Detection of 4 imperiled western North American freshwater mussel species from environmental DNA with multiplex qPCR assays

Abstract

We developed multiplexed, species-specific, quantitative PCR assays for the detection of four freshwater mussel species native to western North America, Gonidea angulata, Margaritifera falcata, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA (eDNA). These species have experienced dramatic declines over the last century and are currently threatened in many portions of their ranges. Therefore, improved tools for detecting and monitoring these species are needed. Speciesspecificity and sensitivity of assays were empirically tested in the lab, and multiplex assays were also validated with field collected eDNA samples. All assays were species-specific, sensitive, and effective for detection from eDNA samples collected from streams and rivers. These assays will aid in the detection, monitoring, management, and conservation of these vulnerable species.

Western Pearlshell (Margaritifera falcata) Extirpation in the Smith River, Montana, with a Possible Link to Warming Water Temperatures

“…Additionally, no recently deceased shells were observed at any site visited in 2014, and eDNA samples collected in 2022 downstream from 2 previously occupied sites tested negative for pearlshell DNA. Environmental DNA (eDNA) analysis has proven to be a useful and efficient tool for detecting rare aquatic organisms that are present but difficult to detect using traditional sampling surveys (Davy et al 2015, Dysthe et al 2018, Preece et al 2019, Rogers et al 2020). But in this case, it appears that eDNA has validated the absence of western pearlshell mussels in previously occupied areas.…”

Freshwater mussel populations in Pacific Coast Watersheds (Oregon, USA): occurrence, condition, habitat, and fish species overlap

“…This study identified a subset of coastal watersheds in which mussels were not observed in 1st-3rd order streams during the eleven year AQI survey period (SM, Figure S1). Environmental DNA (eDNA) monitoring technology has evolved as an effective monitoring tool to assess presence/absence of aquatic species in watersheds, and recent applications incorporate freshwater mussels assays (Rodgers et al, 2020;Preece et al, 2021). Identified watersheds should be prioritized for future monitoring to determine the status of mussel presence and/or extirpation in coastal watersheds to guide future efforts in population dynamics and extinction debt research in functionally isolated populations.…”

Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species

“…This is not surprising since freshwater ecosystems are considered the most imperilled habitats in the world (Reid et al, 2019), and at least in temperate regions they have been subject of intensive monitoring due to legal requirements, as already above-mentioned. In these ecosystems, most studies have been conducted in rivers and small streams (Castañeda et al, 2020;Ma et al, 2016;Mizumoto et al, 2020;Piggott, 2017;Riaz et al, 2020;Rodgers et al, 2020), lentic ponds (Adams et al, 2019;Geerts et al, 2018;Harper et al, 2018b) and lakes (Johansson et al, 2020;Kamoroff and Goldberg, 2018), to a small extent in reservoirs and dams (Nakao et al, 2023;Sepulveda et al, 2022Sepulveda et al, , 2019, channels (Beauclerc et al, 2019;, caves and springs (DiStefano et al, 2020;Vörös et al, 2017) and aquacultures (Deutschmann et al, 2019;Ladell et al, 2019) (Table S2).…”

“…Multiplex approaches have been less adopted but can be more cost-effective than DNA metabarcoding when the target is a few a priori well-known species (Jo et al, 2020;King et al, 2022;Robinson et al, 2018bRobinson et al, , 2018aRodgers et al, 2020;Tsuji et al, 2018;Wozney and Wilson, 2017) (Table S2). The use of multiplex designs can allow the simultaneous detection of numerous species, reducing processing and handling times, as well as the risk of contamination, lowering costs and reducing the amount of DNA extract required for testing (Rodgers et al, 2020;Wozney and Wilson, 2017). For instance, Robinson and co-authors (Robinson et al, 2018a) developed a multiplex assay for the simultaneous detection of the invasive signal (which was not certified by peer review) is the author/funder.…”