Broad‐scale eDNA sampling for describing aquatic species distributions in running waters: Pacific lamprey Entosphenus tridentatus in the upper Snake River, USA

Abstract

One of the most fundamental yet challenging tasks for aquatic ecologists is to precisely delineate the range of species, particularly those that are broadly distributed, require specialized sampling methods, and may be simultaneously declining and increasing in different portions of their range. An exemplar is the Pacific lamprey Entosphenus tridentatus, a jawless anadromous fish of conservation concern that is actively managed in many coastal basins in western North America. To efficiently determine its distribution across the accessible 56,168 km of the upper Snake River basin in the north-western United States, we first delimited potential habitat by using predictions from a species distribution model based on conventionally collected historical data and from the distribution of a potential surrogate, Chinook salmon Oncorhynchus tshawytscha, which yielded a potential habitat network of 10,615 km. Within this area, we conducted a two-stage environmental DNA survey involving 394 new samples and 187 archived samples collected by professional biologists and citizen scientists using a single, standardized method from 2015 to 2021. We estimated that Pacific lamprey occupied 1875 km of lotic habitat in this basin, of which 1444 km may have been influenced by recent translocation efforts. Pacific lamprey DNA was consistently present throughout most river main stems, although detections became weaker or less frequent in the largest and warmest downstream channels and near their headwater extent. Pacific lamprey were detected in nearly all stocked tributaries, but there was no evidence of indigenous populations in such habitats. There was evidence of post-stocking movement because detections were 1.8-36.0 km upstream from release sites. By crafting a model-driven spatial sampling template and executing an eDNA-based sampling campaign led by professionals and volunteers, supplemented by previously collected samples, we established a benchmark for understanding the current range of Pacific lamprey across a large portion of its range in the interior Columbia River basin. This approach could be tailored to refine range estimates for other wide-ranging aquatic species of conservation concern.

Integrating spatial stream network models and environmental DNA to estimate current and future distributions of nonnative Smallmouth Bass

“…Despite offering many advantages for delineating species distributions in rivers, the application of eDNA monitoring also has weaknesses. As discussed above, DNA detections can occur at distances downstream from the source, causing uncertainty in terms of among-site occupancy patterns and the terminus, if present, of habitat occupancy (Pont et al 2018;Young et al 2022). With our eDNA data set alone, we have no population demographic information.…”

“…2021; Young et al. 2022). As a result, many groups are collecting eDNA, thereby creating large spatial data sets useful for SDM estimation (Biggs et al.…”

“…For example, eDNA can provide occurrence information in high-turbidity conditions (Strickland and Roberts 2017) and in large river reaches (Goutte et al 2020), where traditional techniques like snorkeling can underestimate species richness (Plichard et al 2017). Environmental DNA is relatively easy to collect, so rapid sampling across geographic areas relevant to management is possible (Strickland and Roberts 2019;Beng and Corlett 2020;Blackman et al 2021;Young et al 2022). As a result, many groups are collecting eDNA, thereby creating large spatial data sets useful for SDM estimation (Biggs et al 2015;Isaak et al 2018).…”

Molecular identification and environmental DNA detection of gill lice ectoparasites associated with Brook Trout declines

“…Environmental DNA (eDNA) analysis, or the analysis of trace DNA that is shed by organisms into their environment and collected from bulk environmental samples (e.g., soil, water, and air), has emerged as a viable and cost-effective tool for rapidly surveying biodiversity across vast spatial scales without requiring efforts to observe, capture, or identify species at the time of the survey (e.g., Katz et al 2021;West et al 2021;Young et al 2022;Johnson et al 2023). When used in conjunction with conventional survey approaches, eDNA analysis can provide enormous benefits in terms of survey efficiency, especially if there is a need to expand survey coverage and sampling frequency (Bass et al 2015(Bass et al , 2023Evans et al 2017).…”

Cold-water habitats, climate refugia, and their utility for conserving salmonid fishes

“…It is unknown how accurately the distributions of these species could be predicted based on the environmental gradients that appear relevant to salmonids, but exploratory analyses would be intriguing and may yield encouraging results. The limitation for many of these species is sparse occurrence data sets that hinder model development although the rapid adoption of eDNA sampling and growing databases that can be repurposed for multiple species are alleviating this deficiency in many areas (Dysthe et al 2018;Young et al 2018cYoung et al , 2022.…”