1
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Clark AJ, Atkinson SR, Scarponi V, Cane T, Geraldi NR, Hendy IW, Shipway JR, Peck M. Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities. PeerJ 2024; 12:e17091. [PMID: 38708339 PMCID: PMC11067900 DOI: 10.7717/peerj.17091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/20/2024] [Indexed: 05/07/2024] Open
Abstract
Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and conservation monitoring programs around the globe.
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Affiliation(s)
- Alice J. Clark
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sophie R. Atkinson
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Valentina Scarponi
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Tim Cane
- Department of Geography, University of Sussex, Brighton, United Kingdom
| | | | - Ian W. Hendy
- School of Biological Science, University of Portsmouth, Portsmouth, United Kingdom
| | - J. Reuben Shipway
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Mika Peck
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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2
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Stein ED, Jerde CL, Allan EA, Sepulveda AJ, Abbott CL, Baerwald MR, Darling J, Goodwin KD, Meyer RS, Timmers MA, Thielen PM. Critical considerations for communicating environmental DNA science. ENVIRONMENTAL DNA (HOBOKEN, N.J.) 2024; 6:1-12. [PMID: 38784600 PMCID: PMC11110536 DOI: 10.1002/edn3.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/17/2023] [Indexed: 05/25/2024]
Abstract
The economic and methodological efficiencies of environmental DNA (eDNA) based survey approaches provide an unprecedented opportunity to assess and monitor aquatic environments. However, instances of inadequate communication from the scientific community about confidence levels, knowledge gaps, reliability, and appropriate parameters of eDNA-based methods have hindered their uptake in environmental monitoring programs and, in some cases, has created misperceptions or doubts in the management community. To help remedy this situation, scientists convened a session at the Second National Marine eDNA Workshop to discuss strategies for improving communications with managers. These include articulating the readiness of different eDNA applications, highlighting the strengths and limitations of eDNA tools for various applications or use cases, communicating uncertainties associated with specified uses transparently, and avoiding the exaggeration of exploratory and preliminary findings. Several key messages regarding implementation, limitations, and relationship to existing methods were prioritized. To be inclusive of the diverse managers, practitioners, and researchers, we and the other workshop participants propose the development of communication workflow plans, using RACI (Responsible, Accountable, Consulted, Informed) charts to clarify the roles of all pertinent individuals and parties and to minimize the chance for miscommunications. We also propose developing decision support tools such as Structured Decision-Making (SDM) to help balance the benefits of eDNA sampling with the inherent uncertainty, and developing an eDNA readiness scale to articulate the technological readiness of eDNA approaches for specific applications. These strategies will increase clarity and consistency regarding our understanding of the utility of eDNA-based methods, improve transparency, foster a common vision for confidently applying eDNA approaches, and enhance their benefit to the monitoring and assessment community.
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Affiliation(s)
- Eric D Stein
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Christopher L Jerde
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | | | - Adam J Sepulveda
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, USA
| | | | - Melinda R Baerwald
- Division of Integrated Science and Engineering, California Department of Water Resources, West Sacramento, California, USA
| | - John Darling
- U.S. Environmental Protection Agency, Environmental Genomics Branch, Watershed and Ecosystem Characterization Division, Research Triangle Park, North Carolina, USA
| | - Kelly D Goodwin
- National Oceanic and Atmospheric Administration, NOAA Ocean Exploration, Stationed at SWFSC/NMFS, La Jolla, California, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of Santa Cruz, Santa Cruz, California, USA
| | - Molly A Timmers
- Pristine Seas, National Geographic Society, Washington, DC, USA
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Peter M Thielen
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
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3
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Urban P, Jacobsen MW, Bekkevold D, Nielsen A, Storr-Paulsen M, Nijland R, Nielsen EE. eDNA based bycatch assessment in pelagic fish catches. Sci Rep 2024; 14:2976. [PMID: 38316827 PMCID: PMC10844201 DOI: 10.1038/s41598-024-52543-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
Pelagic fish like herring, sardines, and mackerel constitute an essential and nutritious human food source globally. Their sustainable harvest is promoted by the application of precise, accurate, and cost-effective methods for estimating bycatch. Here, we experimentally test the new concept of using eDNA for quantitative bycatch assessment on the illustrative example of the Baltic Sea sprat fisheries with herring bycatch. We investigate the full pipeline from sampling of production water on vessels and in processing factories to the estimation of species weight fractions. Using a series of controlled mixture experiments, we demonstrate that the eDNA signal from production water shows a strong, seasonally consistent linear relationship with herring weight fractions, however, the relationship is influenced by the molecular method used (qPCR or metabarcoding). In four large sprat landings analyzed, despite examples of remarkable consistency between eDNA and visual reporting, estimates of herring bycatch biomass varied between the methods applied, with the eDNA-based estimates having the highest precision for all landings analyzed. The eDNA-based bycatch assessment method has the potential to improve the quality and cost effectiveness of bycatch assessment in large pelagic fisheries catches and in the long run lead to more sustainable management of pelagic fish as a precious marine resource.
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Affiliation(s)
- Paulina Urban
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Silkeborg, Denmark.
| | - Magnus Wulff Jacobsen
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Silkeborg, Denmark
| | - Dorte Bekkevold
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Silkeborg, Denmark
| | - Anders Nielsen
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Lyngby, Denmark
| | - Marie Storr-Paulsen
- Section for Monitoring and Data, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Lyngby, Denmark
| | - Reindert Nijland
- Marine Animal Ecology Group, Wageningen University, Wageningen, The Netherlands
| | - Einar Eg Nielsen
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Silkeborg, Denmark.
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4
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Lodge DM. Conservation in a litre of air. Mol Ecol Resour 2024; 24:e13883. [PMID: 37864493 DOI: 10.1111/1755-0998.13883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/26/2023] [Accepted: 10/06/2023] [Indexed: 10/23/2023]
Abstract
Since Ficetola et al. (2008) alerted ecologists and conservation biologists to the existence of environmental DNA (eDNA), the number of studies using eDNA has exploded, with a rapidly increasing diversity of research, monitoring, and management objectives. Initial applications focused on amphibians and fishes while today's taxonomic targets span the phylogenetic tree. The environmental media that are sampled have expanded from freshwater to saltwater to soils, and, most recently, to air. In this issue of Molecular Ecology Resources, Lynggaard et al. (Molecular Ecology Resources, 2023) use eDNA captured on air filters to census vertebrate biodiversity in a forest. With a three day, six sample period, 143 sample effort in a nature park in a rural area of Zealand, Denmark, their wild species detections comprised about 25% of the terrestrial vertebrates that are known to occur in the area, including about 33% of the mammal, 17% of the bird, and 60% of the amphibian species. This study demonstrates that air sampling for eDNA has the potential to become a powerful standard method for terrestrial biodiversity assessment that is complementary to traditional methods (e.g., trapping, visual and acoustic observation, collection of scat and hair).
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Affiliation(s)
- David M Lodge
- Cornell Atkinson Center for Sustainability, and the Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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5
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Waters T, Gold Z, Obaza A, Ambrose RF, Eagle RA. Environmental DNA metabarcoding reveals distinct fish assemblages supported by seagrass (Zostera marina and Zostera pacifica) beds in different geographic settings in Southern California. PLoS One 2023; 18:e0286228. [PMID: 37796915 PMCID: PMC10553302 DOI: 10.1371/journal.pone.0286228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Seagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these different environments contribute to local biodiversity. This study evaluates the assemblages of fish found at five Zostera beds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.
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Affiliation(s)
- Tanner Waters
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
- Center for Diverse Leadership in Science, University of California, Los Angeles, CA, United States of America
| | - Zachary Gold
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, United States of America
| | - Adam Obaza
- Paua Marine Research Group, Long Beach, CA, United States of America
| | - Richard F. Ambrose
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
- Department of Environmental Health Sciences, Jonathan and Karen Fielding School of Public Health, University of California, Los Angeles, CA, United States of America
| | - Robert A. Eagle
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
- Center for Diverse Leadership in Science, University of California, Los Angeles, CA, United States of America
- Atmospheric and Oceanic Sciences Department, University of California, Los Angeles, CA, United States of America
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6
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Gold Z, Koch MQ, Schooler NK, Emery KA, Dugan JE, Miller RJ, Page HM, Schroeder DM, Hubbard DM, Madden JR, Whitaker SG, Barber PH. A comparison of biomonitoring methodologies for surf zone fish communities. PLoS One 2023; 18:e0260903. [PMID: 37314989 DOI: 10.1371/journal.pone.0260903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/25/2023] [Indexed: 06/16/2023] Open
Abstract
Surf zones are highly dynamic marine ecosystems that are subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines and hook and line surveys are often labor intensive, taxonomically biased, and can be physically hazardous. Emerging techniques, such as baited remote underwater video (BRUV) and environmental DNA (eDNA) are promising nondestructive tools for assessing marine biodiversity in surf zones of sandy beaches. Here we compare the relative performance of beach seines, BRUV, and eDNA in characterizing community composition of bony (teleost) and cartilaginous (elasmobranch) fishes of surf zones at 18 open coast sandy beaches in southern California. Seine and BRUV surveys captured overlapping, but distinct fish communities with 50% (18/36) of detected species shared. BRUV surveys more frequently detected larger species (e.g. sharks and rays) while seines more frequently detected one of the most abundant species, barred surfperch (Amphistichus argenteus). In contrast, eDNA metabarcoding captured 88.9% (32/36) of all fishes observed in seine and BRUV surveys plus 57 additional species, including 15 that frequent surf zone habitats. On average, eDNA detected over 5 times more species than BRUVs and 8 times more species than seine surveys at a given site. eDNA approaches also showed significantly higher sensitivity than seine and BRUV methods and more consistently detected 31 of the 32 (96.9%) jointly observed species across beaches. The four species detected by BRUV/seines, but not eDNA were only resolved at higher taxonomic ranks (e.g. Embiotocidae surfperches and Sygnathidae pipefishes). In frequent co-detection of species between methods limited comparisons of richness and abundance estimates, highlighting the challenge of comparing biomonitoring approaches. Despite potential for improvement, results overall demonstrate that eDNA can provide a cost-effective tool for long-term surf zone monitoring that complements data from seine and BRUV surveys, allowing more comprehensive surveys of vertebrate diversity in surf zone habitats.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - McKenzie Q Koch
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Nicholas K Schooler
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Kyle A Emery
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Jenifer E Dugan
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Robert J Miller
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Henry M Page
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Donna M Schroeder
- Bureau of Ocean Energy Management, Camarillo, CA, United States of America
| | - David M Hubbard
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Jessica R Madden
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Stephen G Whitaker
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
- Channel Islands National Park, Ventura, CA, United States of America
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
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7
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Shelton AO, Gold ZJ, Jensen AJ, D Agnese E, Andruszkiewicz Allan E, Van Cise A, Gallego R, Ramón-Laca A, Garber-Yonts M, Parsons K, Kelly RP. Toward quantitative metabarcoding. Ecology 2023; 104:e3906. [PMID: 36320096 DOI: 10.1002/ecy.3906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/07/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022]
Abstract
Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, and health. At present, amplicon-sequencing studies-known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments of DNA sequenced from many taxa in a mixture-struggle to link genetic observations to the underlying biology in a quantitative way, but many applications require quantitative information about the taxa or systems under scrutiny. As metabarcoding studies proliferate in ecology, it becomes more important to develop ways to make them quantitative to ensure that their conclusions are adequately supported. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying polymerase chain reaction mechanism explains the observed patterns of amplicon data in a general way. By modeling the process through which amplicon-sequence data arise, rather than transforming the data post hoc, we show how to estimate the starting DNA proportions from a mixture of many taxa. We illustrate how to calibrate the model using mock communities and apply the approach to simulated data and a series of empirical examples. Our approach opens the door to improve the use of metabarcoding data in a wide range of applications in ecology, public health, and related fields.
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Affiliation(s)
- Andrew Olaf Shelton
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Zachary J Gold
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA.,CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, USA
| | - Alexander J Jensen
- CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, USA.,School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Erin D Agnese
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | | | - Amy Van Cise
- North Gulf Oceanic Society, Visiting Scientist at Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Ramón Gallego
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA.,Departamento de Biologia, Universidad Autonoma de Madrid, Unidad de Genetica, Madrid, Spain
| | - Ana Ramón-Laca
- CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, USA.,School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Maya Garber-Yonts
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Kim Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
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8
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Gold Z, Shelton AO, Casendino HR, Duprey J, Gallego R, Van Cise A, Fisher M, Jensen AJ, D'Agnese E, Andruszkiewicz Allan E, Ramón-Laca A, Garber-Yonts M, Labare M, Parsons KM, Kelly RP. Signal and noise in metabarcoding data. PLoS One 2023; 18:e0285674. [PMID: 37167310 PMCID: PMC10174484 DOI: 10.1371/journal.pone.0285674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
Metabarcoding is a powerful molecular tool for simultaneously surveying hundreds to thousands of species from a single sample, underpinning microbiome and environmental DNA (eDNA) methods. Deriving quantitative estimates of underlying biological communities from metabarcoding is critical for enhancing the utility of such approaches for health and conservation. Recent work has demonstrated that correcting for amplification biases in genetic metabarcoding data can yield quantitative estimates of template DNA concentrations. However, a major source of uncertainty in metabarcoding data stems from non-detections across technical PCR replicates where one replicate fails to detect a species observed in other replicates. Such non-detections are a special case of variability among technical replicates in metabarcoding data. While many sampling and amplification processes underlie observed variation in metabarcoding data, understanding the causes of non-detections is an important step in distinguishing signal from noise in metabarcoding studies. Here, we use both simulated and empirical data to 1) suggest how non-detections may arise in metabarcoding data, 2) outline steps to recognize uninformative data in practice, and 3) identify the conditions under which amplicon sequence data can reliably detect underlying biological signals. We show with both simulations and empirical data that, for a given species, the rate of non-detections among technical replicates is a function of both the template DNA concentration and species-specific amplification efficiency. Consequently, we conclude metabarcoding datasets are strongly affected by (1) deterministic amplification biases during PCR and (2) stochastic sampling of amplicons during sequencing-both of which we can model-but also by (3) stochastic sampling of rare molecules prior to PCR, which remains a frontier for quantitative metabarcoding. Our results highlight the importance of estimating species-specific amplification efficiencies and critically evaluating patterns of non-detection in metabarcoding datasets to better distinguish environmental signal from the noise inherent in molecular detections of rare targets.
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Affiliation(s)
- Zachary Gold
- Cooperative Institute for Climate, Ocean, & Ecosystem Studies, UW, Seattle, Washington, United States of America
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Andrew Olaf Shelton
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Helen R Casendino
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | - Joe Duprey
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | - Ramón Gallego
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Amy Van Cise
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Mary Fisher
- School of Aquatic Fisheries Science, UW, Seattle, Washington, United States of America
| | - Alexander J Jensen
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Erin D'Agnese
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | | | - Ana Ramón-Laca
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Maya Garber-Yonts
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | - Michaela Labare
- Scripps Institution of Oceanography, UCSD, La Jolla, California, United States of America
| | - Kim M Parsons
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
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9
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Goethel DR, Omori KL, Punt AE, Lynch PD, Berger AM, de Moor CL, Plagányi ÉE, Cope JM, Dowling NA, McGarvey R, Preece AL, Thorson JT, Chaloupka M, Gaichas S, Gilman E, Hesp SA, Longo C, Yao N, Methot RD. Oceans of plenty? Challenges, advancements, and future directions for the provision of evidence-based fisheries management advice. REVIEWS IN FISH BIOLOGY AND FISHERIES 2023; 33:375-410. [PMID: 36124316 PMCID: PMC9476434 DOI: 10.1007/s11160-022-09726-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/18/2022] [Indexed: 05/19/2023]
Abstract
UNLABELLED Marine population modeling, which underpins the scientific advice to support fisheries interventions, is an active research field with recent advancements to address modern challenges (e.g., climate change) and enduring issues (e.g., data limitations). Based on discussions during the 'Land of Plenty' session at the 2021 World Fisheries Congress, we synthesize current challenges, recent advances, and interdisciplinary developments in biological fisheries models (i.e., data-limited, stock assessment, spatial, ecosystem, and climate), management strategy evaluation, and the scientific advice that bridges the science-policy interface. Our review demonstrates that proliferation of interdisciplinary research teams and enhanced data collection protocols have enabled increased integration of spatiotemporal, ecosystem, and socioeconomic dimensions in many fisheries models. However, not all management systems have the resources to implement model-based advice, while protocols for sharing confidential data are lacking and impeding research advances. We recommend that management and modeling frameworks continue to adopt participatory co-management approaches that emphasize wider inclusion of local knowledge and stakeholder input to fill knowledge gaps and promote information sharing. Moreover, fisheries management, by which we mean the end-to-end process of data collection, scientific analysis, and implementation of evidence-informed management actions, must integrate improved communication, engagement, and capacity building, while incorporating feedback loops at each stage. Increasing application of management strategy evaluation is viewed as a critical unifying component, which will bridge fisheries modeling disciplines, aid management decision-making, and better incorporate the array of stakeholders, thereby leading to a more proactive, pragmatic, transparent, and inclusive management framework-ensuring better informed decisions in an uncertain world. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11160-022-09726-7.
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Affiliation(s)
- Daniel R. Goethel
- Auke Bay Laboratories, Marine Ecology and Stock Assessment (MESA) Program, Alaska Fisheries Science Center, NOAA Fisheries, Juneau, AK 99801 USA
| | - Kristen L. Omori
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062 USA
| | - André E. Punt
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195-5020 USA
| | - Patrick D. Lynch
- Office of Science and Technology, NOAA Fisheries, Silver Spring, MD 20910 USA
| | - Aaron M. Berger
- Fisheries Resource, Analysis, and Monitoring (FRAM) Division, Northwest Fisheries Science Center, NOAA Fisheries, Newport, OR 97365 USA
| | - Carryn L. de Moor
- Marine Resource Assessment and Management (MARAM) Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch, 7701 South Africa
| | | | - Jason M. Cope
- Fisheries Resource, Analysis, and Monitoring (FRAM) Division, Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA 98112 USA
| | | | | | - Ann L. Preece
- CSIRO Oceans and Atmosphere, Hobart, TAS 7001 Australia
| | - James T. Thorson
- Habitat and Ecological Process Research (HEPR) Program, Alaska Fisheries Science Center, NOAA Fisheries, Seattle, WA 98115 USA
| | - Milani Chaloupka
- Ecological Modelling Services Pty Ltd & Marine Spatial Ecology Lab, University of Queensland, St Lucia, QLD 4067 Australia
| | - Sarah Gaichas
- Resource Evaluation and Assessment Division, Northeast Fisheries Science Center, NOAA Fisheries, Woods Hole, MA 02543 USA
| | | | - Sybrand A. Hesp
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA 6920 Australia
| | - Catherine Longo
- Science & Standards, Marine Stewardship Council, EC1A 2DH London, U.K
| | - Nan Yao
- Oceanic Fisheries Programme, The Pacific Community (SPC), B.P. D5, 98848 Nouméa, New Caledonia
| | - Richard D. Methot
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA 98112 USA
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10
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Jensen MR, Høgslund S, Knudsen SW, Nielsen J, Møller PR, Rysgaard S, Thomsen PF. Distinct latitudinal community patterns of Arctic marine vertebrates along the East Greenlandic coast detected by environmental
DNA. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Signe Høgslund
- Department of Ecoscience Aarhus University Silkeborg Denmark
| | - Steen Wilhelm Knudsen
- NIVA Denmark Water Research Copenhagen Denmark
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Julius Nielsen
- Department of Fish and Shellfish Greenland Institute of Natural Resources Nuuk Greenland
| | - Peter Rask Møller
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Norwegian College of Fishery Science UiT – The Arctic University of Norway Tromsø Norway
| | - Søren Rysgaard
- Department of Biology, Arctic Research Centre Aarhus University Aarhus Denmark
- Centre for Earth Observation Science, CHR Faculty of Environment Earth and Resources University of Manitoba Winnipeg Manitoba Canada
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Luo M, Ji Y, Warton D, Yu DW. Extracting abundance information from
DNA
‐based data. Mol Ecol Resour 2022; 23:174-189. [PMID: 35986714 PMCID: PMC10087802 DOI: 10.1111/1755-0998.13703] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/31/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022]
Abstract
The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA-based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within-sample across-species quantification describes relative species abundances in one sample. (ii) Across-sample within-species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across-species abundance information (by removing what we call "species pipeline biases") and within-species abundance information (by removing what we call "pipeline noise"). We argue that many ecological questions can be answered with just within-species quantification, and we therefore demonstrate how to use a "DNA spike-in" to correct for pipeline noise and recover within-species abundance information. We also introduce a model-based estimator that can be used on data sets without a physical spike-in to approximate and correct for pipeline noise.
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Affiliation(s)
- Mingjie Luo
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingYunnanChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingYunnanChina
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingYunnanChina
| | - David Warton
- School of Mathematics and StatisticsUNSW SydneySydneyNew South WalesAustralia
- Evolution and Ecology Research Centre, UNSW SydneySydneyNew South WalesAustralia
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingYunnanChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingYunnanChina
- School of Biological SciencesUniversity of East Anglia, Norwich Research ParkNorwichNorfolkUK
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12
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Minamoto T. Environmental DNA analysis for macro-organisms: species distribution and more. DNA Res 2022; 29:6598799. [PMID: 35652724 PMCID: PMC9187915 DOI: 10.1093/dnares/dsac018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/31/2022] [Indexed: 11/14/2022] Open
Abstract
In an era of severe biodiversity loss, biological monitoring is becoming increasingly essential. The analysis of environmental DNA (eDNA) has emerged as a new approach that could revolutionize the biological monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has undergone significant developments and is rapidly becoming established as the golden standard for non-destructive and non-invasive biological monitoring. In this review, I summarize the development of macro-organismal eDNA analysis to date and the techniques used in this field. I also discuss the future perspective of these analytical methods in combination with sophisticated analytical techniques for DNA research developed in the fields of molecular biology and molecular genetics, including genomics, epigenomics, and single-cell technologies. eDNA analysis, which to date has been used primarily for determining the distribution of organisms, is expected to develop into a tool for elucidating the physiological state and behaviour of organisms. The fusion of microbiology and macrobiology through an amalgamation of these technologies is anticipated to lead to the future development of an integrated biology.
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Affiliation(s)
- Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University , Kobe, Hyogo 657-8501, Japan
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