2021] [Indexed: 11/25/2022] Open
Abstract
Uzbekistan is one of two doubly landlocked countries in the world, where all rivers are endorheic basins. Although fish diversity is relatively poor in Uzbekistan, the fish fauna of the region has not yet been fully studied. The aim of this study was to establish a reliable barcoding reference database for fish in Uzbekistan. A total of 666 specimens, belonging to 59 species within 39 genera, 17 families, and 9 orders, were subjected to polymerase chain reaction amplification in the barcode region and sequenced. The length of the 666 barcodes was 682 bp. The average K2P distances within species, genera, and families were 0.22%, 6.33%, and 16.46%, respectively. The average interspecific distance was approximately 28.8 times higher than the mean intraspecific distance. The Barcode Index Number (BIN) discordance report showed that 666 specimens represented 55 BINs, of which five were singletons, 45 were taxonomically concordant, and five were taxonomically discordant. The barcode gap analysis demonstrated that 89.3% of the fish species examined could be discriminated by DNA barcoding. These results provide new insights into fish diversity in the inland waters of Uzbekistan and can provide a basis for the development of further studies on fish fauna.
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20
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Polanco F. A, Mutis Martinezguerra M, Marques V, Villa‐Navarro F, Borrero Pérez GH, Cheutin M, Dejean T, Hocdé R, Juhel J, Maire E, Manel S, Spescha M, Valentini A, Mouillot D, Albouy C, Pellissier L. Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA. Biotropica 2021. [DOI: 10.1111/btp.13009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Andrea Polanco F.
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR, Santa Marta, Colombia, Programa de Biodiversidad y Ecosistemas MarinosMuseo de Historia Natural Marina de Colombia (MHNMC Santa Marta Colombia)
| | - Maria Mutis Martinezguerra
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR, Santa Marta, Colombia, Programa de Biodiversidad y Ecosistemas MarinosMuseo de Historia Natural Marina de Colombia (MHNMC Santa Marta Colombia)
| | - Virginie Marques
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
- CEFE Univ. Montpellier CNRS EPHE‐PSL University IRD Univ. Paul Valéry Montpellier Montpellier France
| | - Francisco Villa‐Navarro
- Grupo de Investigación en Zoología Facultad de Ciencias Universidad del Tolima Ibagué Colombia
| | - Giomar Helena Borrero Pérez
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR, Santa Marta, Colombia, Programa de Biodiversidad y Ecosistemas MarinosMuseo de Historia Natural Marina de Colombia (MHNMC Santa Marta Colombia)
| | - Marie‐Charlotte Cheutin
- CEFE Univ. Montpellier CNRS EPHE‐PSL University IRD Univ. Paul Valéry Montpellier Montpellier France
| | | | - Régis Hocdé
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
| | | | - Eva Maire
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
- Lancaster Environment Centre Lancaster University Lancaster UK
| | - Stéphanie Manel
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
- CEFE Univ. Montpellier CNRS EPHE‐PSL University IRD Univ. Paul Valéry Montpellier Montpellier France
| | - Manuel Spescha
- Landscape Ecology Department of Environmental Systems Science Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
| | | | - David Mouillot
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
| | - Camille Albouy
- IFREMER Unité Écologie et Modèles pour l’Halieutique Nantes cedex 3 France
| | - Loïc Pellissier
- Landscape Ecology Department of Environmental Systems Science Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- Unit of Land Change Science Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
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21
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Macher TH, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F. Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.66557] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.
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22
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Shum P, Palumbi SR. Testing small-scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding. Mol Ecol 2021; 30:3355-3373. [PMID: 33682164 DOI: 10.1111/mec.15851] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 01/27/2021] [Accepted: 02/10/2021] [Indexed: 12/25/2022]
Abstract
DNA metabarcoding has been increasingly used to detail distributions of hundreds of species. Most analyses focus on creating molecular operational taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much less common is use of the sequence diversity within these MOTUs. Here we use the diversity of COI haplotypes within MOTUs from a California kelp forest to infer patterns of population abundance, dispersal and population history from 527 species of animals and algae from 106 samples of benthic habitats in Monterey Bay. Using haplotypes as a unit we show fine-grained differences of abundance across locations for 15 species, and marked aggregation from sample to sample for most of the common species of plants and animals. Previous analyses could not distinguish these patterns from artefacts of amplification or sequence bias. Our haplotype data also reveal strong population genetic differentiation over small spatial scales for 48 species of red algae, sponges and Bryozoa. Last, phylogenetic analysis of mismatch frequencies among haplotypes show a wide variety of demographic histories from recent expansions to long, stable population sizes. These analyses show that abundant, small-bodied marine species that are often overlooked in ecological surveys can have strikingly different patterns of ecological and genetic structure leading to population, ecological and perhaps adaptive differences between habitats. MOTU diversity data from the same sequencing efforts that generate species-level analyses can greatly increase the scope and value of metabarcoding studies.
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Affiliation(s)
- Peter Shum
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - Stephen R Palumbi
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
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23
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eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals. Sci Rep 2021; 11:11362. [PMID: 34131168 PMCID: PMC8206079 DOI: 10.1038/s41598-021-90598-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/13/2021] [Indexed: 11/14/2022] Open
Abstract
Biodiversity monitoring delivers vital information to those making conservation decisions. Comprehensively measuring terrestrial biodiversity usually requires costly methods that can rarely be deployed at large spatial scales over multiple time periods, limiting conservation efficiency. Here we investigated the capacity of environmental DNA (eDNA) from stream water samples to survey terrestrial mammal diversity at multiple spatial scales within a large catchment. We compared biodiversity information recovered using an eDNA metabarcoding approach with data from a dense camera trap survey, as well as the sampling costs of both methods. Via the sampling of large volumes of water from the two largest streams that drained the study area, eDNA metabarcoding provided information on the presence and detection probabilities of 35 mammal taxa, 25% more than camera traps and for half the cost. While eDNA metabarcoding had limited capacity to detect felid species and provide individual-level demographic information, it is a cost-efficient method for large-scale monitoring of terrestrial mammals that can offer sufficient information to solve many conservation problems.
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24
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Nguyen A, Tilker A, Le D, Le HV, Le SV, Luu TH, Tran BV, Wilting A. New records and southern range extension of the Annamite striped rabbit Nesolagus timminsi in Vietnam. MAMMALIA 2021. [DOI: 10.1515/mammalia-2020-0189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The Annamite striped rabbit Nesolagus timminsi is a little-known and Endangered lagomorph endemic to the Annamites ecoregion of Vietnam and Laos. The species’ known distribution extends from the northern to central Annamites. Here, we report the first records of the species from the southern Annamites. We recorded camera-trap photographs of Annamite striped rabbit in Bidoup – Nui Ba National Park, located in Lam Dong province, Vietnam. The photographs represent the first records of the species from the southern Annamites, and a significant southern range extension. We discuss the implications of this finding for Annamite striped rabbit conservation.
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Affiliation(s)
- An Nguyen
- Leibniz Institute for Zoo and Wildlife Research , 10315 Berlin , Germany
- Global Wildlife Conservation , 500 Capital of Texas HWY , Austin , TX 76787 , USA
| | - Andrew Tilker
- Leibniz Institute for Zoo and Wildlife Research , 10315 Berlin , Germany
- Global Wildlife Conservation , 500 Capital of Texas HWY , Austin , TX 76787 , USA
| | - Duy Le
- Southern Institute of Ecology, Vietnam Academy of Science and Technology , Ho Chi Minh City , Vietnam
| | - Huong Van Le
- Bidoup – Nui Ba National Park , Dalat , Lam Dong Province , Vietnam
| | - Son Van Le
- Bidoup – Nui Ba National Park , Dalat , Lam Dong Province , Vietnam
| | - Truong Hong Luu
- Southern Institute of Ecology, Vietnam Academy of Science and Technology , Ho Chi Minh City , Vietnam
| | - Bang Van Tran
- Southern Institute of Ecology, Vietnam Academy of Science and Technology , Ho Chi Minh City , Vietnam
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research , 10315 Berlin , Germany
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25
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Wilcox TM, Caragiulo A, Dysthe JC, Franklin TW, Mason DH, McKelvey KS, Zarn KE, Schwartz MK. Detection of Jaguar (Panthera onca) From Genetic Material in Drinking Water. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.613200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Jaguar (Panthera onca) are of conservation concern and occur at very low densities in the northern portion of their range in northern Mexico and the southwestern United States. Environmental DNA sampling to detect genetic material from drinking water may be an effective approach for jaguar detection in these arid landscapes. Here we develop a qPCR assay for the detection of jaguar mitochondrial DNA, show that large quantities of DNA (mean 66,820 copies/L) can be found in the drinking water of captive animals, and observe detectable levels of DNA (80 copies/L) in a wild habitat with known jaguar populations. We suggest that environmental DNA sampling may represent a useful, complementary sampling tool for detection of rare jaguars, although effective application would require careful consideration of DNA persistence time in the environment.
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26
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Environmental DNA provides higher resolution assessment of riverine biodiversity and ecosystem function via spatio-temporal nestedness and turnover partitioning. Commun Biol 2021; 4:512. [PMID: 33941836 PMCID: PMC8093236 DOI: 10.1038/s42003-021-02031-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Rapidly assessing biodiversity is essential for environmental monitoring; however, traditional approaches are limited in the scope needed for most ecological systems. Environmental DNA (eDNA) based assessment offers enhanced scope for assessing biodiversity, while also increasing sampling efficiency and reducing processing time, compared to traditional methods. Here we investigated the effects of landuse and seasonality on headwater community richness and functional diversity, via spatio-temporal dynamics, using both eDNA and traditional sampling. We found that eDNA provided greater resolution in assessing biodiversity dynamics in time and space, compared to traditional sampling. Community richness was seasonally linked, peaking in spring and summer, with temporal turnover having a greater effect on community composition compared to localized nestedness. Overall, our assessment of ecosystem function shows that community formation is driven by regional resource availability, implying regional management requirements should be considered. Our findings show that eDNA based ecological assessment is a powerful, rapid and effective assessment strategy that enables complex spatio-temporal studies of community diversity and ecosystem function, previously infeasible using traditional methods. Mathew Seymour et al. compare eDNA with traditional biodiversity metrics to assess the functional diversity of a river basin in Wales over space and time and variable land use. Their results show that eDNA can generate greater biodiversity resolution and reliably detect spatio-temporal changes in community and functional diversity.
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27
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Coutant O, Richard-Hansen C, de Thoisy B, Decotte JB, Valentini A, Dejean T, Vigouroux R, Murienne J, Brosse S. Amazonian mammal monitoring using aquatic environmental DNA. Mol Ecol Resour 2021; 21:1875-1888. [PMID: 33787010 DOI: 10.1111/1755-0998.13393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/14/2021] [Accepted: 03/22/2021] [Indexed: 11/26/2022]
Abstract
Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.
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Affiliation(s)
- Opale Coutant
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | | | | | | | | | - Tony Dejean
- VIGILIFE, Le Bourget-du-Lac, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Régis Vigouroux
- Laboratoire Environnement de Petit Saut, HYDRECO, Kourou Cedex, French Guiana
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
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28
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eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Sci Rep 2021; 11:6820. [PMID: 33767219 PMCID: PMC7994446 DOI: 10.1038/s41598-021-85488-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.
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29
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Priestley V, Allen R, Binstead M, Arnold R, Savolainen V. Quick detection of a rare species: Forensic swabs of survey tubes for hazel dormouse
Muscardinus avellanarius
urine. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Lozano Mojica JD, Caballero S. Applications of eDNA Metabarcoding for Vertebrate Diversity Studies in Northern Colombian Water Bodies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.617948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Environmental DNA metabarcoding is a tool with increasing use worldwide. The uses of such technology have been validated several times for diversity census, invasive species detection, and endangered/cryptic/elusive species detection and monitoring. With the help of this technology, water samples collected (n = 37) from several main river basins and other water bodies of the northern part of Colombia, including the Magdalena, Sinú, Atrato, and San Jorge river basins, were filtered and analyzed and processed using universal 12S primers for vertebrate fauna and NGS. Over 200 native taxa were detected, the majority of them being fish species but also including amphibia, reptiles, and several non-aquatic species of birds and mammals (around 78, 3, 2, 9, and 8%, respectively). Among the matches, vulnerable, and endangered species such as the catfish Pseudoplatystoma magdaleniatum and the Antillean manatee (Trichechus manatus) were detected. The manual revision of the data revealed some geographical incongruencies in classification. No invasive species were detected in the filters. This is, to our knowledge, the first time this technique is used in rivers of the country and this tool promises to bring advances in monitoring and conservation efforts, since its low cost and fast deployment allows for sampling in small periods of time, together with the fact that it can detect a wide range of species, allows for a new way of censing the vertebrate diversity in Colombia. Diversity analysis showed how the species identified using this method point to expected community structure although still much needs to be improved in rates of detection and genomic reference databases. This technique could be used in citizen science projects involving local communities in these regions.
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31
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Littlewood NA, Hancock MH, Newey S, Shackelford G, Toney R. Use of a novel camera trapping approach to measure small mammal responses to peatland restoration. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-020-01449-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AbstractSmall mammals, such as small rodents (Rodentia: Muroidea) and shrews (Insectivora: Soricidae), present particular challenges in camera trap surveys. Their size is often insufficient to trigger infra-red sensors, whilst resultant images may be of inadequate quality for species identification. The conventional survey method for small mammals, live-trapping, can be both labour-intensive and detrimental to animal welfare. Here, we describe a method for using camera traps for monitoring small mammals. We show that by attaching the camera trap to a baited tunnel, fixing a close-focus lens over the camera trap lens, and reducing the flash intensity, pictures or videos can be obtained of sufficient quality for identifying species. We demonstrate the use of the method by comparing occurrences of small mammals in a peatland landscape containing (i) plantation forestry (planted on drained former blanket bog), (ii) ex-forestry areas undergoing bog restoration, and (iii) unmodified blanket bog habitat. Rodents were detected only in forestry and restoration areas, whilst shrews were detected across all habitat. The odds of detecting small mammals were 7.6 times higher on camera traps set in plantation forestry than in unmodified bog, and 3.7 times higher on camera traps in restoration areas than in bog. When absolute abundance estimates are not required, and camera traps are available, this technique provides a low-cost survey method that is labour-efficient and has minimal animal welfare implications.
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32
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Blackman RC, Ling KKS, Harper LR, Shum P, Hänfling B, Lawson‐Handley L. Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water. Ecol Evol 2020; 10:13248-13259. [PMID: 33304534 PMCID: PMC7713958 DOI: 10.1002/ece3.6921] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 09/14/2020] [Indexed: 12/29/2022] Open
Abstract
The early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS-particularly during the early stages of an invasion.Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, Dreissena rostriformis bugensis, a high priority INNS, along a density gradient on the River Wraysbury, UK.All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor. Synthesis and application. All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community and consequently the impacts of INNS.
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Affiliation(s)
- Rosetta C. Blackman
- Department of Aquatic EcologyEawagSwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Kar Keun Sean Ling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lynsey R. Harper
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Peter Shum
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Bernd Hänfling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lori Lawson‐Handley
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
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33
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Skorupski J. Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals? Genes (Basel) 2020; 11:E1332. [PMID: 33187363 PMCID: PMC7696698 DOI: 10.3390/genes11111332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
The purpose of this review is to present the current state of knowledge about the genetics of European mink Mustela lutreola L., 1761, which is one of the most endangered mammalian species in the world. This article provides a comprehensive description of the studies undertaken over the last 50 years in terms of cytogenetics, molecular genetics, genomics (including mitogenomics), population genetics of wild populations and captive stocks, phylogenetics, phylogeography, and applied genetics (including identification by genetic methods, molecular ecology, and conservation genetics). An extensive and up-to-date review and critical analysis of the available specialist literature on the topic is provided, with special reference to conservation genetics. Unresolved issues are also described, such as the standard karyotype, systematic position, and whole-genome sequencing, and hotly debated issues are addressed, like the origin of the Southwestern population of the European mink and management approaches of the most distinct populations of the species. Finally, the most urgent directions of future research, based on the research questions arising from completed studies and the implementation of conservation measures to save and restore M. lutreola populations, are outlined. The importance of the popularization of research topics related to European mink genetics among scientists is highlighted.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-914-441-685
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
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34
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Milan DT, Mendes IS, Damasceno JS, Teixeira DF, Sales NG, Carvalho DC. New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment. Sci Rep 2020; 10:17966. [PMID: 33087755 PMCID: PMC7578065 DOI: 10.1038/s41598-020-74902-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
The megadiverse Neotropical fish fauna lacks a comprehensive and reliable DNA reference database, which hampers precise species identification and DNA based biodiversity assessment in the region. Here, we developed a mitochondrial 12S ribosomal DNA reference database for 67 fish species, representing 54 genera, 25 families, and six major Neotropical orders. We aimed to develop mini-barcode markers (i.e. amplicons with less than 200 bp) suitable for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes and to determine a threshold value for fish species delimitation using 12S. Evaluation of the target amplicons demonstrated that both full-length library (565 bp) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish species. For species delimitation, interspecific genetic distance threshold values of 0.4% and 0.55% were defined using full-length and mini-barcodes, respectively. A custom reference database and specific mini-barcode markers are important assets for ecoregion scale DNA based biodiversity assessments (such as environmental DNA) that can help with the complex task of conserving the megadiverse Neotropical ichthyofauna.
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Affiliation(s)
- David T Milan
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil
| | - Izabela S Mendes
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil.,Postgraduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Júnio S Damasceno
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil
| | - Daniel F Teixeira
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil.,Postgraduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Naiara G Sales
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK.,CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Daniel C Carvalho
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil. .,Postgraduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.
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35
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Browett SS, O'Meara DB, McDevitt AD. Genetic tools in the management of invasive mammals: recent trends and future perspectives. Mamm Rev 2020. [DOI: 10.1111/mam.12189] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samuel S. Browett
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| | - Denise B. O'Meara
- Molecular Ecology Research Group Eco‐Innovation Research Centre School of Science and Computing Waterford Institute of Technology Waterford Ireland
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
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