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Sepulveda AJ, Dumoulin CE, Blanchette DL, McPhedran J, Holme C, Whalen N, Hunter ME, Merkes CM, Richter CA, Neilson ME, Daniel WM, Jones DN, Smith DR. When are environmental DNA early detections of invasive species actionable? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 343:118216. [PMID: 37247541 DOI: 10.1016/j.jenvman.2023.118216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/19/2023] [Accepted: 05/19/2023] [Indexed: 05/31/2023]
Abstract
Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an early detection rapid response program because positive eDNA detections are not always indicative of an eventual infestation. We used a structured decision making (SDM) framework to evaluate appropriate response actions to hypothetical eDNA early detections of an introduced aquatic plant in Sebago Lake (Maine, USA). The results were juxtaposed to a recent study that used a similar SDM approach to evaluate response actions to hypothetical eDNA early detections of introduced mussels in Jordanelle Reservoir (Utah, USA). We found that eDNA early detections were not actionable in Sebago Lake because the plant's invasion potential was spatially constrained and the current management activities provided acceptable levels of mitigation. In Jordanelle Reservoir, eDNA detections were actionable due to high invasion potential and analyses supported management actions to contain the invasion. The divergent outcomes of the two case studies are related to the unique attributes of the habitats and species, highlighting the utility of the SDM approach when considering an eDNA monitoring program. We use these two case studies to present a general SDM framework and a set of heuristics that can be efficiently applied to eDNA early detection rapid response scenarios and other instances associated with indeterminant eDNA detections, especially when there is an imperative to make decisions as quickly as possible.
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Affiliation(s)
- Adam J Sepulveda
- U.S. Geological Survey Northern Rocky Mountain Science Center, Bozeman, MT, 59715, USA.
| | - Christine E Dumoulin
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown, WV, 25430, USA
| | | | - John McPhedran
- Maine Department of Environmental Protection, Augusta, ME, 04333, USA
| | - Colin Holme
- Lakes Environmental Association, Bridgton, ME, 04009, USA
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA
| | - Christopher M Merkes
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, WI, 54603, USA
| | - Catherine A Richter
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, 65201, USA
| | - Matthew E Neilson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA
| | - Wesley M Daniel
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA
| | - Devin N Jones
- U.S. Geological Survey Northern Rocky Mountain Science Center, Bozeman, MT, 59715, USA
| | - David R Smith
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown, WV, 25430, USA
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2
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Keller AG, Grason EW, McDonald PS, Ramón-Laca A, Kelly RP. Tracking an invasion front with environmental DNA. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2561. [PMID: 35128750 DOI: 10.1002/eap.2561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 12/14/2021] [Indexed: 05/03/2023]
Abstract
Data from environmental DNA (eDNA) may revolutionize environmental monitoring and management, providing increased detection sensitivity at reduced cost and survey effort. However, eDNA data are rarely used in decision-making contexts, mainly due to uncertainty around (1) data interpretation and (2) whether and how molecular tools dovetail with existing management efforts. We address these challenges by jointly modeling eDNA detection via qPCR and traditional trap data to estimate the density of invasive European green crab (Carcinus maenas), a species for which, historically, baited traps have been used for both detection and control. Our analytical framework simultaneously quantifies uncertainty in both detection methods and provides a robust way of integrating different data streams into management processes. Moreover, the joint model makes clear the marginal information benefit of adding eDNA (or any other) additional data type to an existing monitoring program, offering a path to optimizing sampling efforts for species of management interest. Here, we document green crab eDNA beyond the previously known invasion front and find that the value of eDNA data dramatically increases with low population densities and low traditional sampling effort, as is often the case at leading-edge locations. We also highlight the detection limits of the molecular assay used in this study, as well as scenarios under which eDNA sampling is unlikely to improve existing management efforts.
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Affiliation(s)
- Abigail G Keller
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Emily W Grason
- Washington Sea Grant, University of Washington, Seattle, Washington, USA
| | - P Sean McDonald
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Ana Ramón-Laca
- CICOES, University of Washington at Northwest Fisheries Science Center, Seattle, Washington, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
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3
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Newcomb TJ, Simonin PW, Martinez FA, Chadderton WL, Bossenbroek JM, Cudmore B, Hoff MH, Keller RP, Ridenhour BD, Rothlisberger JD, Rutherford ES, Van Egeren S, Lodge DM. A Best Practices Case Study for Scientific Collaboration between Researchers and Managers. FISHERIES 2021; 46:131-138. [PMID: 33888934 PMCID: PMC8048992 DOI: 10.1002/fsh.10536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 08/15/2020] [Accepted: 09/27/2020] [Indexed: 06/12/2023]
Abstract
Effective engagement among scientists, government agency staff, and policymakers is necessary for solving fisheries challenges, but remains challenging for a variety of reasons. We present seven practices learned from a collaborative project focused on invasive species in the Great Lakes region (USA-CAN). These practices were based on a researcher-manager model composed of a research team, a management advisory board, and a bridging organization. We suggest this type of system functions well when (1) the management advisory board is provided compelling rationale for engagement; (2) the process uses key individuals as communicators; (3) the research team thoughtfully selects organizations and individuals involved; (4) the funding entity provides logistical support and allows for (5) a flexible structure that prioritizes management needs; (6) a bridging organization sustains communication between in-person meetings; and (7) the project team determines and enacts a project endpoint. We predict these approaches apply equally effectively to other challenges at the research-management-policy interface, including reductions of water pollution, transitions to renewable energy, increasing food security, and addressing climate change.
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Affiliation(s)
| | - Paul W. Simonin
- Cornell UniversityDepartment of Ecology and Evolutionary BiologyIthacaNY
| | - Felix A. Martinez
- National Oceanic and Atmospheric Administration, National Centers for Coastal Ocean ScienceAnn ArborMI
| | | | - Jon M. Bossenbroek
- Department of Environmental Sciences and Lake Erie CenterUniversity of ToledoToledoOH
| | | | - Michael H. Hoff
- U.S. Fish and Wildlife Service (retired), Fish and Aquatic ConservationBloomingtonMN
| | - Reuben P. Keller
- Loyola University ChicagoInstitute of Environmental SustainabilityChicagoIL
| | - Berkley D. Ridenhour
- The Nature Conservancy, Great Lakes ProjectSouth BendIN
- The Nature ConservancyMoscowID
| | | | - Edward S. Rutherford
- National Oceanic and Atmospheric AdministrationGreat Lakes Environmental Research LaboratoryAnn ArborMI
| | | | - David M. Lodge
- Cornell UniversityCornell Atkinson Center for SustainabilityIthacaNY
- University of Notre DameEnvironmental Change InitiativeSouth BendIN (former)
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4
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Jerde CL. Can we manage fisheries with the inherent uncertainty from eDNA? JOURNAL OF FISH BIOLOGY 2021; 98:341-353. [PMID: 31769024 DOI: 10.1111/jfb.14218] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
Environmental (e)DNA, as a general approach in aquatic systems, seeks to connect the presence of species' genetic material in the water and hence to infer the species' physical presence. However, fisheries managers face making decisions with risk and uncertainty when eDNA indicates a fish is present but traditional methods fail to capture the fish. In comparison with traditional methods such as nets, electrofishing and piscicides, eDNA approaches have more sources of underlying error that could give rise to false positives. This has resulted in some managers to question whether eDNA can be used to make management decisions because there is no fish in hand. As a relatively new approach, the methods and techniques have quickly evolved to improve confidence in eDNA. By evaluating an eDNA based research programmes through the pattern of the eDNA signal, assay design, experimental design, quality assurance and quality control checks, data analyses and concurrent search for fish using traditional gears, the evidence for fish presence can be evaluated to build confidence in the eDNA approach. The benefits for fisheries management from adopting an eDNA approach are numerous but include cost effectiveness, broader geographic coverage of habitat occupancy, early detection of invasive species, non-lethal stock assessments, exploration of previously inaccessible aquatic environments and discovery of new species hidden beneath the water's surface. At a time when global freshwater and marine fisheries are facing growing threats from over-harvest, pollution and climate change, we anticipate that growing confidence in eDNA will overcome the inherent uncertainty of not having a fish in hand and will empower the informed management actions necessary to protect and restore our fisheries.
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Affiliation(s)
- Christopher L Jerde
- Marine Science Institute, University of California, Santa Barbara, California, USA
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5
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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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6
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Competition between Invasive Ruffe (Gymnocephalus cernua) and Native Yellow Perch (Perca flavescens) in Experimental Mesocosms. FISHES 2020. [DOI: 10.3390/fishes5040033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ruffe (Gymnocephalus cernua) were introduced to North America from Europe in the mid-1980s and based on similar diets and habit use may compete with yellow perch (Perca flavescens). To examine competitive interactions between invasive ruffe and native yellow perch, individually marked perch and ruffe were placed in mesocosms in a small lake. Mesocosms allowed fish to interact and feed on the natural prey populations enclosed. In the first experiment, four treatments were assessed: 28 perch, 14 perch + 14 ruffe, 14 perch, and 7 perch + 7 ruffe. Yellow perch growth was significantly lower in the presence of ruffe (ANOVA, p = 0.005) than in treatments containing only perch. In a second experiment, an increasing density of one species was superimposed upon a constant density of the other in parallel treatment series. Growth rates of both ruffe and perch declined when ruffe density was increased (t test, p = 0.006). However, neither ruffe nor perch growth was affected by increasing perch density. Total stomach content mass of perch was significantly decreased by ruffe in both years (p < 0.02), but no effects of ruffe on the composition of perch diets were observed. Ruffe growth and food consumption was greater than that of perch for both experiments. Ruffe can outcompete yellow perch when both species depend on a limited benthic food resource. Thus there is reason for concern for the ecological effects of ruffe if they expand their range into Lake Erie or North American inland lakes that contain yellow perch.
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Kirtane A, Atkinson JD, Sassoubre L. Design and Validation of Passive Environmental DNA Samplers Using Granular Activated Carbon and Montmorillonite Clay. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11961-11970. [PMID: 32659082 DOI: 10.1021/acs.est.0c01863] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Environmental DNA (eDNA) analysis is gaining prominence as a tool for species and biodiversity monitoring in aquatic environments. eDNA shed by organisms is captured in grab samples, concentrated by filtration, extracted, and analyzed using molecular methods. Conventional capture and filtration methods are limited because (1) filtration does not capture all extracellular DNA, (2) eDNA can degrade during sample transport and storage, (3) filters often clog in turbid waters, reducing the eDNA captured, and (4) grab samples are time sensitive due to pulse eDNA inputs. To address these limitations, this work designs and validates Passive Environmental DNA Samplers (PEDS). PEDS consist of an adsorbent-filled sachet that is suspended in water to collect eDNA over time. Both extracellular and cellular DNA are captured, and the extracellular DNA is protected from degradation. The eDNA captured over time may be more representative than a grab sample. Two adsorbents, Montmorillonite Clay (MC) and Granular Activated Carbon (GAC), are tested. In laboratory experiments, MC-PEDS adsorbed five times more extracellular DNA and desorbed up to four times more than GAC-PEDS (despite high levels of eDNA loss during desorption). In microcosm and field experiments, GAC-PEDS captured over an order of magnitude more eDNA than MC-PEDS. Field results further validated PEDS as an effective eDNA capture method compared to conventional methods.
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Affiliation(s)
- Anish Kirtane
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo, Buffalo, New York 14228, United States
| | - John D Atkinson
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo, Buffalo, New York 14228, United States
| | - Lauren Sassoubre
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo, Buffalo, New York 14228, United States
- Department of Engineering, University of San Francisco, San Francisco, California 94117, United States
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8
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Lopes CM, Baêta D, Valentini A, Lyra ML, Sabbag AF, Gasparini JL, Dejean T, Haddad CFB, Zamudio KR. Lost and found: Frogs in a biodiversity hotspot rediscovered with environmental DNA. Mol Ecol 2020; 30:3289-3298. [PMID: 32786119 DOI: 10.1111/mec.15594] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/25/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Declines and extinctions are increasing globally and challenge conservationists to keep pace with biodiversity monitoring. Organisms leave DNA traces in the environment, e.g., in soil, water, and air. These DNA traces are referred to as environmental DNA (eDNA). The analysis of eDNA is a highly sensitive method with the potential to rapidly assess local diversity and the status of threatened species. We searched for DNA traces of 30 target amphibian species of conservation concern, at different levels of threat, using an environmental DNA metabarcoding approach, together with an extensive sequence reference database to analyse water samples from six montane sites in the Atlantic Coastal Forest and adjacent Cerrado grasslands of Brazil. We successfully detected DNA traces of four declined species (Hylodes ornatus, Hylodes regius, Crossodactylus timbuhy, and Vitreorana eurygnatha); two locally disappeared (Phasmahyla exilis and Phasmahyla guttata); and one species that has not been seen since 1968 (putatively assigned to Megaelosia bocainensis). We confirm the presence of species undetected by traditional methods, underscoring the efficacy of eDNA metabarcoding for biodiversity monitoring at low population densities, especially in megadiverse tropical sites. Our results support the potential application of eDNA in conservation biology, to evaluate persistence and distribution of threatened species in surveyed habitats or sites, and improve accuracy of red lists, especially for species undetected over long periods.
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Affiliation(s)
- Carla Martins Lopes
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Délio Baêta
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | | | - Mariana Lúcio Lyra
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Ariadne Fares Sabbag
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - João Luiz Gasparini
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Macaé, RJ, Brazil
| | | | - Célio Fernando Baptista Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Kelly Raquel Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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9
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Furlan EM, Davis J, Duncan RP. Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes. Mol Ecol Resour 2020; 20:1259-1276. [PMID: 32310337 DOI: 10.1111/1755-0998.13170] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/25/2020] [Accepted: 04/06/2020] [Indexed: 12/18/2022]
Abstract
Environmental DNA (eDNA) metabarcoding surveys enable rapid, noninvasive identification of taxa from trace samples with wide-ranging applications from characterizing local biodiversity to identifying food-web interactions. However, the technique is prone to error from two major sources: (a) contamination through foreign DNA entering the workflow, and (b) misidentification of DNA within the workflow. Both types of error have the potential to obscure true taxon presence or to increase taxonomic richness by incorrectly identifying taxa as present at sample sites, but multiple error sources can remain unaccounted for in metabarcoding studies. Here, we use data from an eDNA metabarcoding study designed to detect vertebrate species at waterholes in Australia's arid zone to illustrate where and how in the workflow errors can arise, and how to mitigate those errors. We detected the DNA of 36 taxa spanning 34 families, 19 orders and five vertebrate classes in water samples from waterholes, demonstrating the potential for eDNA metabarcoding surveys to provide rapid, noninvasive detection in remote locations, and to widely sample taxonomic diversity from aquatic through to terrestrial taxa. However, we initially identified 152 taxa in the samples, meaning there were many false positive detections. We identified the sources of these errors, allowing us to design a stepwise process to detect and remove error, and provide a template to minimize similar errors that are likely to arise in other metabarcoding studies. Our findings suggest eDNA metabarcoding surveys need to be carefully conducted and screened for errors to ensure their accuracy.
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Affiliation(s)
- Elise M Furlan
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Jenny Davis
- Research Institute for Environment and Livelihoods, College of Engineering, IT and Environment, Charles Darwin University, Casuarina, NT, Australia
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
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10
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Furlan EM, Gleeson D, Wisniewski C, Yick J, Duncan RP. eDNA surveys to detect species at very low densities: A case study of European carp eradication in Tasmania, Australia. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elise M. Furlan
- Institute for Applied Ecology University of Canberra Bruce ACT Australia
| | - Dianne Gleeson
- Institute for Applied Ecology University of Canberra Bruce ACT Australia
| | | | - Jonah Yick
- Inland Fisheries Service New Norfolk TAS Australia
| | - Richard P. Duncan
- Institute for Applied Ecology University of Canberra Bruce ACT Australia
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11
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A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11040050] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, and present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have shown mixed results in detecting the presence of these animals under field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored non-avian reptile eDNA quantification by sampling four lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months to detect differences in eDNA using a qPCR assay amplifying the COI gene of the mtDNA genome. Only one sample of the highest-density pond amplified eDNA for a positive detection. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present the “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—as a potential challenge for eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.
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12
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Jerde CL, Wilson EA, Dressler TL. Measuring global fish species richness with eDNA metabarcoding. Mol Ecol Resour 2019; 19:19-22. [PMID: 30701707 DOI: 10.1111/1755-0998.12929] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 06/26/2018] [Indexed: 11/30/2022]
Abstract
Despite mounting threats to global freshwater and marine biodiversity, including climate change, habitat alteration, overharvesting and pollution, we struggle to know which species are present below the water's surface that are suffering from these stressors. However, the idea that a water sample containing environmental DNA (eDNA) can be screened using high-throughput sequencing and bioinformatics to reveal the identity of aquatic species is a revolutionary advance for studying the patterns of species extirpation, invasive species establishment and the dynamics of species richness. To date, many of the critical tests of fisheries diversity using this metabarcoding approach have been conducted in lower diversity systems (<40 fish species), but in this issue of Molecular Ecology Resources, Cilleros et al. (2018) described their eDNA application in the species-rich French Guiana fishery (>200 fish species) and showed the greater potential and some limitations of using eDNA in species-rich environments.
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Affiliation(s)
- Christopher L Jerde
- Marine Science Institute, University of California, Santa Barbara, California
| | - Emily A Wilson
- Marine Science Institute, University of California, Santa Barbara, California
| | - Terra L Dressler
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California
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13
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Bourne SD, Hudson J, Holman LE, Rius M. Marine Invasion Genomics: Revealing Ecological and Evolutionary Consequences of Biological Invasions. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Nevers MB, Byappanahalli MN, Morris CC, Shively D, Przybyla-Kelly K, Spoljaric AM, Dickey J, Roseman EF. Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus). PLoS One 2018; 13:e0191720. [PMID: 29357382 PMCID: PMC5777661 DOI: 10.1371/journal.pone.0191720] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/10/2018] [Indexed: 12/29/2022] Open
Abstract
Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, occupancy estimates, and real-time detections of invasive species. In the Great Lakes, the round goby (Neogobius melanostomus), an invasive benthic fish from the Black Sea, has spread to encompass all five lakes and many tributaries, outcompeting or consuming native species; however, estimates of round goby abundance are confounded by behavior and habitat preference, which impact reliable methods for estimating their population. By integrating eDNA into round goby monitoring, improved estimates of biomass may be obtainable. We conducted mesocosm experiments to estimate rates of goby DNA shedding and decay. Further, we compared eDNA with several methods of traditional field sampling to compare its use as an alternative/complementary monitoring method. Environmental DNA decay was comparable to other fish species, and first-order decay was lower at 12°C (k = 0.043) than at 19°C (k = 0.058). Round goby eDNA was routinely detected in known invaded sites of Lake Michigan and its tributaries (range log10 4.8-6.2 CN/L), but not upstream of an artificial fish barrier. Traditional techniques (mark-recapture, seining, trapping) in Lakes Michigan and Huron resulted in fewer, more variable detections than eDNA, but trapping and eDNA were correlated (Pearson R = 0.87). Additional field testing will help correlate round goby abundance with eDNA, providing insight on its role as a prey fish and its impact on food webs.
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Affiliation(s)
- Meredith B. Nevers
- U.S. Geological Survey, Great Lakes Science Center, Lake Michigan Ecological Research Station, Chesterton, Indiana, United States of America
- * E-mail:
| | - Murulee N. Byappanahalli
- U.S. Geological Survey, Great Lakes Science Center, Lake Michigan Ecological Research Station, Chesterton, Indiana, United States of America
| | - Charles C. Morris
- National Park Service, Indiana Dunes National Lakeshore, Porter, Indiana, United States of America
| | - Dawn Shively
- U.S. Geological Survey, Great Lakes Science Center, Lake Michigan Ecological Research Station, Chesterton, Indiana, United States of America
| | - Kasia Przybyla-Kelly
- U.S. Geological Survey, Great Lakes Science Center, Lake Michigan Ecological Research Station, Chesterton, Indiana, United States of America
| | - Ashley M. Spoljaric
- U.S. Geological Survey, Great Lakes Science Center, Lake Michigan Ecological Research Station, Chesterton, Indiana, United States of America
| | - Joshua Dickey
- National Park Service, Indiana Dunes National Lakeshore, Porter, Indiana, United States of America
| | - Edward F. Roseman
- U.S. Geological Survey, Great Lakes Science Center, Ann Arbor, Michigan, United States of America
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15
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Lugg WH, Griffiths J, Rooyen AR, Weeks AR, Tingley R. Optimal survey designs for environmental DNA sampling. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12951] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- William H. Lugg
- School of BioSciences University of Melbourne Parkville Vic. Australia
| | | | | | - Andrew R. Weeks
- School of BioSciences University of Melbourne Parkville Vic. Australia
- Cesar Pty Ltd Parkville Vic. Australia
| | - Reid Tingley
- School of BioSciences University of Melbourne Parkville Vic. Australia
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16
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Muha TP, Rodríguez-Rey M, Rolla M, Tricarico E. Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00158] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Balasingham KD, Walter RP, Mandrak NE, Heath DD. Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries. Mol Ecol 2017; 27:112-127. [PMID: 29087006 DOI: 10.1111/mec.14395] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 10/03/2017] [Accepted: 10/06/2017] [Indexed: 01/10/2023]
Abstract
The extraction and characterization of DNA from aquatic environmental samples offers an alternative, noninvasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing ("metabarcoding"), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom-designed group-specific primer set and next-generation sequencing for the detection of three species at risk (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada: the Grand River and the Sydenham River. Of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns.
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Affiliation(s)
- Katherine D Balasingham
- Department of Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryan P Walter
- Department of Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.,Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, ON, Canada
| | - Nicholas E Mandrak
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, ON, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Daniel D Heath
- Department of Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
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