eDNA results: Where are the fish?

eDNA shows reduction in tributary habitat

Back in June 2023 we worked with the Boise National Forest to grab some eDNA samples of tributaries to the SF Boise River. This work was adjacent to ongoing bull trout eDNA sampling efforts and for our purposes we were interested in understanding if there are detections of salmonid use of the tributaries. Salmonids include bull trout and other species like rainbow trout.

Results took some time process. The Forest Service sent the samples to its lab in Missoula and the information did not come back for nearly a year. Then it took time to find a way to plot the information on a map.

The information shows in some tributaries there appears to be a reduction of trout use of some of the small tributaries. If the trout were present, and if they shed enough eDNA into the water column, and if the sampling effort works, we should get a signal. Assuming the samples were accurate here is a capsule set of results:

• Pierce Creek samples show trout present at the bridge where the passage reconnection project was implemented in 2011 (a bridge replaced culvert). But further upstream in the mainstem of Pierce Creek and its West Fork the samples were negative. Since the 2013 and 2014 debris flow events there is a waterfall that might be impassible for trout to access the upper reaches. Past fish sampling efforts had shown fish using the upstream reaches. This appears to be a reduction in available habitat.
• Granite Creek sampling shows fish presence upstream of the culvert AND upstream of a water fall that appeared to be a problem for passage. But a kilometer upstream the samples were negative for trout eDNA presence. The positive sample however is encouraging. The culvert could present passage challenges at certain flows given its length.
• Rough Creek tested positive downstream of the culvert for fish using the small stream. Samples one and two kilometers upstream were both negative. A large waterfall is present between the two negative samples. The culvert under the SF Boise River Road is perched and not very surprising the negative sample is a result.
• Cow Creek shows eDNA presence near its confluence with the SF Boise River but negative one kilometer upstream. This is consistent with field observations from recent years.