Environmental DNA Is Effective at Detecting a Salmonid Ectoparasite: A Statewide Survey of the Distribution and Genetic Diversity of the Gill Louse Salmincola californiensis in Colorado, USA

Abstract

ABSTRACT

Invasive species present considerable threats to native biodiversity by disrupting ecosystem processes. The gill louse Salmincola californiensis is a copepod that parasitizes Oncorhynchus species, which includes ecologically, commercially, and recreationally important fishes. As S. californiensis expands its geographic range, there are concerns that conservation efforts focused on Rocky Mountain cutthroat trout Oncorhynchus virginalis may be thwarted. To address these concerns, we (1) assessed upstream range expansions of S. californiensis from known infected waters; (2) compared the efficacy of environmental DNA (eDNA) sampling to traditional sampling methods in detecting S. californiensis; (3) evaluated S. californiensis population genetic structure using DNA barcoding; and (4) assessed gill lice occupancy and detection probabilities using occupancy modeling. We compared the success of detecting S. californiensis using electrofishing versus eDNA sampling methods at 48 sites throughout the state of Colorado. We detected gill lice at 17 sites via electrofishing, and at 10 sites using eDNA. For DNA barcoding, we collected 58 lice at 11 sampling localities and sequenced the mitochondrial cytochrome c oxidase subunit 1 for species identification, to assess genetic diversity across Colorado, and to estimate divergence times. Salmincola californiensis was the only species of gill lice we detected. Divergence time estimates show that it is possible that the highly divergent gill lice lineages originally co‐invaded with cutthroat trout. However, the presence of the most widespread parasite haplotypes across multiple drainages presents a phylogeographic pattern consistent with fish stocking facilitating its range expansion. Occupancy modeling suggests that fluvial processes, temperature, and UV impact gill lice detection using eDNA. We conclude that eDNA is effective at detecting gill lice presence in a system, perhaps best used in conjunction with electrofishing methods for early detection, that gill lice continue to expand their range in Colorado, and that continued monitoring will be an important component of future management efforts.