Development and Validation of an Environmental DNA Method for Detection of the Alligator Snapping Turtle (Macrochelys temminckii)

Feist, Sheena M.; Jones, Robin L.; Copley, Jeremy L.; Pearson, Luke; Berry, Gabrielle; Qualls, Carl P.

doi:10.2744/ccb-1315.1

Cited by 14 publications

(22 citation statements)

References 45 publications

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“…Additionally, an eDNA assay was developed to detect alligator snapping turtle (Macrochelys temminckii) presence in both lentic and lotic environments in the southeastern USA [78]. Filtered water volumes varied according to water sample clogging rates, so two 1.5 µm microfiber glass filters were used to collect between 850 and 1500 mL of field water in total [78]. The Qiagen QIAshredder and DNeasy Blood and Tissue kits were used to extract out DNA which was amplified by a Taqman probe targeting the CR of mtDNA [78].…”

Section: Reptile Ednamentioning

confidence: 99%

“…Filtered water volumes varied according to water sample clogging rates, so two 1.5 µm microfiber glass filters were used to collect between 850 and 1500 mL of field water in total [78]. The Qiagen QIAshredder and DNeasy Blood and Tissue kits were used to extract out DNA which was amplified by a Taqman probe targeting the CR of mtDNA [78]. Technical replicates amplified 1/6 to 2/3 replicates, but technical replicates never amplified in all triplicate or sextuplicate reactions [78].…”

Section: Reptile Ednamentioning

confidence: 99%

“…The Qiagen QIAshredder and DNeasy Blood and Tissue kits were used to extract out DNA which was amplified by a Taqman probe targeting the CR of mtDNA [78]. Technical replicates amplified 1/6 to 2/3 replicates, but technical replicates never amplified in all triplicate or sextuplicate reactions [78]. Furthermore, the replicates that did amplify had a high Cq value (>38), indicating a low eDNA concentration [78].…”

Section: Reptile Ednamentioning

confidence: 99%

“…Technical replicates amplified 1/6 to 2/3 replicates, but technical replicates never amplified in all triplicate or sextuplicate reactions [78]. Furthermore, the replicates that did amplify had a high Cq value (>38), indicating a low eDNA concentration [78]. It is possible that turtle eDNA concentrations may approach the limit of detection in some cases.…”

Section: Reptile Ednamentioning

confidence: 99%

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

et al. 2019

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Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, and present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have shown mixed results in detecting the presence of these animals under field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored non-avian reptile eDNA quantification by sampling four lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months to detect differences in eDNA using a qPCR assay amplifying the COI gene of the mtDNA genome. Only one sample of the highest-density pond amplified eDNA for a positive detection. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present the “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—as a potential challenge for eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

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Section: Reptile Ednamentioning

confidence: 99%

Section: Reptile Ednamentioning

confidence: 99%

Section: Reptile Ednamentioning

confidence: 99%

Section: Reptile Ednamentioning

confidence: 99%

See 2 more Smart Citations

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

et al. 2019

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“…Nonetheless, fish remain the group most studied with eDNA analysis in both freshwater and marine environments (Hansen et al, 2018). Few eDNA studies have investigated aquatic reptiles (Roussel et al, 2015), and those that did focused on freshwater turtles (Davy et al, 2015;de Souza et al, 2016;Lacoursière-Roussel et al, 2016;Feist et al, 2018;Kundu et al, 2018;Raemy and Ursenbacher, 2018;Wilson et al, 2018;Adams et al, 2019;Akre et al, 2019;Ficetola et al, 2019). Only Kelly et al (2014) used eDNA analysis to detect sea turtles and their study was conducted in a mesocosm to census marine fishes, not specifically designed for sea turtles.…”

Section: Introductionmentioning

confidence: 99%

Finding Crush: Environmental DNA Analysis as a Tool for Tracking the Green Sea Turtle Chelonia mydas in a Marine Estuary

et al. 2020

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Environmental DNA (eDNA) analysis is a rapid, non-invasive method for species detection and distribution assessment using DNA released into the surrounding environment by an organism. eDNA analysis is recognised as a powerful tool for detecting endangered or rare species in a range of ecosystems. Although the number of studies using eDNA analysis in marine systems is continually increasing, there appears to be no published studies investigating the use of eDNA analysis to detect sea turtles in natural conditions. We tested the efficacy of two primer pairs known to amplify DNA fragments of differing lengths (488 and 253 bp) from Chelonia mydas tissues for detecting C. mydas eDNA in water samples. The capture, extraction, and amplification of C. mydas eDNA from aquaria (Sea World, San Diego, CA, United States) and natural water (San Diego Bay, CA, United States) were successful using either primer set. The primer pair providing the shorter amplicon, LCMint2/H950g, demonstrated the ability to distinguish cross-reactive species by melt curve analysis and provided superior amplification metrics compared to the other primer set (LTCM2/HDCM2); although primer dimer was observed, warranting future design refinement. Results indicated that water samples taken from deeper depths might improve detection frequency, consistent with C. mydas behaviour. Overall, this pilot study suggests that with refinement of sampling methodology and further assay optimisation, eDNA analysis represents a promising tool to monitor C. mydas. Potential applications include rapid assessment across broad geographical areas to pinpoint promising locations for further evaluation with traditional methods.

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A review of applications of environmental DNA for reptile conservation and management

Nordstrom

Mitchell

Byrne

et al. 2022

Ecology and Evolution

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Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio‐temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.

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Development and Validation of an Environmental DNA Method for Detection of the Alligator Snapping Turtle (Macrochelys temminckii)

Cited by 14 publications

References 45 publications

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

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

Finding Crush: Environmental DNA Analysis as a Tool for Tracking the Green Sea Turtle Chelonia mydas in a Marine Estuary

A review of applications of environmental DNA for reptile conservation and management

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