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Investigating the Potential Utility of Environmental DNA to Provide a Relative Abundance Index for the Depleted Teleost, Mulloway, Argyrosomus japonicus. DIVERSITY 2023. [DOI: 10.3390/d15030322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Non-invasive, low-cost methods for censusing depleted fish populations are being prioritised among many jurisdictions worldwide. Collecting environmental DNA (eDNA) could offer one such option for augmenting fish population assessments. However, candidate species need to be carefully selected because species-specific DNA shedding and decay rates are affected by many biotic and abiotic factors that may influence relative abundance estimates. In this study, we sought to ascertain if the eDNA of a depleted Australian teleost, mulloway, Argyrosomus japonicus, reflects its weight under controlled aquaria conditions. With four experiments, we investigated the relationships between mulloway eDNA concentrations and their weight tank−1 as a function of: (1) time post-tank establishment; (2) water temperatures (within the species’ tolerance range); (3) stocking densities; and (4) among individual, similar-sized fish. The concentrations of eDNA in tanks stabilised after six days, and a positive relationship was found between fish weight and eDNA concentration, despite some variability in shedding rates by similar-sized fish. There was also a positive effect of water temperature on eDNA concentrations, which reinforces the need to control for such abiotic factors. We conclude that there is strong utility in applying eDNA concentrations as an index of relative abundance for mulloway under controlled conditions, which justifies future field-based investigations.
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2
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Ahmed SF, Kumar PS, Kabir M, Zuhara FT, Mehjabin A, Tasannum N, Hoang AT, Kabir Z, Mofijur M. Threats, challenges and sustainable conservation strategies for freshwater biodiversity. ENVIRONMENTAL RESEARCH 2022; 214:113808. [PMID: 35798264 DOI: 10.1016/j.envres.2022.113808] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/06/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Increasing human population, deforestation and man-made climate change are likely to exacerbate the negative effects on freshwater ecosystems and species endangerment. Consequently, the biodiversity of freshwater continues to dwindle at an alarming rate. However, this particular topic lacks sufficient attention from conservation ecologists and policymakers, resulting in a dearth of data and comprehensive reviews on freshwater biodiversity, specifically. Despite the widespread awareness of risks to freshwater biodiversity, organized action to reverse this decline has been lacking. This study reviews prospective conservation and management strategies for freshwater biodiversity and their associated challenges, identifying current key threats to freshwater biodiversity. Engineered nanomaterials pose a significant threat to aquatic species, and will make controlling health risks to freshwater biodiversity increasingly challenging in the future. When fish are exposed to nanoparticles, the surface area of their respiratory and ion transport systems can decline to 60% of their total surface area, posing serious health risks. Also, about 50% of freshwater fish species are threatened by climate change, globally. Freshwater biodiversity that is heavily reliant on calcium perishes when the calcium content of their environments degrades, posing another severe threat to world biodiversity. To improve biodiversity, variables such as species diversity, population and water quality, and habitat are essential components that must be monitored continuously. Existing research on freshwater biota and ecosystems is still lacking. Therefore, data collection and the establishment of specialized policies for the conservation of freshwater biodiversity should be prioritized.
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Affiliation(s)
- Shams Forruque Ahmed
- Science and Math Program, Asian University for Women, Chattogram, 4000, Bangladesh.
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, Chennai, 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, Chennai, 603110, India; Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, India
| | - Maliha Kabir
- Science and Math Program, Asian University for Women, Chattogram, 4000, Bangladesh
| | - Fatema Tuz Zuhara
- Science and Math Program, Asian University for Women, Chattogram, 4000, Bangladesh
| | - Aanushka Mehjabin
- Science and Math Program, Asian University for Women, Chattogram, 4000, Bangladesh
| | - Nuzaba Tasannum
- Science and Math Program, Asian University for Women, Chattogram, 4000, Bangladesh
| | - Anh Tuan Hoang
- Institute of Engineering, HUTECH University, Ho Chi Minh City, Viet Nam.
| | - Zobaidul Kabir
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - M Mofijur
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia; Mechanical Engineering Department, Prince Mohammad Bin Fahd University, Al Khobar, 31952, Saudi Arabia.
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3
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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4
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Smyth ERB, Drake DAR. A classification framework for interspecific trade-offs in aquatic ecology. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13762. [PMID: 34057237 DOI: 10.1111/cobi.13762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 04/27/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
In some cases, wildlife management objectives directed at multiple species can conflict with one another, creating species trade-offs. For managers to effectively identify trade-offs and avoid their undesirable outcomes, they must understand the agents involved and their corresponding interactions. A literature review of interspecific trade-offs within freshwater and marine ecosystems was conducted to illustrate the scope of potential interspecific trade-offs that may occur. We identified common pitfalls that lead to failed recognition of interspecific trade-offs, including, single-species management and limited consideration of the spatial and temporal scale of ecosystems and their management regimes. We devised a classification framework of common interspecific trade-offs within aquatic systems. The classification can help managers determine whether the conflict is species based through direct relationships (i.e., predator-prey, competition, other antagonistic relationships) or indirect relationships involving intermediate species (i.e., conflict-generating species) or whether the conflict is driven by opposing management objectives for species that would otherwise not interact (i.e., nontarget management effects). Once the nature and scope of trade-offs are understood, existing decision-making tools, such as structured decision-making and real-options analysis, can be incorporated to improve the management of aquatic ecosystems. Article Impact Statement: A synthesis of interspecific trade-offs in aquatic ecosystems supports their identification and resolution.
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Affiliation(s)
- Eric R B Smyth
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, Ontario, Canada
| | - D Andrew R Drake
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, Ontario, Canada
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5
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Mariac C, Duponchelle F, Miranda G, Ramallo C, Wallace R, Tarifa G, Garcia-Davila C, Ortega H, Pinto J, Renno JF. Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA. PLoS One 2022; 17:e0262357. [PMID: 34982802 PMCID: PMC8726463 DOI: 10.1371/journal.pone.0262357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
To date, more than 2400 valid fish species have been recorded in the Amazon basin. However, some regions remain poorly documented. This is the case in the Beni basin and in particular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlapping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species compositions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the different hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possible to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a baseline for future studies, including on other Andean tributaries.
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Affiliation(s)
- Cédric Mariac
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- * E-mail:
| | - Fabrice Duponchelle
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Guido Miranda
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
- Unidad de Limnología, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Camila Ramallo
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
| | - Robert Wallace
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
| | - Gabriel Tarifa
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
| | - Carmen Garcia-Davila
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- Instituto de Investigaciones de la Amazonía Peruana (IIAP), Laboratorio de Biología y Genética Molecular (LBGM), Iquitos, Perú
| | - Hernán Ortega
- Departamento de Ictiología, Museo de Historia Natural, Universidad Nacional Mayor San Marcos, Lima, Peru
| | - Julio Pinto
- Unidad de Limnología, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Jean-François Renno
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
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6
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Zhao B, van Bodegom PM, Trimbos K. The particle size distribution of environmental DNA varies with species and degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149175. [PMID: 34303977 DOI: 10.1016/j.scitotenv.2021.149175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) analysis is frequently used as a non-invasive method to investigate species and biodiversity in ecosystems. However, such eDNA may represent both organisms currently present as well as species that released their DNA some point in the past, thereby representing a mix of current and historic biodiversity. This may lead to a false-positive detection of organisms' presence. As the eDNA particle size distribution (PSD) changes along with the decay process, it may facilitate solving the above problem. Here, we set up tank experiments with snails, zebrafish and daphnids, respectively, to monitor the change in eDNA PSD and eDNA degradation through time after removing organisms. We found that zebrafish eDNA decays more slowly for larger particle sizes. Across all species tested, the percentage of large size ranges tended to increase over time while the smaller sizes showed relatively fast decay rates. As a result, PSD changed consistently with eDNA decay, although initial PSD varied between species. In combination, we propose that eDNA PSD can be used to assess the current prevalence of organisms at an eDNA sampling location while avoiding false-positives on the presence of species. Our findings expand the applicability of eDNA for monitoring target species in freshwater ecosystems.
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Affiliation(s)
- Beilun Zhao
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands.
| | - Peter M van Bodegom
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands
| | - Krijn Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands
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7
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Yates MC, Cristescu ME, Derry AM. Integrating physiology and environmental dynamics to operationalize environmental DNA (eDNA) as a means to monitor freshwater macro-organism abundance. Mol Ecol 2021; 30:6531-6550. [PMID: 34592014 DOI: 10.1111/mec.16202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/03/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022]
Abstract
Research has demonstrated consistent positive correlations between organism abundance and absolute environmental DNA (eDNA) concentrations. Robust correlations in laboratory experiments indicate strong functional links, suggesting the potential for eDNA to monitor organism abundance in nature. However, correlations between absolute eDNA concentrations and organism abundance in nature tend to be weaker because myriad biotic and abiotic factors influence steady-state eDNA concentrations, decoupling its direct functional link with abundance. Additional technical challenges can also weaken correlations between relative organism abundance and relative eDNA data derived from metabarcoding. Future research must account for these factors to improve the inference of organism abundance from eDNA, including integrating the effects of organism physiology on eDNA production, eDNA dynamics in lentic/lotic systems, and key environmental parameters that impact estimated steady-state concentrations. Additionally, it is critical to manage expectations surrounding the accuracy and precision that eDNA can provide - eDNA, for example, cannot provide abundance estimates comparable to intensively managed freshwater fisheries that enumerate every individual fish. Recent developments, however, are encouraging. Current methods could provide meaningful information regarding qualitative conservation thresholds and emergent research has demonstrated that eDNA concentrations in natural ecosystems can provide rough quantitative estimates of abundance, particularly when models integrate physiology and/or eDNA dynamics. Operationalizing eDNA to infer abundance will probably require more than simple correlations with organism biomass/density. Nevertheless, the future is promising - models that integrate eDNA dynamics in nature could represent an effective means to infer abundance, particularly when traditional methods are considered too "costly" or difficult to obtain.
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Affiliation(s)
| | | | - Alison M Derry
- Université du Québec à Montréal, Montréal, Québec, Canada
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8
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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] [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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9
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Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data. Foods 2021; 10:foods10061425. [PMID: 34205462 PMCID: PMC8235475 DOI: 10.3390/foods10061425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 01/10/2023] Open
Abstract
The decline in wild-caught fisheries paired with increasing global seafood demand is pushing the need for seafood sustainability to the forefront of national and regional priorities. Validation of species identity is a crucial early step, yet conventional monitoring and surveillance tools are limited in their effectiveness because they are extremely time-consuming and require expertise in fish identification. DNA barcoding methods are a versatile tool for the genetic monitoring of wildlife products; however, they are also limited by requiring individual tissue samples from target specimens which may not always be possible given the speed and scale of seafood operations. To circumvent the need to individually sample organisms, we pilot an approach that uses forensic environmental DNA (eDNA) metabarcoding to profile fish species composition from the meltwater in fish holds on industrial and artisanal fishing vessels in Ecuador. Fish identified genetically as present were compared to target species reported by each vessel’s crew. Additionally, we contrasted the geographic range of identified species against the satellite-based fishing route data of industrial vessels to determine if identified species could be reasonably expected in the catch.
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10
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Nevers MB, Przybyla-Kelly K, Shively D, Morris CC, Dickey J, Byappanahalli MN. Influence of sediment and stream transport on detecting a source of environmental DNA. PLoS One 2020; 15:e0244086. [PMID: 33370371 PMCID: PMC7769486 DOI: 10.1371/journal.pone.0244086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/02/2020] [Indexed: 12/22/2022] Open
Abstract
Environmental DNA (eDNA) can be used for early detection, population estimations, and assessment of potential spread of invasive species, but questions remain about factors that influence eDNA detection results. Efforts are being made to understand how physical, chemical, and biological factors-settling, resuspension, dispersion, eDNA stability/decay-influence eDNA estimations and potentially population abundance. In a series of field and controlled mesocosm experiments, we examined the detection and accumulation of eDNA in sediment and water and the transport of eDNA in a small stream in the Lake Michigan watershed, using the invasive round goby fish (Neogobius melanostomus) as a DNA source. Experiment 1: caged fish (average n = 44) were placed in a stream devoid of round goby; water was collected over 24 hours along 120-m of stream, including a simultaneous sampling event at 7 distances from DNA source; stream monitoring continued for 24 hours after fish were removed. Experiment 2: round goby were placed in laboratory tanks; water and sediment were collected over 14 days and for another 150 days post-fish removal to calculate eDNA shedding and decay rates for water and sediment. For samples from both experiments, DNA was extracted, and qPCR targeted a cytochrome oxidase I gene (COI) fragment specific to round goby. Results indicated that eDNA accumulated and decayed more slowly in sediment than water. In the stream, DNA shedding was markedly lower than calculated in the laboratory, but models indicate eDNA could potentially travel long distances (up to 50 km) under certain circumstances. Collectively, these findings show that the interactive effects of ambient conditions (e.g., eDNA stability and decay, hydrology, settling-resuspension) are important to consider when developing comprehensive models. Results of this study can help resource managers target representative sites downstream of potential invasion sites, thereby maximizing resource use.
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Affiliation(s)
- Meredith B. Nevers
- Great Lakes Science Center, U.S. Geological Survey, Chesterton, Indiana, United States of America
| | - Kasia Przybyla-Kelly
- Great Lakes Science Center, U.S. Geological Survey, Chesterton, Indiana, United States of America
| | - Dawn Shively
- Great Lakes Science Center, U.S. Geological Survey, Chesterton, Indiana, United States of America
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Charles C. Morris
- Indiana Dunes National Park, National Park Service, Porter, Indiana, United States of America
| | - Joshua Dickey
- Indiana Dunes National Park, National Park Service, Porter, Indiana, United States of America
| | - Murulee N. Byappanahalli
- Great Lakes Science Center, U.S. Geological Survey, Chesterton, Indiana, United States of America
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11
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Samplonius JM, Atkinson A, Hassall C, Keogan K, Thackeray SJ, Assmann JJ, Burgess MD, Johansson J, Macphie KH, Pearce-Higgins JW, Simmonds EG, Varpe Ø, Weir JC, Childs DZ, Cole EF, Daunt F, Hart T, Lewis OT, Pettorelli N, Sheldon BC, Phillimore AB. Strengthening the evidence base for temperature-mediated phenological asynchrony and its impacts. Nat Ecol Evol 2020; 5:155-164. [PMID: 33318690 DOI: 10.1038/s41559-020-01357-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/23/2020] [Indexed: 11/10/2022]
Abstract
Climate warming has caused the seasonal timing of many components of ecological food chains to advance. In the context of trophic interactions, the match-mismatch hypothesis postulates that differential shifts can lead to phenological asynchrony with negative impacts for consumers. However, at present there has been no consistent analysis of the links between temperature change, phenological asynchrony and individual-to-population-level impacts across taxa, trophic levels and biomes at a global scale. Here, we propose five criteria that all need to be met to demonstrate that temperature-mediated trophic asynchrony poses a growing risk to consumers. We conduct a literature review of 109 papers studying 129 taxa, and find that all five criteria are assessed for only two taxa, with the majority of taxa only having one or two criteria assessed. Crucially, nearly every study was conducted in Europe or North America, and most studies were on terrestrial secondary consumers. We thus lack a robust evidence base from which to draw general conclusions about the risk that climate-mediated trophic asynchrony may pose to populations worldwide.
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Affiliation(s)
- Jelmer M Samplonius
- Institute for Evolutionary Biology, The University of Edinburgh, Edinburgh, UK.
| | | | - Christopher Hassall
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Katharine Keogan
- Institute for Evolutionary Biology, The University of Edinburgh, Edinburgh, UK.,Marine Scotland Science, Marine Laboratory, Aberdeen, UK
| | | | | | - Malcolm D Burgess
- RSPB Centre for Conservation Science, Sandy, UK.,Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | | | - Kirsty H Macphie
- Institute for Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
| | - James W Pearce-Higgins
- British Trust for Ornithology, Thetford, UK.,Conservation Science Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Emily G Simmonds
- Department of Mathematical Sciences and Centre for Biodiversity Dynamics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Øystein Varpe
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Norwegian Institute for Nature Research, Bergen, Norway
| | - Jamie C Weir
- Institute for Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
| | - Dylan Z Childs
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Ella F Cole
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, UK
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Ben C Sheldon
- Department of Zoology, University of Oxford, Oxford, UK
| | - Albert B Phillimore
- Institute for Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
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12
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Halvorsen S, Korslund L, Gustavsen PØ, Slettan A. Environmental DNA analysis indicates that migration barriers are decreasing the occurrence of European eel (Anguilla anguilla) in distance from the sea. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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13
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van Rees CB, Waylen KA, Schmidt‐Kloiber A, Thackeray SJ, Kalinkat G, Martens K, Domisch S, Lillebø AI, Hermoso V, Grossart H, Schinegger R, Decleer K, Adriaens T, Denys L, Jarić I, Janse JH, Monaghan MT, De Wever A, Geijzendorffer I, Adamescu MC, Jähnig SC. Safeguarding freshwater life beyond 2020: Recommendations for the new global biodiversity framework from the European experience. Conserv Lett 2020. [DOI: 10.1111/conl.12771] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
| | - Kerry A. Waylen
- Social, Economic and Geographical Sciences Department The James Hutton Institute Aberdeen Scotland UK
| | - Astrid Schmidt‐Kloiber
- Institute of Hydrobiology and Aquatic Ecosystem Management University of Natural Resources and Life Sciences Vienna (BOKU) Vienna Austria
| | | | - Gregor Kalinkat
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences Brussels Belgium
- University of Ghent, Biology Ghent Belgium
| | - Sami Domisch
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
| | - Ana I. Lillebø
- Department of Biology & CESAM University of Aveiro Aveiro Portugal
| | - Virgilio Hermoso
- Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC) Solsona Spain
| | - Hans‐Peter Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Institute of Biochemistry and Biology University of Potsdam Germany
| | - Rafaela Schinegger
- Institute of Hydrobiology and Aquatic Ecosystem Management University of Natural Resources and Life Sciences Vienna (BOKU) Vienna Austria
| | - Kris Decleer
- Research Institute for Nature and Forest (INBO) Brussels Belgium
| | - Tim Adriaens
- Research Institute for Nature and Forest (INBO) Brussels Belgium
| | - Luc Denys
- Research Institute for Nature and Forest (INBO) Brussels Belgium
| | - Ivan Jarić
- Biology Centre of the Czech Academy of Sciences Institute of Hydrobiology České Budějovice Czech Republic
- Faculty of Science Department of Ecosystem Biology, University of South Bohemia České Budějovice Czech Republic
| | - Jan H. Janse
- PBL Netherlands Environmental Assessment Agency The Hague The Netherlands
- Netherlands Institute of Ecology, NIOO‐KNAW Wageningen The Netherlands
| | - Michael T. Monaghan
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Institut für Biologie Freie Universität Berlin Germany
| | - Aaike De Wever
- Research Institute for Nature and Forest (INBO) Brussels Belgium
| | - Ilse Geijzendorffer
- Tour du Valat Research Institute for the Conservation of Mediterranean Wetlands Arles France
| | - Mihai C. Adamescu
- Research Centre in Systems Ecology and Sustainability University of Bucharest Bucharest Romania
| | - Sonja C. Jähnig
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Geography Department Humboldt‐Universität zu Berlin, Berlin Germany
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14
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Goutte A, Molbert N, Guérin S, Richoux R, Rocher V. Monitoring freshwater fish communities in large rivers using environmental DNA metabarcoding and a long-term electrofishing survey. JOURNAL OF FISH BIOLOGY 2020; 97:444-452. [PMID: 32412670 DOI: 10.1111/jfb.14383] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Monitoring freshwater fish communities in a large human-impacted river is a challenging task. The structure of fish assemblages has been monitored yearly in the Marne and the Seine Rivers, across the Paris conurbation, France, using traditional electrofishing (EF) surveys since 1990, in accordance with the European Water Framework Directive. In addition, metabarcoding of DNA extracted from environmental samples (eDNA) was concomitantly conducted in nine sampling sites in 2017 and in 2018 to compare the estimates of species richness and relative abundance among three methods: annual, long-term EF monitoring and eDNA. The present study confirms better detection of fish species using eDNA compared to annual EF. eDNA metabarcoding was also more efficient for species detection than a 3-6-year EF survey but was similar or less efficient than a long-term EF survey of 14 years of monitoring. In addition, the numbers of reads per species relative to the total number of reads significantly increased with (a) increasing relative abundance (relative percentage of individuals caught per species) and (b) increasing number of years that a fish species was detected during the 2000-2018 period. These results suggest that eDNA could reflect local population persistence.
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Affiliation(s)
- Aurélie Goutte
- Sorbonne Université, CNRS, EPHE, UMR METIS, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Noëlie Molbert
- Sorbonne Université, CNRS, EPHE, UMR METIS, Paris, France
| | - Sabrina Guérin
- Syndicat Interdépartemental pour l'Assainissement de l'Agglomération Parisienne (SIAAP), Colombes, France
| | - Robin Richoux
- Syndicat Interdépartemental pour l'Assainissement de l'Agglomération Parisienne (SIAAP), Colombes, France
| | - Vincent Rocher
- Syndicat Interdépartemental pour l'Assainissement de l'Agglomération Parisienne (SIAAP), Colombes, France
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