Using environmental DNA methods to improve winter surveys for rare carnivores: DNA from snow and improved noninvasive techniques

Thomas W Franklin,Kevin S Mckelvey,Jessie D Golding,Daniel H Mason,Joseph C Dysthe,Kristine L Pilgrim,John R Squires,Keith B Aubry,Robert A Long,Samuel E Greaves,Catherine M Raley,Scott Jackson,Paula Mackay,Joshua Lisbon,Joel D Sauder,Michael T Pruss,Don Heffington,Michael K Schwartz

doi:10.1016/j.biocon.2018.11.006

Abstract

The management of rare species is a conservation priority worldwide, but this task is made difficult by detection errors in population surveys. Both false positive (misidentification) and false negative (missed detection) errors are prevalent in surveys for rare species and can affect resulting inferences about their population status or distribution. Environmental DNA (eDNA)—DNA shed from an organism in its environment—coupled with quantitative PCR (qPCR) analyses, has become a reliable and extremely sensitive mean for identifying rare species in aquatic systems. Due to the demonstrated effectiveness of these methods, we tested their efficacy in surveys for rare species in terrestrial settings to reduce detection errors for three rare forest carnivores of conservation concern: Canada lynx (Lynx canadensis), fisher (Pekania pennanti), and wolverine (Gulo gulo). We specifically investigated our ability to reliably: 1) identify species directly from snow samples collected within tracks; 2) identify species by collecting snow in locations where an animal had been photographed; and 3) identify species from hair samples collected during the summer after being deployed throughout the winter (i.e., overwinter surveys). Our findings indicated that qPCR assays can effectively detect DNA of all three species, including from snow-track surveys, snow collected at camera stations, and overwinter samples that failed to amplify with conventional PCR techniques. All results indicate that the sources of targeted DNA collection provided adequate quantities of DNA for robust species detection. We suggest that using qPCR methods to detect DNA has the potential to revolutionize winter surveys for rare species in terrestrial settings by reducing or eliminating misidentifications and missed detections.

Highlights

Wildlife conservationists, federal and state agencies, and non-governmental organizations spend significant amounts of time and money managing rare species (e.g., Miller et al, 2002; McCarthy et al, 2012)
We successfully developed quantitative PCR (qPCR) assays for each species that were efficient and highly sensitive
The in vivo analyses using the Canada lynx assay resulted in detection of Canada lynx DNA in 11/11 samples collected from snow-tracks identified as Canada lynx in the field; analyses with the fisher assay resulted in detection of fisher DNA in 3/3 samples collected from snow-tracks identified as fisher in the field; analyses with the wolverine assay resulted in detection of wolverine DNA in 13/17 samples collected from snow-tracks identified as wolverine in the field (Table 2)

Summary

Introduction

Federal and state agencies, and non-governmental organizations spend significant amounts of time and money managing rare species (e.g., Miller et al, 2002; McCarthy et al, 2012). Prior to the development of these methods, there was limited information on rare carnivores (Zielinski and Kucera, 1995; Long et al, 2008). Most carnivores are reliably attracted to baited stations in winter, resulting in high detection rates (e.g., Mulders et al, 2007). These methods, combined with the advantages of conducting surveys in the winter season, have allowed new insights into carnivore ecology and monitoring (e.g., Squires et al, 2004; McKelvey et al, 2006; Ulizio et al, 2006)

Methods

Results

Conclusion