An evaluation of the efficacy of using environmental DNA (eDNA) to detect giant gartersnakes (Thamnophis gigas)

Abstract

For more information on the USGS-the Federal source for science about the Earth, its natural and living resources, natural hazards, and the environment-visit https://www.usgs.gov or call 1-888-ASK-USGS (1-888-275-8747).For an overview of USGS information products, including maps, imagery, and publications, visit https://store.usgs.gov.The findings and conclusions in this article are those of the author(s) and do not necessarily represent the views of the U.S. Fish and Wildlife Service.Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner. Abstract Detecting populations of rare or cryptic species is essential for their conservation. For species like giant gartersnakes (Thamnophis gigas), conventional survey methods can be expensive and inefficient. These sampling difficulties might be overcome by modern techniques that detect deoxyribonucleic acid (DNA) shed by organisms into the environment (eDNA). We evaluated the efficacy of detecting giant gartersnake eDNA in water samples from the laboratory and at locations with known giant gartersnake populations in the Sacramento Valley of California, and failed to detect giant gartersnake DNA in most laboratory and all field samples. Aspects of giant gartersnake biology-such as highly keratinized skin and spending extensive time in the terrestrial environment, as well as hot, sunny, and turbid conditions in wetlands and canals of the Sacramento Valley-likely contributed to low detection probabilities. Although detection of eDNA shows promise under many conditions, further development is needed before sampling for eDNA is a viable option for detecting giant gartersnake populations.

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

“…In this study, laboratory experiments detected T. gigas eDNA from tanks with snake skin and snake feces in water, but curiously eDNA was not detected in tanks with live snakes in the water [74]. This qPCR Taqman assay used 1 L water samples which were filtered with a 0.45 µm nitrocellulose filter, although precipitation with sodium acetate methods were also tested [74]. The Taqman assay amplified the ND4 region of mitochondrial DNA (mtDNA), although cytochrome B (CytB) and NADH dehydrogenase 2 (ND2) regions were also considered [74].…”

“…These snakes inhabit canals and marsh-like habitats [75]. In this study, laboratory experiments detected T. gigas eDNA from tanks with snake skin and snake feces in water, but curiously eDNA was not detected in tanks with live snakes in the water [74]. This qPCR Taqman assay used 1 L water samples which were filtered with a 0.45 µm nitrocellulose filter, although precipitation with sodium acetate methods were also tested [74].…”

“…The Taqman assay amplified the ND4 region of mitochondrial DNA (mtDNA), although cytochrome B (CytB) and NADH dehydrogenase 2 (ND2) regions were also considered [74]. T. gigas eDNA was not detected in water at field locations, despite capture with traps at the same sites [74]. Overall, this assay was not effective at detecting T. gigas eDNA in field settings compared to traditional methods.…”

“…Similarly, giant garter snake (Thamnophis gigas) eDNA assays were created for presence detection [74]. These snakes inhabit canals and marsh-like habitats [75].…”

“…This qPCR Taqman assay used 1 L water samples which were filtered with a 0.45 µm nitrocellulose filter, although precipitation with sodium acetate methods were also tested [74]. The Taqman assay amplified the ND4 region of mitochondrial DNA (mtDNA), although cytochrome B (CytB) and NADH dehydrogenase 2 (ND2) regions were also considered [74]. T. gigas eDNA was not detected in water at field locations, despite capture with traps at the same sites [74].…”