Environmental DNA (eDNA): a valuable tool for ecological inference and management of sharks and their relatives

Le Port, Agnes, Bakker, Judith, Cooper, Madalyn K., Huerlimann, Roger, and Mariani, Stefano (2018) Environmental DNA (eDNA): a valuable tool for ecological inference and management of sharks and their relatives. In: Carrier, Jeffrey C., Heithaus, Michael R., and Simpfendorfer, Colin A., (eds.) Shark Research: emerging technologies and applications for the field and laboratory. Marine Biology Series . CRC Press, Boca Raton, FL, USA, pp. 255-283.

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Abstract

Knowledge of spatial and temporal variation in abundance is critical for the implementation of effective protective measures for organisms that are both naturally rare and vulnerable to exploitation. The development of management and conservation strategies for elasmobranchs depends on accurate assessment and monitoring of the distribution and abundance of target species in the field, but detecting species occurrences is often even more challenging in the aquatic environment than on land (Webb and Mindel, 2015). Consequently, as is the case for many large, mobile and rare vertebrates, shark detection is inherently difficult.

All organisms continuously leave traces of themselves behind in the environment in the form of shed skin cells, bodily fluids, metabolic waste, gametes, or blood. Any of these materials can contain pieces of the organism's DNA. Environmental DNA (eDNA) analysis is based on the retrieval of this naturally released genetic material from the environment. It generally refers to bulk DNA extracted from an environmental sample such as water but also from soil, sediment, snow, or even from air (Taberlet et al., 2012a). In aquatic systems, macroorganismal-derived eDNA can be present as free DNA, cellular debris, or particle-bound DNA and is mostly present in small fragments, due to rapid degradation (Barnes et al., 2014); however, much of the eDNA is retrieved from cellular material and may therefore contain still relatively undamaged nucleic acid molecules. Nevertheless, eDNA studies focus primarily on the detection of short fragments, as currently available parallel sequencing and qPCR platforms have short-read capabilities limited to a few hundred base pairs. When DNA is present at low concentrations, mitochondrial DNA (mtDNA) is often targeted, as there are substantially more mitochondrial than nuclear DNA copies per cell (Wilcox et al., 2013). Commonly employed mtDNA genes include cytochrome b, cytochrome c oxidase subunit 1 (COI), 12S rRNA, and 16S rRNA (Kelly et al., 2014; Thomsen et al., 2012b; Valentini et al., 2016), and targeted fragments typically fall within the range of 79 to 285 bp (Ficetola et al., 2008; Minamoto et al., 2012). The level of target specificity is often the main determining factor when choosing or designing primers for eDNA analysis.

Item ID: 55841
Item Type: Book Chapter (Research - B1)
ISBN: 978-1-1380-3292-7
Date Deposited: 23 Oct 2018 01:13
FoR Codes: 06 BIOLOGICAL SCIENCES > 0602 Ecology > 060205 Marine and Estuarine Ecology (incl Marine Ichthyology) @ 100%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 100%
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