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Fernandes K, Bateman PW, Saunders BJ, Gibberd M, Bunce M, Bohmann K, Nevill P. Analysing the effects of distance, taxon and biomass on vertebrate detections using bulk-collected carrion fly iDNA. R Soc Open Sci 2024; 11:231286. [PMID: 38577218 PMCID: PMC10987983 DOI: 10.1098/rsos.231286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 11/23/2023] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
Invertebrate-derived DNA (iDNA) metabarcoding from carrion flies is a powerful, non-invasive tool that has value for assessing vertebrate diversity. However, unknowns exist around the factors that influence vertebrate detections, such as spatial limits to iDNA signals or if detections are influenced by taxonomic class or estimated biomass of the vertebrates of interest. Using a bulk-collection method, we captured flies from within a zoo and along transects extending 4 km away from this location. From 920 flies, we detected 28 vertebrate species. Of the 28 detected species, we identified 9 species kept at the zoo, 8 mammals and 1 bird, but no reptiles. iDNA detections were highly geographically localized, and only a few zoo animals were detected outside the zoo setting. However, due to the low number of detections in our dataset, we found no influence of the taxonomic group or the estimated biomass of animals on their detectability. Our data suggest that iDNA detections from bulk-collected carrion flies, at least in urban settings in Australia, are predominantly determined by geographic proximity to the sampling location. This study presents an important step in understanding how iDNA techniques can be used in biodiversity monitoring.
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Affiliation(s)
- Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia6102, Australia
- Section for Molecular Ecology and Evolution, Faculty of Health and Medical Sciences, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Food Agility CRC Ltd, Sydney, New South Wales2000, Australia
- Department of Anatomy, University of Otago, Dunedin9016, New Zealand
| | - Philip W. Bateman
- Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia6102, Australia
- MBioMe - Mine Site Biomonitoring using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia6102, Australia
| | - Benjamin J. Saunders
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia6102, Australia
| | - Mark Gibberd
- Food Agility CRC Ltd, Sydney, New South Wales2000, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia6102, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia6102, Australia
- Environmental Science and Research (ESR), Porirua5022, New Zealand
| | - Kristine Bohmann
- Section for Molecular Ecology and Evolution, Faculty of Health and Medical Sciences, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Paul Nevill
- MBioMe - Mine Site Biomonitoring using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia6102, Australia
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [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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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Mwakasungula S, Rougeron V, Arnathau C, Boundenga L, Miguel E, Boissière A, Jiolle D, Durand P, Msigwa A, Mswata S, Olotu A, Sterkers Y, Roche B, Killeen G, Cerqueira F, Bitome‐Essono PY, Bretagnolle F, Masanja H, Paupy C, Sumaye R, Prugnolle F. Using haematophagous fly blood meals to study the diversity of blood-borne pathogens infecting wild mammals. Mol Ecol Resour 2022; 22:2915-2927. [PMID: 35730337 PMCID: PMC9796008 DOI: 10.1111/1755-0998.13670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/25/2022] [Accepted: 05/17/2022] [Indexed: 12/30/2022]
Abstract
Many emerging infectious diseases originate from wild animals, so there is a profound need for surveillance and monitoring of their pathogens. However, the practical difficulty of sample acquisition from wild animals tends to limit the feasibility and effectiveness of such surveys. Xenosurveillance, using blood-feeding invertebrates to obtain tissue samples from wild animals and then detect their pathogens, is a promising method to do so. Here, we describe the use of tsetse fly blood meals to determine (directly through molecular diagnostic and indirectly through serology), the diversity of circulating blood-borne pathogens (including bacteria, viruses and protozoa) in a natural mammalian community of Tanzania. Molecular analyses of captured tsetse flies (182 pools of flies totalizing 1728 flies) revealed that the blood meals obtained came from 18 different vertebrate species including 16 non-human mammals, representing approximately 25% of the large mammal species present in the study area. Molecular diagnostic demonstrated the presence of different protozoa parasites and bacteria of medical and/or veterinary interest. None of the six virus species searched for by molecular methods were detected but an ELISA test detected antibodies against African swine fever virus among warthogs, indicating that the virus had been circulating in the area. Sampling of blood-feeding insects represents an efficient and practical approach to tracking a diversity of pathogens from multiple mammalian species, directly through molecular diagnostic or indirectly through serology, which could readily expand and enhance our understanding of the ecology and evolution of infectious agents and their interactions with their hosts in wild animal communities.
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Affiliation(s)
- Solomon Mwakasungula
- Department of Environmental Health and Ecological SciencesIfakara Health InstituteIfakaraTanzania
| | - Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance,IRL REHABSNelson Mandela UniversityGeorgeSouth Africa
| | - Céline Arnathau
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance
| | - Larson Boundenga
- Centre Interdisciplinaire de Recherches de FrancevilleFrancevilleGabon,Department of AnthropologyDurham UniversityDurhamUK
| | - Eve Miguel
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance
| | - Anne Boissière
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance,UMR CIRAD‐INRA ASTRECIRADMontpellierFrance
| | - Davy Jiolle
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance
| | - Patrick Durand
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance,IRL REHABSNelson Mandela UniversityGeorgeSouth Africa
| | - Alphonce Msigwa
- Tanzania National ParksBurigi‐Chato National ParkBiharamuloTanzania
| | - Sarah Mswata
- Department of Environmental Health and Ecological SciencesIfakara Health InstituteIfakaraTanzania
| | - Ally Olotu
- Department of Environmental Health and Ecological SciencesIfakara Health InstituteIfakaraTanzania
| | - Yvon Sterkers
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance
| | - Benjamin Roche
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance
| | - Gerard Killeen
- Department of Environmental Health and Ecological SciencesIfakara Health InstituteIfakaraTanzania,School of Biological, Earth & Environmental Sciences and Environmental Research InstituteUniversity College CorkCorkIreland
| | - Frédérique Cerqueira
- Plateforme Génotypage – SéquençageInstitut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHEMontpellierFrance
| | | | | | - Honorati Masanja
- Department of Environmental Health and Ecological SciencesIfakara Health InstituteIfakaraTanzania
| | - Christophe Paupy
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance
| | - Robert Sumaye
- Department of Environmental Health and Ecological SciencesIfakara Health InstituteIfakaraTanzania
| | - Franck Prugnolle
- Laboratoire MIVEGEC (Université de Montpellier‐CNRS‐IRD)MontpellierFrance,IRL REHABSNelson Mandela UniversityGeorgeSouth Africa
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5
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Nelaballi S, Finkel BJ, Bernard AB, Estrada GR, Setiawan E, Setia TM, Susanto TW, Rhanda R, Surya, Jakaria, Andika D, Lemoine S, Jaffe SM, Barrow EJ, Justinek Ž, Wittmer HU, Marshall AJ. Impacts of abiotic and biotic factors on terrestrial leeches in Indonesian Borneo. Biotropica 2022. [DOI: 10.1111/btp.13146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Swapna Nelaballi
- Department of Anthropology University of Michigan Ann Arbor Michigan USA
| | - Benjamin J. Finkel
- Department of Anthropology University of Michigan Ann Arbor Michigan USA
| | - Andrew B. Bernard
- Department of Anthropology University of Michigan Ann Arbor Michigan USA
| | - Gene R. Estrada
- Department of Anthropology University of Michigan Ann Arbor Michigan USA
| | - Endro Setiawan
- Department of Biology Graduate School, Universitas Nasional Jakarta Indonesia
- Gunung Palung National Park Bureau Ketapang, West Kalimantan Indonesia
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
| | - Tatang Mitra Setia
- Department of Biology Graduate School, Universitas Nasional Jakarta Indonesia
- Faculty of Biology Universitas Nasional Jakarta Indonesia
| | - Tri Wahyu Susanto
- Faculty of Biology Universitas Nasional Jakarta Indonesia
- Gunung Palung Orangutan Conservation Program Ketapang, West Kalimantan Indonesia
| | - Raden Rhanda
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
| | - Surya
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
| | - Jakaria
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
| | - Dika Andika
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
| | - Sylvain Lemoine
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
- Department of Archaeology University of Cambridge Cambridge UK
| | - Sarah M. Jaffe
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
- Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Boulder Colorado USA
| | - Elizabeth J. Barrow
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
- Gunung Palung Orangutan Conservation Program Ketapang, West Kalimantan Indonesia
- Department of Social Sciences Oxford Brookes University Headington, Oxford UK
| | - Živa Justinek
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
- Programme Selamatkan Yaki Yayasan Kinatouan Pelestarian Alam Sulawesi Manado, North Sulawesi Indonesia
| | - Heiko U. Wittmer
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
- School of Biological Sciences Victoria University of Wellington Wellington New Zealand
| | - Andrew J. Marshall
- Department of Anthropology University of Michigan Ann Arbor Michigan USA
- One Forest Project Gunung Palung National Park West Kalimantan Indonesia
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan USA
- School of Environment and Sustainability University of Michigan Ann Arbor Michigan USA
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6
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Jambari A, Nakabayashi M, Numata S, Hosaka T. Spatio‐temporal patterns in the abundance of active terrestrial leeches in a Malaysian rainforest. Biotropica 2022. [DOI: 10.1111/btp.13120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Asrulsani Jambari
- Graduate School for International Development and Cooperation Hiroshima University Hiroshima Japan
| | - Miyabi Nakabayashi
- Graduate School for International Development and Cooperation Hiroshima University Hiroshima Japan
- Graduate School of Advanced Science and Engineering Hiroshima University Hiroshima Japan
| | - Shinya Numata
- Department of Tourism Science, Graduate School of Urban Environmental Sciences Tokyo Metropolitan University Tokyo Japan
| | - Tetsuro Hosaka
- Graduate School for International Development and Cooperation Hiroshima University Hiroshima Japan
- Graduate School of Advanced Science and Engineering Hiroshima University Hiroshima Japan
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7
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Rieseberg L, Warschefsky E, O'Boyle B, Taberlet P, Ortiz-Barrientos D, Kane NC, Sibbett B. Editorial 2022. Mol Ecol 2021; 31:1-30. [PMID: 34957606 DOI: 10.1111/mec.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Loren Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Univ. Grenoble Alpes, Grenoble Cedex 9, France
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queenland, St. Lucia, Queensland, Australia
| | - Nolan C Kane
- University of Colorado at Boulder, Boulder, Colorado, USA
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8
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Wang J, Liu P, Chang J, Li C, Xie F, Jiang J. Development of an eDNA metabarcoding tool for surveying the world’s largest amphibian. Curr Zool 2021; 68:608-614. [PMID: 36324541 PMCID: PMC9616075 DOI: 10.1093/cz/zoab094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
Due to the overexploitation of farming, as well as habitat destruction, the wild population of Chinese giant salamander (CGS) Andrias davidianus, a species with seven genetically distinct lineages, has decreased by over 80% in the past 70 years. Traditional survey methods have proven to be unsuitable for finding this rare and elusive species. We evaluated the efficacy of environmental DNA (eDNA) sampling to detect CGS indirectly from its aquatic environment. We developed several species-specific primer sets; validated their specificity and sensitivity; and assessed their utility in silico, in the laboratory, and at two field sites harboring released farm-bred CGS. We detected the presence of CGS DNA by using polymerase chain reaction and Sanger sequencing. We also sequenced an amplicon mixture of seven haplotype-represented samples using high-throughput sequencing. Our eDNA methods could detect the presence of CGS at moderate densities reported across its range, proving them as a cost-effective way to establish broad-scale patterns of occupancy for CGS. In addition, our primers enabled the detection of mitochondrial lineage mixture or introduced individuals from geographically isolated populations of CGS.
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Affiliation(s)
- Jie Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Ping Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Cheng Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Feng Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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9
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Massey AL, Bronzoni RVDM, da Silva DJF, Allen JM, de Lázari PR, Dos Santos-Filho M, Canale GR, Bernardo CSS, Peres CA, Levi T. Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers. Mol Ecol Resour 2021; 22:962-977. [PMID: 34601818 DOI: 10.1111/1755-0998.13525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 11/30/2022]
Abstract
Metabarcoding of environmental DNA (eDNA) is now widely used to build diversity profiles from DNA that has been shed by species into the environment. There is substantial interest in the expansion of eDNA approaches for improved detection of terrestrial vertebrates using invertebrate-derived DNA (iDNA) in which hematophagous, sarcophagous, and coprophagous invertebrates sample vertebrate blood, carrion, or faeces. Here, we used metabarcoding and multiple iDNA samplers (carrion flies, sandflies, and mosquitos) collected from 39 forested sites in the southern Amazon to profile gamma and alpha diversity. Our main objectives were to (1) compare diversity found with iDNA to camera trapping, which is the conventional method of vertebrate diversity surveillance; and (2) compare each of the iDNA samplers to assess the effectiveness, efficiency, and potential biases associated with each sampler. In total, we collected and analysed 1759 carrion flies, 48,686 sandflies, and 4776 mosquitos. Carrion flies revealed the greatest total vertebrate species richness at the landscape level, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, followed by sandflies. Camera traps had the highest median species richness at the site-level but showed strong bias towards carnivore and ungulate species and missed much of the diversity described by iDNA methods. Mosquitos showed a strong feeding preference for humans as did sandflies for armadillos, thus presenting potential utility to further study related to host-vector interactions.
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Affiliation(s)
- Aimee L Massey
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | | | | | - Jennifer M Allen
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Patrick Ricardo de Lázari
- Centro de Estudos de Limnologia e Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso, Cáceres, Brazil
| | - Manoel Dos Santos-Filho
- Centro de Estudos de Limnologia e Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso, Cáceres, Brazil
| | - Gustavo Rodrigues Canale
- Instituto de Ciências Naturais, Humanas e Sociais, Universidade Federal de Mato Grosso, Sinop, Brazil
| | | | - Carlos Augusto Peres
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Instituto Juruá, Manaus, Brazil
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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10
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Drinkwater R, Williamson J, Clare EL, Chung AYC, Rossiter SJ, Slade E. Dung beetles as samplers of mammals in Malaysian Borneo-a test of high throughput metabarcoding of iDNA. PeerJ 2021; 9:e11897. [PMID: 34447624 PMCID: PMC8366524 DOI: 10.7717/peerj.11897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespread, with most terrestrial studies relying on DNA derived from the gut contents of blood-feeding invertebrates, such as leeches and mosquitoes. Dung beetles (superfamily Scarabaeoidea) primarily feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps, are globally distributed, and occur in a wide range of habitats. To build on the few existing studies demonstrating the potential of dung beetles as sources of mammalian DNA, we subjected the large-bodied, Bornean dung beetle (Catharsius renaudpauliani) to a controlled feeding experiment. We analysed DNA from gut contents at different times after feeding using qPCR techniques. Here, we first describe the window of DNA persistence within a dung beetle digestive tract. We found that the ability to successfully amplify cattle DNA decayed over relatively short time periods, with DNA copy number decreasing by two orders of magnitude in just 6 h. In addition, we sampled communities of dung beetles from a lowland tropical rainforest in Sabah, Malaysia, in order to test whether it is possible to identify vertebrate sequences from dung beetle iDNA. We sequenced both the gut contents from large dung beetle species, as well as whole communities of smaller beetles. We successfully identified six mammalian species from our samples, including the bearded pig (Sus barbatus) and the sambar deer (Rusa unicolor)—both vulnerable species on the IUCN red list. Our results represent the first use of dung beetle iDNA to sample Southeast Asian vertebrate fauna, and highlight the potential for dung beetle iDNA to be used in future biodiversity monitoring surveys.
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Affiliation(s)
- Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Joseph Williamson
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Arthur Y C Chung
- Sabah Forestry Department, Forest Research Centre, Sandakan, Malaysia
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Eleanor Slade
- Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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Affiliation(s)
- Jan Pawlowski
- Department of Genetics and EvolutionUniversity of GenevaGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
| | - Aurélie Bonin
- Department of Environmental Science and PolicyUniversità degli Studi di MilanoMilanItaly
| | - Frédéric Boyer
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesGrenobleFrance
| | - Tristan Cordier
- Department of Genetics and EvolutionUniversity of GenevaGenevaSwitzerland
- NORCE ClimateNORCE Norwegian Research Centre ASBjerknes Centre for Climate ResearchBergenNorway
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesGrenobleFrance
- Tromsø MuseumUiT – The Arctic University of NorwayTromsøNorway
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12
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Wang Y, Sentis A, Tüzün N, Stoks R. Thermal evolution ameliorates the long‐term plastic effects of warming, temperature fluctuations and heat waves on predator–prey interaction strength. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13810] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ying‐Jie Wang
- Evolutionary Stress Ecology and Ecotoxicology University of Leuven Leuven Belgium
| | - Arnaud Sentis
- INRAE, Aix‐Marseille Université, UMR RECOVER Aix‐en‐Provence France
| | - Nedim Tüzün
- Evolutionary Stress Ecology and Ecotoxicology University of Leuven Leuven Belgium
| | - Robby Stoks
- Evolutionary Stress Ecology and Ecotoxicology University of Leuven Leuven Belgium
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13
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Drinkwater R, Jucker T, Potter JHT, Swinfield T, Coomes DA, Slade EM, Gilbert MTP, Lewis OT, Bernard H, Struebig MJ, Clare EL, Rossiter SJ. Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats. Mol Ecol 2020; 30:3299-3312. [PMID: 33171014 PMCID: PMC8359290 DOI: 10.1111/mec.15724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 12/29/2022]
Abstract
The application of metabarcoding to environmental and invertebrate‐derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is particularly promising for sampling in the biodiverse humid tropics, where rapid land‐use change for agriculture means there is a growing need to understand the conservation value of the remaining mosaic and degraded landscapes. Here we use iDNA from blood‐feeding leeches (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 mammalian genera. We recorded lower mammal diversity in the most heavily degraded forest compared to higher quality twice logged forest. Although the accumulation curves of diversity estimates were comparable across these habitat types, diversity was higher in twice logged forest, with more taxa of conservation concern. In addition, our analysis revealed differences between the community recorded in the heavily logged forest and that of the twice logged forest. By revealing differences in mammal diversity across a human‐modified tropical landscape, our study demonstrates the value of iDNA as a noninvasive biomonitoring approach in conservation assessments.
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Affiliation(s)
- Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tommaso Jucker
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tom Swinfield
- Department of Plant Sciences, Forest and Ecology Conservation Group, University of Cambridge, Cambridge, UK
| | - David A Coomes
- Department of Plant Sciences, Forest and Ecology Conservation Group, University of Cambridge, Cambridge, UK
| | - Eleanor M Slade
- Department of Zoology, University of Oxford, Oxford, UK.,Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore
| | - M Thomas P Gilbert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | - Henry Bernard
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Sabah, Malaysia
| | - Matthew J Struebig
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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