Abstract
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.
Highlights
All sea turtles are threatened species (IUCN, 2019), but there is a fundamental lack of understanding of their biology and distribution that can be attributed primarily to the logistical challenges associated with study in open ocean environments (Hamann et al, 2010)
We developed quantitative PCR (qPCR) assays that were first tested under controlled aquaria conditions and at a field site were C. mydas are known to be present
Given the potentially low shedding rates of aquatic reptiles, further method comparisons are needed to determine the methodology that maximises Environmental DNA (eDNA) yield and detection for C. mydas. The goal of this pilot study was to determine whether eDNA analysis could be applied to the detection of C. mydas in a natural marine environment
Summary
All sea turtles are threatened species (IUCN, 2019), but there is a fundamental lack of understanding of their biology and distribution that can be attributed primarily to the logistical challenges associated with study in open ocean environments (Hamann et al, 2010). Sea turtles are highly migratory and characterised by a complex life history which includes nesting, developmental, and foraging populations. They tend to be present in low numbers and elusive, making them difficult to physically locate. These challenges have resulted in sea turtle population assessments being typically limited to surveys of females and their activity on nesting beaches (National Research Council et al, 2010), instead of surveys in the marine environment where they spend the majority of their time (Hamann et al, 2010; Rees et al, 2016). Greater occurrence of sea turtles within urbanised environments can result in more interactions with humans and associated risks, including drowning from entanglement (National Oceanic and Atmospheric Administration Marine Debris Program, 2014; Godoy and Stockin, 2018), ship strikes (Hazel and Gyuris, 2006), and exposure to toxins (Komoroske et al, 2011)
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