A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (&lt;em&gt;Chrysemys picta&lt;/em&gt;) eDNA under Field Conditions

Adams, Clare I. M.; Hoekstra, Luke A.; Muell, Morgan R.; Janzen, Fredric J.

doi:10.20944/preprints201902.0261.v1

Cited by 5 publications

References 135 publications

(225 reference statements)

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Towards a framework to unify the relationship between numerical abundance, biomass, and quantitative eDNA

Yates

Wilcox

Kay

et al. 2022

Preprint

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Does environmental DNA (eDNA) correlate more closely with numerical abundance (N) or biomass in aquatic organisms? We hypothesize that the answer is neither: eDNA production likely scales allometrically, reflecting key physiological rates and surface area-to-body mass relationships. Building on individual-level frameworks developed from the Metabolic Theory of Ecology, we derive a general framework through which quantitative eDNA data can be transformed to simultaneously reflect both population-level N and biomass. Notably, our framework demonstrates that even under circumstances where eDNA is assumed to scale linearly with either numerical abundance or biomass (e.g. the allometric scaling coefficient (b) is equal to 0 or 1, respectively), deriving the other metric necessitates a correction based on population/species mean mass if size-structure variation exists among populations. We then validated our general framework using data from two previously published studies: (i) a marine eDNA metabarcoding dataset; and (ii) a freshwater single-species qPCR dataset. Using a Bayesian modeling framework, we estimated the value of the allometric scaling coefficient that jointly optimized the relationship between N, biomass, and corrected eDNA data to be 0.82 and 0.77 in Case Studies (i) and (ii), respectively. These estimates closely match expected scaling coefficients estimated in previous work on Teleost fish metabolic rates. We also demonstrate that correcting quantitative eDNA can significantly improve correspondence between eDNA- and traditionally-derived quantitative community biodiversity metrics (e.g., Shannon index and Bray-Curtis dissimilarity) under some circumstances. Collectively, we show that quantitative eDNA data is unlikely to correspond exactly to either N or biomass, but can be corrected to reflect both through our unifying joint modelling framework. This framework can also be further expanded to include other variables that might impact eDNA pseudo-steady-state concentrations in natural ecosystems (e.g., temperature, pH, and phenology).

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Towards a framework to unify the relationship between numerical abundance, biomass, and quantitative eDNA

Yates

Wilcox

Kay

et al. 2022

Preprint

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Use of Environmental DNA to Determine Fantail Darter (Etheostoma flabellare) Density in a Laboratory Setting: Effects of Biomass and Filtration Method

Guivas

Brammell

2020

International Journal of Zoology

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Estimating fish abundance/biomass holds great importance for freshwater ecology and fisheries management, but current techniques can be expensive, time-consuming, and potentially harmful to target organisms. Environmental DNA (eDNA) has proven an effective and efficient technique for presence/absence detection of freshwater vertebrates. Additionally, recent studies report correlations between target organism density/biomass and eDNA levels, although widespread application of this technique is limited by the number of studies examining this relationship in various species and settings. Additionally, filter clogging is a commonly encountered issue in eDNA studies in environments with significant sediment and/or phytoplankton algae. Frequently, a sample must be split into multiple aliquots and filtered separately in order to process the entire sample. The present study examines both the relationship between biomass and eDNA and the effects of single versus multiple filter sampling on eDNA concentrations of fantail darters (Etheostoma flabellare) in a laboratory setting. Tank tests were performed in quadruplicate at four environmentally relevant fantail biomass levels. eDNA samples were collected and processed in parallel (one as a whole through a single filter and one in parts through multiple filters). Species-specific primers and a probe were developed for E. flabellare from cytochrome b sequences obtained from locally collected specimens, and real-time quantitative PCR was used to analyze eDNA levels at each biomass. Significant correlations were observed with increasing biomass for both methods, although this relationship was stronger for samples processed by the multiple filter method. These data should be useful in eDNA studies in which turbidity necessitates the use of multiple filters per sample as well as in the use of eDNA to estimate darter populations.

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Exploration of Environmental DNA (eDNA) to Detect Kirtland’s Snake (Clonophis kirtlandii)

Ratsch

Kingsbury

Jordan

2020

Animals

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Environmental DNA (eDNA) surveys utilize DNA shed by organisms into their environment in order to detect their presence. This technique has proven effective in many systems for detecting rare or cryptic species that require high survey effort. One potential candidate for eDNA surveying is Kirtland’s Snake (Clonophis kirtlandii), a small natricine endemic to the midwestern USA and threatened throughout its range. Due to its cryptic and fossorial lifestyle, it is also a notoriously difficult snake to survey, which has limited efforts to understand its ecology. Our goal was to utilize eDNA surveys for this species to increase detection probability and improve survey efficiency to assist future conservation efforts. We conducted coverboard surveys and habitat analyses to determine the spatial and temporal activity of snakes, and used this information to collect environmental samples in areas of high and low snake activity. In addition, we spiked artificial crayfish burrows with Kirtland’s Snake feces to assess the persistence of eDNA under semi-natural conditions. A quantitative PCR (qPCR) assay using a hydrolysis probe was developed to screen the environmental samples for Kirtland’s Snake eDNA that excluded closely related and co-occurring species. Our field surveys showed that snakes were found in the spring during the first of two seasons, and in areas with abundant grass, herbaceous vegetation, and shrubs. We found that eDNA declines within a week under field conditions in artificial crayfish burrows. In environmental samples of crayfish burrow water and sediment, soil, and open water, a single detection was found out of 380 samples. While there may be physicochemical and biological explanations for the low detection observed, characteristics of assay performance and sampling methodology may have also increased the potential for false negatives. We explored these outcomes in an effort to refine and advance the successful application of eDNA surveying in snakes and groundwater microhabitats.

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A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (<em>Chrysemys picta</em>) eDNA under Field Conditions

Cited by 5 publications

References 135 publications

Towards a framework to unify the relationship between numerical abundance, biomass, and quantitative eDNA

Towards a framework to unify the relationship between numerical abundance, biomass, and quantitative eDNA

Use of Environmental DNA to Determine Fantail Darter (Etheostoma flabellare) Density in a Laboratory Setting: Effects of Biomass and Filtration Method

Exploration of Environmental DNA (eDNA) to Detect Kirtland’s Snake (Clonophis kirtlandii)

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