Use of environmental DNA (eDNA) in streams to detect feral swine (Sus scrofa)

Amberly N Hauger; Karmen M Hollis-Etter; Dwayne R Etter; Gary J Roloff; Andrew R Mahon

doi:10.7717/peerj.8287

Use of environmental DNA (eDNA) in streams to detect feral swine (Sus scrofa)

PeerJ. 2020 Jan 2:8:e8287. doi: 10.7717/peerj.8287. eCollection 2020.

Authors

Amberly N Hauger^#¹, Karmen M Hollis-Etter^#¹, Dwayne R Etter², Gary J Roloff³, Andrew R Mahon⁴

Affiliations

¹ Biology Department, University of Michigan-Flint, Flint, MI, United States of America.
² Wildlife Division, Michigan Department of Natural Resources, East Lansing, MI, United States of America.
³ Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States of America.
⁴ Department of Biology, Central Michigan University, Mount Pleasant, MI, United States of America.

^# Contributed equally.

Abstract

Invasive feral swine can damage ecosystems, disrupt plant and animal populations, and transmit diseases. Monitoring of feral swine populations requires expensive and labor-intensive techniques such as aerial surveys, field surveys for sign, trail cameras, and verifying landowner reports. Environmental DNA (eDNA) provides an alternative method for locating feral swine. To aid in detection of this harmful invasive species, a novel assay was developed incorporating molecular methods. From August 2017 to April 2018, water samples and stream data were collected along 400 m transects in two different stream types where swine DNA was artificially introduced to investigate potential factors affecting detection. A generalized linear model (family binomial) was used to characterize environmental conditions affecting swine DNA detection; detection was the dependent variable and stream measurements included stream type, distance downstream, water temperature, velocity, turbidity, discharge, and pH as independent variables. Parameters from the generalized linear model were deemed significant if 95% confidence intervals did not overlap 0. Detection probability for swine DNA negatively related to water temperature (β = - 0.21, 95% CI [-0.35 to -0.09]), with the highest detection probability (0.80) at 0 °C and lowest detection probability (0.05) at 17.9 °C water temperature. Results indicate that sampling for swine eDNA in free-flowing stream systems should occur at lower water temperatures to maximize detection probability. This study provides a foundation for further development of field and sampling techniques for utilizing eDNA as a viable alternative to monitoring a terrestrial invasive species in northern regions of the United States.

Keywords: Environmental DNA; Feral swine; Invasive species; Streams; Sus scrofa; Terrestrial mammal; Water samples; Water temperature; eDNA.

Grants and funding

This research was supported by the Michigan Department of Natural Resources (MDNR) through financial support from U.S. Fish and Wildlife Service through the Pittman-Robertson Wildlife Restoration Act Grant MI W-155-R. Additional support was provided by the University of Michigan—Flint Biology Start-Up Funds, Graduate Office, and Undergraduate Research Opportunity Program. Amberly N. Hauger received scholarship support from the University of Michigan—Flint Dean’s Graduate Student Fund, Emmalyn E. Freeman MS in Biology Award, and Safari Club International Schotthoefer Student Award. Michigan Statute (PA 451-1994-III-2-1-WILDLIFE-CONSERVATION-401) authorizes the Michigan Department of Natural Resources (MDNR) to conduct wildlife research projects in cooperation with the federal government under the Pittman-Robertson Wildlife Restoration Act. Department employees (Wildlife Research Specialists) are required to design and participate in all aspects of research projects including study design, data collection and analysis, decision to publish, and assist in preparation of manuscripts. Co-PI Dr. Dwayne Etter was project manager for MDNR and has no competing interests related to this project.