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

Abstract

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.

Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes

“…This detection failure is unlikely to be a result of poor primer match (see Supporting Information) and, while failed detection may reflect the recent absence of reptiles from the site, it is also possible that these taxa do not shed DNA as readily as other terrestrial vertebrates because of water conservation adaptations and strategies evolved to cope with arid conditions (Mayhew, 1968). Indeed, other studies have recorded similarly low eDNA detection rates among reptiles (Adams, Hoekstra, Muell, & Janzen, 2019; Raemy & Ursenbacher, 2018).…”

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

“…Finally, although there are few eDNA studies on reptiles, it appears that detection rates are low relative to other aquatic vertebrates [ 22 ]. For example, two recent studies on Eastern Massasauga ( Sistrurus catenatus ), a species with an overlapping geographic range and similar use of wetlands and crayfish burrows [ 42 , 70 ], found limited eDNA detection.…”

“…The one snake species where eDNA detection has had some success is the Burmese Python [ 8 , 67 , 69 ], a species that is significantly larger in size than C. kirtlandii or S. catenatus, suggesting that eDNA detection may be a function of body size within snakes [ 71 ]. More broadly, the greater amount and frequency of shed skin, mucus, and waste from amphibians and fish are hypothesized to make their detection much more tractable relative to snakes and turtles in freshwater systems [ 22 ]. Research aimed at identifying where, when, and how snakes slough tissues into the environment will aid in the development of more targeted sampling schemes.…”

“…Production rates have been shown to vary with the abundance or biomass [ 17 , 18 , 19 ] and seasonal activity [ 11 , 20 , 21 ]. It also appears to vary among taxa in relation to the intrinsic rate that cells are shed from individuals [ 22 ]. Once produced, the persistence or degradation rate is critical for detection of DNA in the environment.…”

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

“…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.…”