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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

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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.

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Acknowledgements

We would like the thank the following people and institutions for providing tissues that contributed to the development of the multiprobe qPCR assay in this study: T. Hibbits and the Texas A&M University Biodiversity Research and Teaching Collection, J. K. Braun and B. S. Coyner and the Oklahoma Collection of Genomic Resources, R. Brown and A. Motta and the University of Kansas Herpetology collection, T. Lott and the Florida Museum of Natural History Genetic Resource Repository, and the non-profit group Texas Turtles. This is publication 36 of the Marine Genomics Laboratory.

Funding

Funding was provided by the Coastal Bend Bays & Estuaries Program (#2126).

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Authors and Affiliations

  1. Marine Genomics Laboratory, Texas A&M Corpus Christi, 6300 Ocean Dr, Corpus Christi, TX, USA

    Andrew T. Fields, Elizabeth P. Hunt, Katherine Lanoue, Riley S. Sebby & David S. Portnoy

  2. Coastal Bend Bays & Estuaries Program, 1305 N Shoreline Blvd #205, Corpus Christi, TX, USA

    Aaron S. Baxter

  3. Palacios Marine Agricultural Research Inc, 555 N Carancahua St, Ste 240, Corpus Christi, TX, USA

    W. Jay Tarkington

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Contributions

DP, AB, AF, EH and JT contributed to the study conception and design. DP and AB secured the funding. Material preparation, data collection and analysis were performed by AB, AF, EH, KL, RS and JT. The first draft of the manuscript was written by AF and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Andrew T. Fields or David S. Portnoy.

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Fields, A.T., Hunt, E.P., Lanoue, K. et al. 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. Conservation Genet Resour 16, 147–157 (2024). https://doi.org/10.1007/s12686-023-01343-1

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