Improving Detection and Community Assessment of Rare and At-risk Fishes

Freshwater fishes are a globally imperiled natural resource.To aid conservation, natural resource agencies frequently assess changes in fish biodiversity and distribution.However, detection probabilities for fishes are frequently low when sampled via traditional methods.In this dissertation, I demonstrate how novel sampling approaches can complement traditional sampling to improve detection of fishes.

First, I evaluated the effects of road-crossing culvert removal on longitudinal connectivity of fish assemblages in three tributary streams in the Manistee River watershed of Michigan.Upstream versus downstream assemblage similarity increased following culvert replacement by bridges.In addition, relatively small sample sizes of fishes were needed to detect an increase in assemblage similarity.

The remainder of my dissertation focused on how environmental DNA (eDNA) can improve the detection of fishes.I compared the financial costs and sampling effort required to assess the distribution of at-risk Brook Trout (Salvelinus fontinalis) in the Namekagon River watershed, Wisconsin, using both electrofishing and eDNA.Brook Trout distribution was accurately determined with both eDNA and electrofishing, but eDNA analysis incurred up to 92% lower effort and up to 67% less cost than electrofishing.

I then evaluated how eDNA metabarcoding can be used to estimate fish species richness.In a replicated mesocosm experiment, I demonstrated that metabarcoding could detect all the species present regardless of species relative abundance or density.Further, I found a positive statistical relationship between species abundance and sequence read abundance.In a field study of a small impoundment, I then compared species richness estimates derived from metabarcoding and capture-based sampling.Metabarcoding detected all 10 species that were observed via capture-based sampling plus an additional 11 uncaptured species.The detection of stream-dwelling species in the impoundment suggests downstream transport of viable eDNA.Additional research on eDNA transport will improve our ability to infer the source of eDNA in aquatic ecosystems.

Overall, my dissertation illustrates that eDNA analysis can be an effective supplement to traditional sampling.I, however, caution that eDNA should not be viewed as a replacement for traditional sampling methods that provide unique information.Research and management objectives should be carefully assessed when selecting a sampling approach.