Development, verification, and implementation of an eDNA detection assay for emydids with a case study on diamondback terrapins, Malaclemys terrapin, and red eared slider, Trachemys script elegans

Abstract

Globally, many pond turtles (Family Emydidae) are of conservation concern due to contracting ranges, increasingly fragmented habitats, and declining populations. One of these turtles, the diamondback terrapin (Malaclemys terrapin), is of concern within the United States, but surveying potential estuarine habitat for the presence of the species requires high levels of time and effort. Here a species-specific, probe-based qPCR assay for identifying terrapin DNA from environmental DNA (eDNA) is described. To expand the utility of this tool, the assay was designed to allow for potential detection of at least 19 other pond turtles taxa and the utility was tested by designing a second species-specific probe for red-eared slider (Trachemys scripta elegans) with a different fluorophore, which can be used simultaneously with the terrapin probe to detect either species. Probes were found to be species-specific and effective at detecting low levels of DNA for the target species, the diamondback terrapin (10 fg/µL) and the red-eared slider (100 fg/µL) in laboratory conditions. The assay also showed species-specific detection in environmental samples taken from field locations where one species or the other were known to reside. Through citizen science approaches, this assay could be used for discovering novel terrapin habitats, monitoring invasive red-eared slider populations or surveying other emydids, with species-specific probes, at a fraction of the cost of traditional surveys.