Placing environmental DNA monitoring for new detections into perspective: Fishes in the Milwaukee River, Wisconsin

Abstract

Invasive species management frameworks, such as the early detection of and rapid response to invasive species, use monitoring programs to detect new species occurrences. Resource managers use environmental DNA (eDNA) as one tool for these monitoring programs. An eDNA detection in a new location may lack perspective for resource managers and researchers because of the rarity of potential invaders and the randomness in their dispersal and detection. An example monitoring program is the eDNA-based sampling approach used by the U.S. Fish and Wildlife Service for bigheaded carps Hypophthalmichthys spp. in the upper Mississippi River and Great Lakes Basins that collects hundreds of water samples per event. The U.S. Fish and Wildlife Service detected a single positive sample for Bighead Carp Hypophthalmichthys nobilis during the spring 2021 sampling event in the Kinnickinnic River within the Milwaukee River Basin, and detected a second single positive sample for bigheaded carps during the fall 2021 sampling event in the Milwaukee River. The U.S. Fish and Wildlife Service did not detect any bigheaded carps in previous years (2015 to 2020) or in either the spring or fall 2022 sampling events. These detections lacked perspective, such as detection numbers for other species. We reanalyzed the 2021 and 2022 samples for four existing species of fish: two fairly common species (Common Carp Cyprinus carpio and Gizzard Shad Dorosoma cepedianum ) and two fairly rare species (Burbot Lota lota and Grass Carp Ctenopharyngodon idella ). We detected Common Carp during all four sampling events, Gizzard Shad during three of four sampling events, and Burbot and Grass Carp during two of four sampling events. These results demonstrated that current sampling efforts could detect other species, and bigheaded carp eDNA was not common in the Milwaukee River compared to these species. More specifically, this finding indicates bigheaded carp eDNA detections are as rare as, or rarer than, Grass Carp eDNA detections, a recent invader to the basin. Our findings also demonstrated how reanalyzing eDNA samples after positive detections for targeted species can help managers understand the context of the detections and provide perspective for the relative abundance of the targeted species. Additionally, our results highlight the importance of completing long-term eDNA-based monitoring rather than a single sampling or inventory event. These detections may have been missed in a single year or sampling event, whereas a multiyear monitoring program provides an opportunity to observe trends through time.