Distribution and seasonal differences in Pacific Lamprey andLampetraspp eDNA across 18 Puget Sound watersheds

Abstract

Lampreys have a worldwide distribution, are functionally important to ecological communities and serve significant roles in many cultures. In Pacific coast drainages of North America, lamprey populations have suffered large declines. However, lamprey population status and trends within many areas of this region are unknown and such information is needed for advancing conservation goals. We developed two quantitative PCR-based, aquatic environmental DNA (eDNA) assays for detection of Pacific Lamprey (Entosphenus tridentatus) and Lampetra spp, using locked nucleic acids (LNAs) in the probe design. We used these assays to characterize the spatial distribution of lamprey in 18 watersheds of Puget Sound, Washington, by collecting water samples in spring and fall. Pacific Lamprey and Lampetra spp were each detected in 14 watersheds and co-occurred in 10 watersheds. Lamprey eDNA detection rates were much higher in spring compared to fall. Specifically, the Pacific Lamprey eDNA detection rate was 3.5 times higher in spring and the Lampetra spp eDNA detection rate was 1.5 times higher in spring even though larval lamprey are present in streams year-round. This significant finding highlights the importance of seasonality on eDNA detection. Higher stream discharge in the fall likely contributed to reduced eDNA detection rates, although seasonal life history events may have also contributed. These eDNA assays differentiate Pacific Lamprey and Lampetra spp across much of their range along the west coast of North America. Sequence analysis indicates the Pacific Lamprey assay also targets other Entosphenus spp and indicates the Lampetra spp assay may have limited or no capability of detecting Lampetra in some locations south of the Columbia River Basin. Nevertheless, these assays will serve as a valuable tool for resource managers and have direct application to lamprey conservation efforts, such as mapping species distributions, occupancy modeling, and monitoring translocations and reintroductions.

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

“…When we performed denoising by dada2 , there was one false‐negative result and some reference haplotypes with low detection probability in multiple filters and/or PCR replications (Figures 4 and S1). It is considered that the false‐negative result and decrease in detection probability among multiple replications of filters and PCRs were caused by three main reasons: (i) failure of eDNA capture during the water sampling because of the scarcity or degradation of eDNA molecules (Evans, Shirey, Wieringa, Mahon, & Lamberti, 2017); (ii) failure of PCR amplification of eDNA in the sample because of scarcity of DNA molecules or the PCR inhibition (Jane et al., 2014; Ostberg, Chase, Hayes, & Duda, 2018); and (iii) incorrect elimination in denoising of HTS data using denoising software based on the ASV method (Rosen, Callahan, Fisher, & Holmes, 2012).…”

Evaluation of environmental DNA surveys for identifying occupancy and spatial distribution of Pacific Lamprey (Entosphenus tridentatus) and Lampetra spp. in a Washington coast watershed

“…Our findings indicate that sampling eDNA at one or few sites at lower ends of drainages can also accurately detect lamprey when present in a drainage. Further, Ostberg et al () used eDNA to replicate known lamprey distributions in Puget Sound watersheds by sampling single sites within each watershed. However, the number and spatial distribution of sample sites in an eDNA survey design will ultimately depend on specific study objectives.…”

“…We used an LOD of 1 copy/qPCR for the E. tridentatus and Lampetra spp. assay as identified in Ostberg et al ().…”

“…The eDNA concentration for each qPCR that exceeded the limit of quantification (LOQ) was estimated from the standard curve. We used an LOQ of six copies/qPCR for each assay as identified in Ostberg et al (). For qPCRs that exceeded the LOD but did not exceed the LOQ, we assigned a quantity of half the LOQ (three copies/qPCR) following the method of Klymus, Richter, Chapman, and Paukert (), because DNA concentrations below the LOQ cannot be accurately estimated, even though target DNA is detected (i.e., above LOD).…”

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

“…S1). It is considered that the false-negative result and decrease in detection probability among multiple replications of filters and PCRs were caused by three main reason: (1) failure of eDNA capture during the water sampling because of the scarcity or degradation of eDNA molecules (Evans et al, 2017), (2) failure of PCR amplification of eDNA in the sample because of scarcity of DNA molecules or the PCR inhibition (Jane et al, 2014, Ostberg et al, 2018), and (3) incorrect elimination in denoising of HTS data using denoising software based on the ASV method (Rosen et al, 2012).…”