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Detection of fish s...
Detection of fish sedimentary DNA in aquatic systems : A review of methodological challenges and future opportunities
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- Huston, Grayson P. (author)
- School of Biology and Ecology, University of Maine, ME, Orono, United States; Maine Center for Genetics in the Environment, University of Maine, ME, Orono, United States
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- Lopez, Mark Louie D. (author)
- Department of Biochemistry & Microbiology, University of Victoria, BC, Victoria, Canada
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- Cheng, Yuanyu (author)
- Department of Biology, McGill University, QC, Montreal, Canada; Groupe de recherche interuniversitaire en limnologie (GRIL), Canada
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- King, Leighton (author)
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland; Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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- Duxbury, Lucinda C. (author)
- School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, Australia; ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), The University of Adelaide, Adelaide, Australia
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- Picard, Maïlys (author)
- Cawthron Institute, Nelson, New Zealand; Department of Biological Sciences, School of Biological Sciences, University of Waikato, Hamilton, New Zealand
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- Thomson-Laing, Georgia (author)
- Cawthron Institute, Nelson, New Zealand; School of Geography, Environment, and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand
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- Myler, Erika (author)
- Department of Integrative Biology, College of Biological Science, University of Guelph, ON, Guelph, Canada
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- Helbing, Caren C. (author)
- Department of Biochemistry & Microbiology, University of Victoria, BC, Victoria, Canada
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- Kinnison, Michael T. (author)
- School of Biology and Ecology, University of Maine, ME, Orono, United States; Maine Center for Genetics in the Environment, University of Maine, ME, Orono, United States
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- Saros, Jasmine E. (author)
- School of Biology and Ecology, University of Maine, ME, Orono, United States; Climate Change Institute, University of Maine, ME, Orono, United States
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- Gregory-Eaves, Irene (author)
- Department of Biology, McGill University, QC, Montreal, Canada; Groupe de recherche interuniversitaire en limnologie (GRIL), Canada
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- Monchamp, Marie-Eve (author)
- Department of Biology, McGill University, QC, Montreal, Canada; Groupe de recherche interuniversitaire en limnologie (GRIL), Canada
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- Wood, Susanna A. (author)
- Cawthron Institute, Nelson, New Zealand
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- Armbrecht, Linda (author)
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Battery Point, Australia
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- Ficetola, Gentile Francesco (author)
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy; Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes and Université Savoie Mont Blanc, Grenoble, France
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- Kurte, Lenka (author)
- Núcleo Milenio INVASAL, University of Concepción, Concepción, Chile
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- Von Eggers, Jordan (author)
- Department of Geology and Geophysics, University of Wyoming, WY, Laramie, United States
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- Brahney, Janice (author)
- Watershed Sciences and Ecology Center, Utah State University, UT, Logan, United States
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- Parent, Genevieve (author)
- Laboratory of Genomics, Maurice Lamontagne Institute, Fisheries and Oceans Canada, QC, Mont-Joli, Canada
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- Sakata, Masayuki K. (author)
- Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan
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- Doi, Hideyuki (author)
- Graduate School of Informatics, Kyoto University, Kyoto, Japan
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- Capo, Eric (author)
- Umeå universitet,Institutionen för ekologi, miljö och geovetenskap,Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain
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(creator_code:org_t)
- John Wiley & Sons, 2023
- 2023
- English.
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In: Environmental DNA. - : John Wiley & Sons. - 2637-4943. ; 5:6, s. 1449-1472
- Related links:
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https://doi.org/10.1...
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https://umu.diva-por... (primary) (Raw object)
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https://urn.kb.se/re...
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Abstract
Subject headings
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- Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short- and long-term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro-organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.
Subject headings
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
Keyword
- environmental DNA
- fish monitoring
- lake sediment
- marine sediment
- paleolimnology
- sedimentary DNA
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Huston, Grayson ...
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Lopez, Mark Loui ...
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Cheng, Yuanyu
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King, Leighton
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Duxbury, Lucinda ...
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Picard, Maïlys
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show more...
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Thomson-Laing, G ...
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Myler, Erika
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Helbing, Caren C ...
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Kinnison, Michae ...
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Saros, Jasmine E ...
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Gregory-Eaves, I ...
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Monchamp, Marie- ...
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Wood, Susanna A.
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Armbrecht, Linda
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Ficetola, Gentil ...
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Kurte, Lenka
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Von Eggers, Jord ...
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Brahney, Janice
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Parent, Geneviev ...
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Sakata, Masayuki ...
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Doi, Hideyuki
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Capo, Eric
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Ecology
- Articles in the publication
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Environmental DN ...
- By the university
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Umeå University