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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 DOI: 10.1098/rstb.2023.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Chen X, Li S, Zhao J, Yao M. Passive eDNA sampling facilitates biodiversity monitoring and rare species detection. Environ Int 2024; 187:108706. [PMID: 38696978 DOI: 10.1016/j.envint.2024.108706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024]
Abstract
Environmental DNA (eDNA) technology has revolutionized biomonitoring, but challenges remain regarding water sample processing. The passive eDNA sampler (PEDS) represents a viable alternative to active, water filtration-based eDNA enrichment methods, but the effectiveness of PEDS for surveying biodiverse and complex natural water bodies is unknown. Here, we collected eDNA using filtration and glass fiber filter-based PEDS (submerged in water for 1 d) from 27 sites along the final reach of the Yangtze River and the coast of the Yellow Sea, followed by eDNA metabarcoding analysis of fish biodiversity and quantitative PCR (qPCR) for a critically endangered aquatic mammal, the Yangtze finless porpoise. We ultimately detected 98 fish species via eDNA metabarcoding. Both eDNA sampling methods captured comparable local species richness and revealed largely similar spatial variation in fish assemblages and community partitions between the river and sea sites. Notably, the Yangtze finless porpoise was detected only in the metabarcoding of eDNA collected by PEDS at five sites. Also, species-specific qPCR revealed that the PEDS captured porpoise eDNA at more sites (7 vs. 2), in greater quantities, and with a higher detection probability (0.803 vs. 0.407) than did filtration. Our results demonstrate the capacity of PEDS for surveying fish biodiversity, and support that continuous eDNA collection by PEDS can be more effective than instantaneous water sampling at capturing low abundance and ephemeral species in natural waters. Thus, the PEDS approach can facilitate more efficient and convenient eDNA-based biodiversity surveillance and rare species detection.
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Affiliation(s)
- Xiaoyu Chen
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871
| | - Sheng Li
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871.
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Saranholi BH, França FM, Vogler AP, Barlow J, Vaz de Mello FZ, Maldaner ME, Carvalho E, Gestich CC, Howes B, Banks-Leite C, Galetti PM. Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics. Mol Ecol Resour 2024:e13961. [PMID: 38646932 DOI: 10.1111/1755-0998.13961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/16/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.
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Affiliation(s)
- Bruno H Saranholi
- Department of Life Sciences, Imperial College London, Ascot, UK
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Filipe M França
- School of Biological Sciences, University of Bristol, Bristol, UK
- Graduate Program in Ecology, Biological Sciences Institute, Federal University of Pará, Belém, Pará, Brazil
| | - Alfried P Vogler
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Life Sciences, Natural History Museum, London, UK
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Fernando Z Vaz de Mello
- Departamento de Biologia e Zoologia, Universidade Federal de Mato Grosso, Instituto de Biociências, Cuiabá, MT, Brazil
| | - Maria E Maldaner
- Programa de Pós-Graduação Em Ecologia e Conservação da Biodiversidade (PPGECB), Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brazil
| | - Edrielly Carvalho
- Programa de Pós-Graduação Em Entomologia, Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Carla C Gestich
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Benjamin Howes
- Department of Life Sciences, Imperial College London, Ascot, UK
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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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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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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Fernandes K, Bateman PW, Saunders BJ, Bunce M, Bohmann K, Nevill P. Use of carrion fly iDNA metabarcoding to monitor invasive and native mammals. Conserv Biol 2023; 37:e14098. [PMID: 37186093 DOI: 10.1111/cobi.14098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 05/17/2023]
Abstract
Severely fragmented habitats increase the risk of extirpation of native mammal populations through isolation, increased edge effects, and predation. Therefore, monitoring the movement of mammal populations through anthropogenically altered landscapes can inform conservation. We used metabarcoding of invertebrate-derived DNA (iDNA) from carrion flies (Calliphoridae and Sarcophagidae) to track mammal populations in the wheat belt of southwestern Australia, where widespread clearing for agriculture has removed most of the native perennial vegetation and replaced it with an agricultural system. We investigated whether the localization of the iDNA signal reflected the predicted distribution of 4 native species-echidna (Tachyglossus aculeatus), numbat (Myrmecobius fasciatus), woylie (Bettongia penicillata), and chuditch (Dasyurus geoffroii)-and 2 non-native, invasive mammal species-fox (Vulpes vulpes) and feral cat (Felis catus). We collected bulk iDNA samples (n = 150 samples from 3428 carrion flies) at 3 time points from 3 conservation reserves and 35 road edges between them. We detected 14 of the 40 mammal species known from the region, including our target species. Most detections of target taxa were in conservation reserves. There were a few detections from road edges. We detected foxes and feral cats throughout the study area, including all conservation reserves. There was a significant difference between the diversity (F3, 98 = 5.91, p < 0.001) and composition (F3, 43 = 1.72, p < 0.01) of taxa detections on road edges and conservation reserves. Conservation reserves hosted more native biodiversity than road edges. Our results suggest that the signals from iDNA reflect the known distribution of target mammals in this region. The development of iDNA methods shows promise for future noninvasive monitoring of mammals. With further development, iDNA metabarcoding could inform decision-making related to conservation of endangered taxa, invasive species management, and impacts of habitat fragmentation.
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Affiliation(s)
- Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Food Agility CRC Ltd, Sydney, New South Wales, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Behavioural Ecology Research Group, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, 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 Australia, Australia
| | - Benjamin J Saunders
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Institute of Environmental Science and Research (ESR), Kenepuru, Porirua, New Zealand
| | - Kristine Bohmann
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, 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 Australia, Australia
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Lee PS, Dong MH, Yan XL, He TY, Yu SF, Wee SL, Wilson JJ. Blowfly-derived mammal DNA as mammal diversity assessment tool: Determination of dispersal activity and flight range of tropical blowflies. Biodivers Data J 2023; 11:e108438. [PMID: 37736305 PMCID: PMC10509675 DOI: 10.3897/bdj.11.e108438] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023] Open
Abstract
Mammalian DNA extracted from the invertebrates, especially blowfly-derived DNA, has been suggested as a useful tool to complement traditional field methods for terrestrial mammal monitoring. However, the accuracy of the estimated location of the target mammal detected from blowfly-derived DNA is largely dependent on the knowledge of blowflies' dispersal range. Presently, published data on adult blowfly dispersal capabilities remain scarce and mostly limited to temperate and subtropical regions, with no published report on the adult blowfly dispersal range in the Tropics. We seek to determine the blowfly flight range and dispersal activity in a tropical plantation in Malaysia by mark-release-recapture of approximately 3000 wild blowflies by use of rotten fish-baited traps for nine consecutive days. Out of the 3000 marked Chrysomya spp., only 1.5% (43) were recaptured during the 9-day sampling period. The majority of the blowflies (79%) were recaptured 1 km from the release point, while 20.9% were caught about 2-3 km from the release point. One individual blowfly travelled as far as 3 km and before being recaptured, which was the maximum dispersal distance recorded in this study. This result suggests that the estimated locations of the mammals detected from blowfly-derived iDNA is likely to be within 1-2 km radius from the origin of the blowfly sampling location. However, a more accurate estimated distance between the target mammal and the blowfly sampling location requires further investigation due to various factors, such as blowfly species, wind speed and direction that may potentially affect the blowfly dispersal activities. This study contributes further understanding on the development of a blowfly-derived DNA method as a mammalian monitoring tool in the tropical forests.
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Affiliation(s)
- Ping Shin Lee
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, ChinaCollege of Life Sciences, Anhui Normal UniversityWuhu 241000, AnhuiChina
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal UniversityWuhu 241000, AnhuiChina
| | - Min Hui Dong
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, ChinaCollege of Life Sciences, Anhui Normal UniversityWuhu 241000, AnhuiChina
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal UniversityWuhu 241000, AnhuiChina
| | - Xin Lei Yan
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, ChinaCollege of Life Sciences, Anhui Normal UniversityWuhu 241000, AnhuiChina
| | - Tian Yi He
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, ChinaCollege of Life Sciences, Anhui Normal UniversityWuhu 241000, AnhuiChina
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, ChinaAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal UniversityWuhu 241000, AnhuiChina
| | - Shang Fei Yu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, ChinaCollege of Life Sciences, Anhui Normal UniversityWuhu 241000, AnhuiChina
| | - Suk Ling Wee
- Centre for Insect Systematics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaCentre for Insect Systematics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600 Bangi, SelangorMalaysia
| | - John James Wilson
- Vertebrate Zoology at World Museum, National Museums Liverpool, William Brown Street, Liverpool, United KingdomVertebrate Zoology at World Museum, National Museums Liverpool, William Brown StreetLiverpoolUnited Kingdom
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Riaz M, Warren D, Wittwer C, Cocchiararo B, Hundertmark I, Reiners TE, Klimpel S, Pfenninger M, Khaliq I, Nowak C. Using eDNA to understand predator-prey interactions influenced by invasive species. Oecologia 2023; 202:757-767. [PMID: 37594600 PMCID: PMC10474997 DOI: 10.1007/s00442-023-05434-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Invasive predatory species may alter population dynamic processes of their prey and impact biological communities and ecosystem processes. Revealing biotic interactions, however, including the relationship between predator and prey, is a difficult task, in particular for species that are hard to monitor. Here, we present a case study that documents the utility of environmental DNA analysis (eDNA) to assess predator-prey interactions between two invasive fishes (Lepomis gibbosus, Pseudorasbora parva) and two potential amphibian prey species, (Triturus cristatus, Pelobates fuscus). We used species-specific TaqMan assays for quantitative assessment of eDNA concentrations from water samples collected from 89 sites across 31 ponds during three consecutive months from a local amphibian hotspot in Germany. We found a negative relationship between eDNA concentrations of the predators (fishes) and prey (amphibians) using Monte-Carlo tests. Our study highlights the potential of eDNA application to reveal predator-prey interactions and confirms the hypothesis that the observed local declines of amphibian species may be at least partly caused by recently introduced invasive fishes. Our findings have important consequences for local conservation management and highlight the usefulness of eDNA approaches to assess ecological interactions and guide targeted conservation action.
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Affiliation(s)
- Maria Riaz
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany.
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany.
| | - Dan Warren
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Claudia Wittwer
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany
| | - Berardino Cocchiararo
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Inga Hundertmark
- Hessische Gesellschaft Für Ornithologie Und Naturschutz (HGON E. V.), Lindenstrasse 5, 61209, Echzell, Germany
| | - Tobias Erik Reiners
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- Hessische Gesellschaft Für Ornithologie Und Naturschutz (HGON E. V.), Lindenstrasse 5, 61209, Echzell, Germany
| | - Sven Klimpel
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Imran Khaliq
- Department of Education, Punjab, Pakistan
- Department of Aquatic Ecology Eawag (Swiss Federal Institute of Aquatic Science and Technology) Überlandstrasse 133, 8600, Dübendorf, Switzerland
- Snow and Landscape Research (WSL), Swiss Federal Institute for Forest, Flüelastr. 11, 7260, Davos Dorf, Switzerland
| | - Carsten Nowak
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
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9
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. Sci Total Environ 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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10
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Hassan S, Sabreena, Poczai P, Ganai BA, Almalki WH, Gafur A, Sayyed RZ. Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity. Biology 2022; 11:1297. [PMID: 36138776 PMCID: PMC9495823 DOI: 10.3390/biology11091297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance. Abstract The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
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11
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Bohmann K, Elbrecht V, Carøe C, Bista I, Leese F, Bunce M, Yu DW, Seymour M, Dumbrell AJ, Creer S. Strategies for sample labelling and library preparation in DNA metabarcoding studies. Mol Ecol Resour 2022; 22:1231-1246. [PMID: 34551203 PMCID: PMC9293284 DOI: 10.1111/1755-0998.13512] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022]
Abstract
Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one-step PCR, two-step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications.
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Affiliation(s)
- Kristine Bohmann
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Vasco Elbrecht
- Department of Environmental Systems ScienceETH ZurichZürichSwitzerland
| | - Christian Carøe
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Iliana Bista
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Tree of LifeWellcome Sanger InstituteHinxtonUK
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- School of Biological SciencesNorwich Research ParkUniversity of East AngliaNorwichUK
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming YunnanChina
| | - Mathew Seymour
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Simon Creer
- Molecular Ecology and Evolution GroupSchool of Natural SciencesBangor UniversityGwyneddUK
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12
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Ji Y, Baker CCM, Popescu VD, Wang J, Wu C, Wang Z, Li Y, Wang L, Hua C, Yang Z, Yang C, Xu CCY, Diana A, Wen Q, Pierce NE, Yu DW. Measuring protected-area effectiveness using vertebrate distributions from leech iDNA. Nat Commun 2022; 13:1555. [PMID: 35322033 PMCID: PMC8943135 DOI: 10.1038/s41467-022-28778-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 01/31/2022] [Indexed: 11/09/2022] Open
Abstract
Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. From 30,468 leeches collected by 163 park rangers across 172 patrol areas, we identify 86 vertebrate species, including amphibians, mammals, birds and squamates. Multi-species occupancy modelling shows that species richness increases with elevation and distance to reserve edge. Most large mammals (e.g. sambar, black bear, serow, tufted deer) follow this pattern; the exceptions are the three domestic mammal species (cows, sheep, goats) and muntjak deer, which are more common at lower elevations. Vertebrate occupancies are a direct measure of conservation outcomes that can help guide protected-area management and improve the contributions that protected areas make towards global biodiversity goals. Here, we show the feasibility of using invertebrate-derived DNA to estimate spatially-resolved vertebrate occupancies across entire protected areas. Invertebrate-derived eDNA (iDNA) is an emerging tool for taxonomic and spatial biodiversity monitoring. Here, the authors use metabarcoding of leech-derived iDNA to estimate vertebrate occupancy over an entire protected area, the Ailaoshan Nature Reserve, China.
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Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Christopher C M Baker
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA. .,US Army ERDC Cold Regions Research and Engineering Laboratory, 72 Lyme Road, Hanover, NH, 03755, USA.
| | - Viorel D Popescu
- Department of Biological Sciences and Sustainability Studies Theme, Ohio University, 107 Irvine Hall, Athens, OH, 45701, USA.,Center for Environmental Studies (CCMESI), University of Bucharest, 1 N. Balcescu Blvd., Bucharest, Romania
| | - Jiaxin Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Chunying Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Yuanheng Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China.,Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Lin Wang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Mengla, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 666303, Mengla, China
| | - Chaolang Hua
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Zhongxing Yang
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Charles C Y Xu
- Redpath Museum and Department of Biology, McGill University, 859 Sherbrooke Street West, Montreal, PQ, H3A2K6, Canada
| | - Alex Diana
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Sibson Building, Canterbury, Kent, CT27FS, UK
| | - Qingzhong Wen
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK.
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13
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Dowling SN, Skaggs CL, Owings CG, Moctar K, Picard CJ, Manicke NE. Insects as Chemical Sensors: Detection of Chemical Warfare Agent Simulants and Hydrolysis Products in the Blow Fly Using LC-MS/MS. Environ Sci Technol 2022; 56:3535-3543. [PMID: 35188758 DOI: 10.1021/acs.est.1c07381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this work, blow flies were investigated as environmental chemical sample collectors following a chemical warfare attack (CWA). Blow flies sample the environment as they search for water and food sources and can be trapped from kilometers away using baited traps. Three species of blow flies were exposed to CWA simulants to determine the persistence and detectability of these compounds under varying environmental conditions. A liquid chromatography mass spectrometry (LC-MS/MS) method was developed to detect CWA simulants and hydrolysis products from fly guts. Flies were exposed to the CWA simulants dimethyl methylphosphonate and diethyl phosphoramidate as well as the pesticide dichlorvos, followed by treatment-dependent temperature and humidity conditions. Flies were sacrificed at intervals within a 14 day postexposure period. Fly guts were extracted and analyzed with the LC-MS/MS method. The amount of CWA simulant in fly guts decreased with time following exposure but were detectable 14 days following exposure, giving a long window of detectability. In addition to the analysis of CWA simulants, isopropyl methylphosphonic acid, the hydrolysis product of sarin, was also detected in blow flies 14 days post exposure. This work demonstrates the potential to obtain valuable samples from remote or access-restricted areas without risking lives.
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Affiliation(s)
- Sarah N Dowling
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Christine L Skaggs
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Charity G Owings
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Khadija Moctar
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Christine J Picard
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Nicholas E Manicke
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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14
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Lynggaard C, Bertelsen MF, Jensen CV, Johnson MS, Frøslev TG, Olsen MT, Bohmann K. Airborne environmental DNA for terrestrial vertebrate community monitoring. Curr Biol 2022; 32:701-707.e5. [PMID: 34995490 PMCID: PMC8837273 DOI: 10.1016/j.cub.2021.12.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/11/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Biodiversity monitoring at the community scale is a critical element of assessing and studying species distributions, ecology, diversity, and movements, and it is key to understanding and tracking environmental and anthropogenic effects on natural ecosystems.1, 2, 3, 4 Vertebrates in terrestrial ecosystems are experiencing extinctions and declines in both population numbers and sizes due to increasing threats from human activities and environmental change.5, 6, 7, 8 Terrestrial vertebrate monitoring using existing methods is generally costly and laborious, and although environmental DNA (eDNA) is becoming the tool of choice to assess biodiversity, few sample types effectively capture terrestrial vertebrate diversity. We hypothesized that eDNA captured from air could allow straightforward collection and characterization of terrestrial vertebrate communities. We filtered air at three localities in the Copenhagen Zoo: a stable, outside between the outdoor enclosures, and in the Rainforest House. Through metabarcoding of airborne eDNA, we detected 49 vertebrate species spanning 26 orders and 37 families: 30 mammal, 13 bird, 4 fish, 1 amphibian, and 1 reptile species. These spanned animals kept at the zoo, species occurring in the zoo surroundings, and species used as feed in the zoo. The detected species comprise a range of taxonomic orders and families, sizes, behaviors, and abundances. We found shorter distance to the air sampling device and higher animal biomass to increase the probability of detection. We hereby show that airborne eDNA can offer a fundamentally new way of studying and monitoring terrestrial communities. 49 vertebrate species detected through metabarcoding of airborne eDNA from the zoo Detections included 30 mammal, 13 bird, 4 fish, 1 amphibian, and 1 reptile species 6 to 21 vertebrate species were detected per air filtering sample Shorter geographical distance and higher biomass increased probability of detection
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Affiliation(s)
- Christina Lynggaard
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
| | | | - Casper V Jensen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Matthew S Johnson
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark; Airlabs Denmark, 2200 Copenhagen, Denmark
| | - Tobias Guldberg Frøslev
- Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
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15
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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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16
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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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17
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Tosa MI, Dziedzic EH, Appel CL, Urbina J, Massey A, Ruprecht J, Eriksson CE, Dolliver JE, Lesmeister DB, Betts MG, Peres CA, Levi T. The Rapid Rise of Next-Generation Natural History. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.
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18
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Fediajevaite J, Priestley V, Arnold R, Savolainen V. Meta-analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards. Ecol Evol 2021; 11:4803-4815. [PMID: 33976849 PMCID: PMC8093654 DOI: 10.1002/ece3.7382] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/01/2021] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost-effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta-analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently "better."Environmental DNA publications for multiple species or single macro-organism detection were identified using the Web of Science, by searching "eDNA" and "environmental DNA" across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa-dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance. Synthesis and applications: The results of this meta-analysis demonstrate that where there is a direct comparison, eDNA surveys of macro-organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods-based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.
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Affiliation(s)
| | | | - Richard Arnold
- Thomson Environmental Consultants Compass House Surrey Research Park Guildford UK
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19
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Owings CG, Gilhooly WP, Picard CJ. Blow fly stable isotopes reveal larval diet: A case study in community level anthropogenic effects. PLoS One 2021; 16:e0249422. [PMID: 33852607 PMCID: PMC8046228 DOI: 10.1371/journal.pone.0249422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/18/2021] [Indexed: 11/18/2022] Open
Abstract
Response to human impacts on the environment are typically initiated too late to remediate negative consequences. We present the novel use of stable isotope analysis (SIA) of blow flies to determine human influences on vertebrate communities in a range of human-inhabited environments, from a pristine national park to a dense metropolitan area. The refrain "you are what you eat" applies to the dietary isotope record of all living organisms, and for carrion-breeding blow flies, this translates to the type of carcasses present in an environment. Specifically, we show that carnivore carcasses make up a large proportion of the adult fly's prior larval diet, which contrasts to what has been reportedly previously for the wild adult fly diet (which consists of mostly herbivore resources). Additionally, we reveal the potential impact of human food on carcasses that were fed on by blow flies, underscoring the human influences on wild animal populations. Our results demonstrate that using SIA in conjunction with other methods (e.g., DNA analysis of flies) can reveal a comprehensive snapshot of the vertebrate community in a terrestrial ecosystem.
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Affiliation(s)
- Charity G. Owings
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - William P. Gilhooly
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Christine J. Picard
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, United States of America
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20
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Cutajar TP, Rowley JJ. Surveying frogs from the bellies of their parasites: Invertebrate-derived DNA as a novel survey method for frogs. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e00978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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21
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Huerlimann R, Cooper MK, Edmunds RC, Villacorta‐Rath C, Le Port A, Robson HLA, Strugnell JM, Burrows D, Jerry DR. Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non‐environmental DNA specialists. Anim Conserv 2020. [DOI: 10.1111/acv.12583] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- R. Huerlimann
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - M. K. Cooper
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - R. C. Edmunds
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - C. Villacorta‐Rath
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - A. Le Port
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - H. L. A. Robson
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - J. M. Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - D. Burrows
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - D. R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Tropical Futures Institute James Cook University Singapore Singapore
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22
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Zemanova MA. Towards more compassionate wildlife research through the 3Rs principles: moving from invasive to non-invasive methods. Wildlife Biology 2020. [DOI: 10.2981/wlb.00607] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Miriam A. Zemanova
- M. A. Zemanova (https://orcid.org/0000-0002-5002-3388) ✉ , Dept of Philosophy, Univ. of Basel, Steinengraben 5, CH-4051 Basel, Switzerland
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23
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Tilker A, Abrams JF, Nguyen A, Hörig L, Axtner J, Louvrier J, Rawson BM, Nguyen HAQ, Guegan F, Nguyen TV, Le M, Sollmann R, Wilting A. Identifying conservation priorities in a defaunated tropical biodiversity hotspot. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13029] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Andrew Tilker
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Global Wildlife Conservation Austin TX USA
| | - Jesse F. Abrams
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - An Nguyen
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Lisa Hörig
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Jan Axtner
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Julie Louvrier
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | | | | | | | - Thanh Van Nguyen
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- VNU-Central Institute for Natural Resources and Environmental Studies Vietnam National University Hanoi Vietnam
| | - Minh Le
- VNU-Central Institute for Natural Resources and Environmental Studies Vietnam National University Hanoi Vietnam
- Department of Environmental Ecology Faculty of Environmental Sciences VNU-University of Science, Vietnam National University Hanoi Vietnam
| | - Rahel Sollmann
- Department of Wildlife, Fish, and Conservation Biology University of California Davis Davis CA USA
| | - Andreas Wilting
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
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24
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Zinger L, Donald J, Brosse S, Gonzalez MA, Iribar A, Leroy C, Murienne J, Orivel J, Schimann H, Taberlet P, Lopes CM. Advances and prospects of environmental DNA in neotropical rainforests. Tropical Ecosystems in the 21st Century. Elsevier; 2020. pp. 331-73. [DOI: 10.1016/bs.aecr.2020.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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25
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Hanya G, Morishima K, Koide T, Otani Y, Hongo S, Honda T, Okamura H, Higo Y, Hattori M, Kondo Y, Kurihara Y, Jin S, Otake A, Shiroisihi I, Takakuwa T, Yamamoto H, Suzuki H, Kajimura H, Hayakawa T, Suzuki‐Hashido N, Nakano T. Host selection of hematophagous leeches (
Haemadipsa japonica
): Implications for iDNA studies. Ecol Res 2019. [DOI: 10.1111/1440-1703.12059] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Goro Hanya
- Primate Research Institute Kyoto University Inuyama Japan
| | - Kaori Morishima
- United Graduate School of Agricultural Science Tokyo University of Agriculture and Technology Utsunomiya Japan
| | | | - Yosuke Otani
- Center for the Study of Co* Design Osaka University Toyonaka Japan
| | - Shun Hongo
- The Center for African Area Studies Kyoto University Kyoto Japan
| | - Takeaki Honda
- Primate Research Institute Kyoto University Inuyama Japan
| | - Hiroki Okamura
- Primate Research Institute Kyoto University Inuyama Japan
| | - Yuma Higo
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
| | - Masamichi Hattori
- Graduate School of Natural Science and Technology Gifu University Gifu Japan
| | - Yuki Kondo
- Graduate School of Education Gifu University Gifu Japan
- Graduate School of Science Osaka City University Osaka Japan
| | - Yosuke Kurihara
- Primate Research Institute Kyoto University Inuyama Japan
- Center for Education and Research in Field Sciences, Faculty of Agriculture Shizuoka University Hamamatsu Japan
| | - Sakura Jin
- Faculty of Agriculture Iwate University Morioka Japan
| | - Aji Otake
- Faculty of Agriculture Iwate University Morioka Japan
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | | | - Tomomi Takakuwa
- Faculty of Agriculture Tokyo University of Agriculture and Technology Fuchu Japan
| | | | - Hanami Suzuki
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
| | - Hisashi Kajimura
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
| | - Takashi Hayakawa
- Primate Research Institute Kyoto University Inuyama Japan
- Faculty of Environmental Earth Science Hokkaido University Sapporo Japan
- Japan Monkey Centre Inuyama Japan
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26
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Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
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Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
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27
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Owings CG, Banerjee A, Asher TMD, Gilhooly WP, Tuceryan A, Huffine M, Skaggs CL, Adebowale IM, Manicke NE, Picard CJ. Female Blow Flies As Vertebrate Resource Indicators. Sci Rep 2019; 9:10594. [PMID: 31332240 PMCID: PMC6646386 DOI: 10.1038/s41598-019-46758-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/02/2019] [Indexed: 11/09/2022] Open
Abstract
Rapid vertebrate diversity evaluation is invaluable for monitoring changing ecosystems worldwide. Wild blow flies naturally recover DNA and chemical signatures from animal carcasses and feces. We demonstrate the power of blow flies as biodiversity monitors through sampling of flies in three environments with varying human influences: Indianapolis, IN and two national parks (the Great Smoky Mountains and Yellowstone). Dissected fly guts underwent vertebrate DNA sequencing (12S and 16S rRNA genes) and fecal metabolite screening. Integrated Nested Laplace Approximation (INLA) was used to determine the most important abiotic factor influencing fly-derived vertebrate richness. In 720 min total sampling time, 28 vertebrate species were identified, with 42% of flies containing vertebrate resources: 23% DNA, 5% feces, and 14% contained both. The species of blow fly used was not important for vertebrate DNA recovery, however the use of female flies versus male flies directly influenced DNA detection. Temperature was statistically relevant across environments in maximizing vertebrate detection (mean = 0.098, sd = 0.048). This method will empower ecologists to test vertebrate community ecology theories previously out of reach due practical challenges associated with traditional sampling.
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Affiliation(s)
- Charity G Owings
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, SL 306, Indianapolis, IN, 46202, USA.
| | - Aniruddha Banerjee
- Department of Geography, Indiana University-Purdue University Indianapolis, 425 University Blvd, Cavanaugh Hall 441, Indianapolis, IN, 46202, USA
| | - Travis M D Asher
- Department of Geography, Indiana University-Purdue University Indianapolis, 425 University Blvd, Cavanaugh Hall 441, Indianapolis, IN, 46202, USA
| | - William P Gilhooly
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis, 723 W Michigan St, SL 118, Indianapolis, IN, 46202, USA
| | - Anais Tuceryan
- International School of Indiana, 4330 N Michigan Rd, Indianapolis, IN, 46208, USA
| | - Mary Huffine
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, SL 306, Indianapolis, IN, 46202, USA
| | - Christine L Skaggs
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford, LD 326, Indianapolis, IN, 46202, USA
| | - Iyun M Adebowale
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford, LD 326, Indianapolis, IN, 46202, USA
| | - Nicholas E Manicke
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford, LD 326, Indianapolis, IN, 46202, USA
| | - Christine J Picard
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, SL 306, Indianapolis, IN, 46202, USA
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28
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Kinoshita G, Yonezawa S, Murakami S, Isagi Y. Environmental DNA Collected from Snow Tracks is Useful for Identification of Mammalian Species. Zoolog Sci 2019; 36:198-207. [DOI: 10.2108/zs180172] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/20/2018] [Indexed: 11/17/2022]
Affiliation(s)
- Gohta Kinoshita
- Laboratory of Forest Biology Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyoku, Kyoto 606-8502, Japan
| | - Satoru Yonezawa
- Laboratory of Forest Biology Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyoku, Kyoto 606-8502, Japan
| | - Shota Murakami
- Course in Forest Field Science, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan
| | - Yuji Isagi
- Laboratory of Forest Biology Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyoku, Kyoto 606-8502, Japan
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29
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Abrams JF, Hörig LA, Brozovic R, Axtner J, Crampton‐Platt A, Mohamed A, Wong ST, Sollmann R, Yu DW, Wilting A. Shifting up a gear with
iDNA
: From mammal detection events to standardised surveys. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13411] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [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)
- Jesse F. Abrams
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Lisa A. Hörig
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Robert Brozovic
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Jan Axtner
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | | | - Azlan Mohamed
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Seth T. Wong
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Rahel Sollmann
- Department of Wildlife, Fish, and Conservation Biology University of California Davis Davis California
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan China
- School of Biological Sciences University of East AngliaNorwich Research Park Norwich Norfolk UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research Berlin Germany
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30
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Gueuning M, Ganser D, Blaser S, Albrecht M, Knop E, Praz C, Frey JE. Evaluating next-generation sequencing (NGS) methods for routine monitoring of wild bees: Metabarcoding, mitogenomics or NGS barcoding. Mol Ecol Resour 2019; 19:847-862. [PMID: 30912868 PMCID: PMC6850489 DOI: 10.1111/1755-0998.13013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/15/2019] [Indexed: 12/26/2022]
Abstract
Implementing cost‐effective monitoring programs for wild bees remains challenging due to the high costs of sampling and specimen identification. To reduce costs, next‐generation sequencing (NGS)‐based methods have lately been suggested as alternatives to morphology‐based identifications. To provide a comprehensive presentation of the advantages and weaknesses of different NGS‐based identification methods, we assessed three of the most promising ones, namely metabarcoding, mitogenomics and NGS barcoding. Using a regular monitoring data set (723 specimens identified using morphology), we found that NGS barcoding performed best for both species presence/absence and abundance data, producing only few false positives (3.4%) and no false negatives. In contrast, the proportion of false positives and false negatives was higher using metabarcoding and mitogenomics. Although strong correlations were found between biomass and read numbers, abundance estimates significantly skewed the communities' composition in these two techniques. NGS barcoding recovered the same ecological patterns as morphology. Ecological conclusions based on metabarcoding and mitogenomics were similar to those based on morphology when using presence/absence data, but different when using abundance data. In terms of workload and cost, we show that metabarcoding and NGS barcoding can compete with morphology, but not mitogenomics which was consistently more expensive. Based on these results, we advocate that NGS barcoding is currently the seemliest NGS method for monitoring of wild bees. Furthermore, this method has the advantage of potentially linking DNA sequences with preserved voucher specimens, which enable morphological re‐examination and will thus produce verifiable records which can be fed into faunistic databases.
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Affiliation(s)
- Morgan Gueuning
- Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland.,Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Dominik Ganser
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Simon Blaser
- Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | | | - Eva Knop
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Christophe Praz
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Juerg E Frey
- Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland
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31
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Axtner J, Crampton-Platt A, Hörig LA, Mohamed A, Xu CCY, Yu DW, Wilting A. An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies. Gigascience 2019; 8:giz029. [PMID: 30997489 PMCID: PMC6461710 DOI: 10.1093/gigascience/giz029] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/12/2018] [Accepted: 03/07/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation. FINDINGS Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a "twin-tagging," 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in >50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples. CONCLUSIONS Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods.
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Affiliation(s)
- Jan Axtner
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Alex Crampton-Platt
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Lisa A Hörig
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Azlan Mohamed
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Charles C Y Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd, Kunming, Yunnan 650223, China
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
- Redpath Museum and Department of Biology, McGill University 859 Sherbooke Street West, Montreal, PQ, Canada H3A 2K6
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd, Kunming, Yunnan 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
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Wearn OR, Glover-Kapfer P. Snap happy: camera traps are an effective sampling tool when compared with alternative methods. R Soc Open Sci 2019; 6:181748. [PMID: 31032031 PMCID: PMC6458413 DOI: 10.1098/rsos.181748] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/12/2019] [Indexed: 05/11/2023]
Abstract
Camera traps have become a ubiquitous tool in ecology and conservation. They are routinely deployed in wildlife survey and monitoring work, and are being advocated as a tool for planetary-scale biodiversity monitoring. The camera trap's widespread adoption is predicated on the assumption of its effectiveness, but the evidence base for this is lacking. Using 104 past studies, we recorded the qualitative overall recommendations made by study authors (for or against camera traps, or ambiguous), together with quantitative data on the effectiveness of camera traps (e.g. number of species detected or detection probabilities) relative to 22 other methods. Most studies recommended the use of camera traps overall and they were 39% more effective based on the quantitative data. They were significantly more effective compared with live traps (88%) and were otherwise comparable in effectiveness to other methods. Camera traps were significantly more effective than other methods at detecting a large number of species (31% more) and for generating detections of species (91% more). This makes camera traps particularly suitable for broad-spectrum biodiversity surveys. Film camera traps were found to be far less effective than digital models, which has led to an increase in camera trap effectiveness over time. There was also evidence from the authors that the use of attractants with camera traps reduced their effectiveness (counter to their intended effect), while the quantitative data indicated that camera traps were more effective in closed than open habitats. Camera traps are a highly effective wildlife survey tool and their performance will only improve with future technological advances. The images they produce also have a range of other benefits, for example as digital voucher specimens and as visual aids for outreach. The evidence-base supports the increasing use of camera traps and underlines their suitability for meeting the challenges of global-scale biodiversity monitoring.
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Affiliation(s)
- Oliver R. Wearn
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Paul Glover-Kapfer
- WWF-UK, The Living Planet Centre, Rufford House, Brewery Road, Woking, UK
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Ruppert KM, Kline RJ, Rahman MS. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 2019; 17:e00547. [DOI: 10.1016/j.gecco.2019.e00547] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Egeter B, Peixoto S, Brito JC, Jarman S, Puppo P, Velo-Antón G. Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNA. Genome 2018; 61:807-814. [DOI: 10.1139/gen-2018-0071] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful tool for species detection and is being increasingly used to conduct biodiversity assessments. However, there are a number of difficulties with sampling eDNA from such turbid water-bodies and it is often not feasible to rely on electrical tools in remote desert environments. We trialled a manually powered filtering method in Mauritania, using pre-filtration to circumvent problems posed by turbid water in remote arid areas. From nine vertebrate species expected in the water-bodies, four were detected visually, two via metabarcoding, and one via both methods. Difficulties filtering turbid water led to severe constraints, limiting the sampling protocol to only one sampling point per study site, which alone may largely explain why many of the expected vertebrate species were not detected. The amplification of human DNA using general vertebrate primers is also likely to have contributed to the low number of taxa identified. Here we highlight a number of challenges that need to be overcome to successfully conduct metabarcoding eDNA studies for vertebrates in desert environments in Africa.
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Affiliation(s)
- Bastian Egeter
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - Sara Peixoto
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- Departamento de Biologia da Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - José C. Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- Departamento de Biologia da Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Simon Jarman
- Trace and Environmental DNA (TrEnD) Laboratory, Molecular and Life Sciences, Curtin University, WA, 6102, Australia
- Environomics Future Science Platform, CSIRO National Collections and Marine Infrastructure, Crawley, WA, 6009, Australia
| | - Pamela Puppo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
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Kerley GIH, Landman M, Ficetola GF, Boyer F, Bonin A, Rioux D, Taberlet P, Coissac E. Diet shifts by adult flightless dung beetles Circellium bacchus, revealed using DNA metabarcoding, reflect complex life histories. Oecologia 2018; 188:107-115. [PMID: 29961180 DOI: 10.1007/s00442-018-4203-6] [Citation(s) in RCA: 12] [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: 08/24/2017] [Accepted: 06/06/2018] [Indexed: 12/18/2022]
Abstract
Life history changes may change resource use. Such shifts are not well understood in the dung beetles, despite recognised differences in larval and adult feeding ability. We use the flightless dung beetle Circellium bacchus to explore such shifts, identifying dung sources of adults using DNA metabarcoding, and comparing these with published accounts of larval dung sources. C. bacchus is traditionally considered to specialise on the dung of large herbivores for both larval and adult feeding. We successfully extracted mammal DNA from 151 adult C. bacchus fecal samples, representing 16 mammal species (ranging from elephants to small rodents), many of which are hitherto undescribed in the diet. Adult C. bacchus showed clear dung source preferences, especially for large herbivores inhabiting dense-cover vegetation. Our approach also confirmed the presence of cryptic taxa in the study area, and we propose that this may be used for biodiversity survey and monitoring purposes. Murid rodent feces were the most commonly fed-upon dung source (77.5%) for adult C. bacchus, differing markedly from the large and megaherbivore dung sources used for larval rearing. These findings support the hypothesis of life history-specific shifts in resource use in dung beetles, and reveal a hitherto unsuspected, but ecologically important, role of these dung beetles in consuming rodent feces. The differences in feeding abilities of the larval and adult life history stages have profound consequences for their resource use and foraging strategies, and hence the ecological role of dung beetles. This principle and its ecological consequences should be explored in other scarabaeids.
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Affiliation(s)
- Graham I H Kerley
- Centre for African Conservation Ecology, Nelson Mandela University, P O Box 77000, Port Elizabeth, 6013, South Africa.
| | - Marietjie Landman
- Centre for African Conservation Ecology, Nelson Mandela University, P O Box 77000, Port Elizabeth, 6013, South Africa
| | - Gentile F Ficetola
- Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Department of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Frédéric Boyer
- Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Aurélie Bonin
- Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Delphine Rioux
- Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Pierre Taberlet
- Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Eric Coissac
- Centre National de la Recherche Scientifique, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
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