Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

• Published in: Canadian journal of fisheries and aquatic sciences Vol. 70; no. 8; pp. 1123 - 1130
• Main Authors: Pilliod, David S., Goldberg, Caren S., Arkle, Robert S., Waits, Lisette P.
• Format: Journal Article
• Language: English
• Published: Ottawa, ON NRC Research Press 01.08.2013; National Research Council of Canada; Canadian Science Publishing NRC Research Press
• Subjects: Amphibia. Reptilia; Amphibians; Animal and plant ecology; Animal, plant and microbial ecology; Applied ecology; aquatic organisms; Aquatic sciences; Ascaphus montanus; Biological and medical sciences; biomass; Creeks & streams; Deoxyribonucleic acid; Dicamptodon aterrimus; DNA; Environmental aspects; Environmental DNA; Exploitation and management of natural biological resources (hunting, fishing and exploited populations survey, etc.); Fresh water ecosystems; Freshwater; Fundamental and applied biological sciences. Psychology; Genetic research; Habitats; Idaho; Methods; monitoring; Monitoring methods; Reptiles & amphibians; streams; Synecology; Vertebrates; Vertebrates: general zoology, morphology, phylogeny, systematics, cytogenetics, geographical distribution; Water analysis; Water sampling; United States; USA, Idaho; Idaho; Freshwater environment; Vertebrata; Filter; DNA; Amphibia; Abundance; Stream
• ISSN: 0706-652X; 1205-7533; 1205-7533
• DOI: 10.1139/cjfas-2013-0047

Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.