Exploring the Use of Environmental DNA to Determine the Species of Salmon Redds

Abstract

Annual redd counts are used to monitor the status and trends of salmonid populations, but methods to easily and reliably determine which of sympatric species made specific redds are lacking. We explored whether environmental DNA (eDNA) analysis might prove useful for assigning salmon redds to the species of origin. We collected eDNA samples from the interstitial spaces of redds constructed by Chinook Salmon Oncorhynchus tshawytscha, redds constructed by Coho Salmon O. kisutch, and areas of undisturbed gravel (n = 10 of each type) as well as from the water column adjacent to each of those sites in the Sandy River basin, Oregon, during fall 2013. The concentrations of Chinook Salmon and Coho Salmon eDNA were quantified within each sample by using real-time PCR. The water in the interstitial spaces of redds contained significantly higher concentrations of eDNA from the species that made the redd than from the other species; concentrations of eDNA from the species that built the redd were also significantly higher in the redd than in the adjacent water column. In contrast, within samples of water from the interstitial spaces of undisturbed gravel, neither Chinook Salmon eDNA nor Coho Salmon eDNA was significantly more concentrated than the other. The interstitial water of undisturbed gravel contained significantly higher Coho Salmon eDNA concentrations than the adjacent water column. In contrast, Chinook Salmon eDNA concentrations in the interstitial water of undisturbed gravel and in the adjacent water column were similar. Both species’ redds had significantly higher concentrations of their respective eDNA than did undisturbed gravel, but conclusions were confounded by differences in the timing and locations of sampling. This initial investigation highlights the potential value and some of the complexities involved in using eDNA analysis to identify the species that constructed a given redd.

Received November 18, 2016; accepted May 20, 2017Published online August 4, 2017

ACKNOWLEDGMENTS

The Portland Water Bureau and U.S. Geological Survey provided funding for this project. We are grateful to Steve Schaaf, Jon Mueller, Den Fraser, and Kathryn Arendt for helping collect field samples. We appreciate Robert Arkle, Carl Ostberg, and the anonymous reviewers for their helpful comments on earlier versions of the manuscript. We also thank Hossein Parandvash and Benjamin Beal for assistance with statistical analyses. Any use of trade names is for descriptive purposes only and does not imply endorsement by the U.S. Government.