Harnessing DNA to improve environmental management

Kelly, Ryan P.; Port, Jesse A.; Yamahara, Kevan M.; Martone, Rebecca G.; Lowell, Natalie; Thomsen, Philip Francis; Mach, Megan E.; Bennett, Meredith; Prahler, Erin; Caldwell, Margaret R.; Crowder, Larry B.

doi:10.1126/science.1251156

Cited by 217 publications

(186 citation statements)

References 13 publications

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“…1, 2). The application of eDNA-based technology is already beginning to influence conservation, management, and policy decisions, despite existing uncertainty (Kelly et al 2014a). Nevertheless, there is much work to be done to continue close the gap between research and management considering the application and interpretation of genetic methods including eDNA applications (Darling 2015), and the present review has provided a framework to guide research and organize understanding as eDNA frontiers continue to advance.…”

Section: Resultsmentioning

confidence: 93%

The ecology of environmental DNA and implications for conservation genetics

2015

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Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

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Section: Resultsmentioning

confidence: 93%

The ecology of environmental DNA and implications for conservation genetics

2015

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“…This technique, albeit still subject to some limitations, will likely become a cornerstone in decision making of management bodies in the near future (Kelly et al, 2014a;Danovaro et al, 2016). In the marine realm, eukaryotic diversity has been analysed using metabarcoding in plankton and sediment communities (reviewed in Carugati et al, 2015;Bucklin et al, 2016;Sinniger et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Wangensteen

Cebrián

Palacín

et al. 2018

Marine Pollution Bulletin

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Running title: community-wide effects of invasive algae in MPAs Highlights  Hard-bottom communities dominated by invasive algae were studied with metabarcoding  A size-fractionation method is developed for the metabarcoding of complex samples  A modified primer set is used for the amplification of a COI fragment  A semiquantitave abundance index is proposed for statistical analyses  Results show effects of canopy-forming invasive algae on the underlying communities AbstractWe analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.

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“…Environmental DNA (eDNA) rely on the presence of DNA fragments that have been shed by organisms via metabolic waste, damaged or decomposing tissue, sloughed skin cells, and gametes into various habitats without having to isolate or invasively sample focal taxa (Kelly et al 2014). The amount and geographical range of eDNA can thereby be used to infer species distributions and/or the conservation status of a population, and has been widely applied for ecological surveillance of rare, cryptic, or otherwise hard-to-study taxa, including endangered (Jerde et al 2011;Thomsen et al 2012b;Laramie et al 2015), endemic (Fukumoto et al 2015), and recently colonized invasive species Piaggio et al 2014;Dejean et al 2012;Hunter et al 2015).…”

Section: Introductionmentioning

confidence: 99%