Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non‐environmental DNA specialists

Huerlimann, Roger; Cooper, Madalyn K.; Edmunds, Richard C.; Villacorta‐Rath, Cecilia; Port, Agnès Le; Robson, Heather; Strugnell, Jan M.; Burrows, Damien; Jerry, Dean R.

doi:10.1111/acv.12583

Cited by 40 publications

(37 citation statements)

References 97 publications

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“…The sensitivity, non-invasiveness, and cost-efficiency of environmental DNA (eDNA) based methods have been proven for diverse habitats and species making them powerful new tools for conservation biology and biodiversity assessments (Barnes and Turner, 2016;Deiner et al, 2017;Huerlimann et al, 2020). Regarding the detection of fish species, eDNA-based monitoring outperforms traditional methods such as electrofishing: for example, for the detection of the endangered European weather loach, Misgurnus fossilis (Sigsgaard et al, 2015), the assessment of fish communities in Australian streams (McColl-Gausden et al, 2020), and the distribution of brook trout, Salvelinus fontinalis in a US watershed (Evans et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

et al. 2021

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The quantitative measurement of environmental DNA (eDNA) from field-collected water samples is gaining importance for the monitoring of fish communities and populations. The interpretation of these signal strengths depends, among other factors, on the amount of target eDNA shed into the water. However, shedding rates are presumably associated with species-specific traits such as physiology and behavior. Although such differences between juvenile and adult fish have been previously detected, the general impact of movement and energy use in a resting state on eDNA release into the surrounding water remains hardly addressed. In an aquarium experiment, we compared eDNA shedding between seven fish species occurring in European freshwaters. The investigated salmonids, cyprinids, and sculpin exhibit distinct adaptions to microhabitats, diets, and either solitary or schooling behavior. The fish were housed in aquaria with constant water flow and their activity was measured by snapshots taken every 30 s. Water samples for eDNA analysis were taken every 3 h and energy use was determined in an intermittent flow respirometer. After controlling for the effect of fish mass, our results demonstrate a positive correlation between target eDNA quantities as measured with digital PCR, fish activity, and energy use, as well as species-specific differences. For cyprinids, the model based on data from individual fish was only partly transferable to groups, which showed lower activity and higher energy use. Our findings highlight the importance of fish physiology and behavior for the comparative interpretation of taxon-specific eDNA quantities. Species traits should therefore be incorporated into eDNA-based monitoring and conservation efforts.

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Section: Introductionmentioning

confidence: 99%

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

et al. 2021

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“…Sequences are then taxonomically assigned using a genetic reference database, which provides an integrative inventory of species and composition in aquatic systems (Deiner et al., 2017; Harrison et al., 2019). A recent synthesis counted 54 papers on tropical eDNA, whereas only 15 focused on marine systems (Bakker et al., 2019; Huerlimann et al., 2020; Sigsgaard et al., 2019; West et al., 2020). Compared to freshwater systems, the marine environment has a larger water volume to fish biomass ratio, the movement of molecules in suspension is influenced by various currents, and reef systems can contain up to hundreds of species, which might challenge the detection of individual species (Collins et al., 2019; Hansen et al., 2018; Harrison et al., 2019).…”

Section: Introductionmentioning

confidence: 99%

“…Tropical ecosystems have historically been underrepresented in research (Collen et al., 2008), and increased monitoring efforts in these regions are urgently needed, particularly under ongoing global change (Barlow et al., 2018). Different abiotic conditions and high species richness might challenge the application of eDNA in the tropics (Huerlimann et al., 2020; Jerde et al., 2019). Studies of eDNA on coral reefs have shown a strong potential for biodiversity detection (Nguyen et al., 2020; Sigsgaard et al., 2019; West et al., 2020), but the scope of methodological testing remains narrow.…”

Section: Introductionmentioning

confidence: 99%

Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

Marques

Fopp

et al. 2020

Environmental DNA

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Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems such as coral reefs is a prerequisite for their application in long‐term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to species using a public reference database, we detected the presence of 107 and 85 fish species, 106 and 92 genera, and 73 and 57 families in Providencia and Gayraca Bay, respectively. Of the species identified using eDNA, 32.7% (Providencia) and 18.8% (Gayraca) were also found in the UVCs. We further found congruence in genus and species richness and abundance between eDNA and UVC approaches in Providencia but not in Gayraca Bay. Mismatches between eDNA and UVC had a phylogenetic and ecological signal, with eDNA detecting a broader phylogenetic diversity and more effectively detecting smaller species, pelagic species and those in deeper habitats. Altogether, eDNA can be used for fast and broad biodiversity surveys and is applicable to species‐rich ecosystems in the tropics, but improved coverage of the reference database is required before this new method could serve as an effective complement to traditional census methods.

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“…The sensitivity, non-invasiveness and cost-efficiency of environmental DNA (eDNA) based methods has been proven for diverse habitats and species making them powerful new tools for conservation biology and biodiversity assessments (Barnes and Turner, 2016; Deiner et al, 2017; Huerlimann et al, 2020). Regarding the detection of fish species, eDNA-based monitoring outperforms traditional methods such as electrofishing: for example, for the detection of the endangered European weather loach, Misgurnus fossilis (Sigsgaard et al, 2015), the assessment of fish communities in Australian streams (McColl‐Gausden et al, 2020), and the distribution of brook trout, Salvelinus fontinalis in a US watershed (Evans et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

The effect of activity, energy use, and species identity on environmental DNA shedding of freshwater fish

Thalinger

Rieder

Teuffenbach

et al. 2020

Preprint

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The quantitative measurement of eDNA form field-collected water samples is gaining importance for the monitoring of fish communities and populations. The interpretation of these signal strengths depends, among other factors, on the amount of target eDNA shed into the water. However, shedding rates are presumably associated with species-specific traits such as physiology and behavior. Although such differences between juvenile and adult fish have been previously detected, the general impact of movement and energy use in a resting state on eDNA release into the surrounding water remains hardly addressed. In an aquarium experiment, we compared eDNA shedding between seven fish species occurring in European freshwaters. The investigated salmonids, cyprinids and sculpin exhibit distinct adaptions to microhabitats, diets, and either solitary or schooling behavior. The fish were housed in aquaria with constant water flow and their activity was measured by snapshots taken every 30 s. Water samples for eDNA analysis were taken every 3 h and energy use was determined in an intermittent flow respirometer. After controlling for the effect of fish mass, our results demonstrate a positive correlation between target eDNA quantities as measured with digital PCR, fish activity and energy use, as well as species-specific differences. For cyprinids, the model based on data from individual fish was only partly transferable to groups, which exhibited lower activity and higher energy use. Our findings highlight the importance of fish physiology and behavior for the comparative interpretation of taxon-specific eDNA quantities. Species traits should therefore be incorporated into eDNA-based monitoring and conservation efforts.

show abstract

Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non‐environmental DNA specialists

Cited by 40 publications

References 97 publications

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

The effect of activity, energy use, and species identity on environmental DNA shedding of freshwater fish

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