Including environmental covariates clarifies the relationship between endangered Atlantic salmon (Salmo salar) abundance and environmental DNA

Abstract

Collecting environmental DNA (eDNA) as a nonlethal sampling approach has been valuable in detecting the presence/absence of many imperiled taxa; however, its application to indicate species abundance poses many challenges. A deeper understanding of eDNA dynamics in aquatic systems is required to better interpret the substantial variability often associated with eDNA samples. Our sampling design took advantage of natural variation in juvenile Atlantic salmon (Salmo salar) distribution and abundance along 9 km of a single river in the Province of New Brunswick (Canada), covering different spatial and temporal scales to address the unknown seasonal impacts of environmental variables on the quantitative relationship between eDNA concentration and species abundance. First, we asked whether accounting for environmental variables strengthened the relationship between eDNA and salmon abundance by sampling eDNA during their spring seaward migration. Second, we asked how environmental variables affected eDNA dynamics during the summer as the parr abundance remained relatively constant. Spring eDNA samples were collected over a 6‐week period (12 times) near a rotary screw trap that captured approximately 18.6% of migrating smolts, whereas summer sampling occurred (i) at three distinct salmon habitats (9 times) and (ii) along the full 9 km (3 times). We modeled eDNA concentration as a product of fish abundance and environmental variables, demonstrating that (1) with inclusion of abundance and environmental covariates, eDNA was highly correlated with spring smolt abundance and (2) the relationships among environmental covariates and eDNA were affected by seasonal variation with relatively constant parr abundance in summer. Our findings underscore that with appropriate study design that accounts for seasonal environmental variation and life history phenology, eDNA salmon population assessments may have the potential to evaluate abundance fluctuations in spring and summer.

Environmental DNA captures diurnal fluctuations of surface eukaryotes on a tropical coral reef

“…However, in the natural environment, these relationships have been found to be weaker, most likely due to more dilute DNA concentrations and stochasticity in environmental parameters and organism behavior that are known to impact the release, transport, and degradation of eDNA (Rourke et al, 2021;Yates et al, 2019). With careful consideration of key environmental parameters however, there is a promising outlook for answering quantitative questions in natural environments using eDNA (Morrison et al, 2023;Yates et al, 2023).…”

Streamside detection of Chinook salmon (Oncorhynchus tshawytscha) environmental DNA with CRISPR technology

“…Robust Chinook salmon eDNA detection technologies have been developed and widely utilized to monitor stream and localized habitat distribution (Duda et al., 2021; Laramie et al., 2015; Matter et al., 2018). There is even a growing area of research utilizing eDNA to estimate salmon abundance (Lacoursière‐Roussel, Côté, et al., 2016; Lacoursière‐Roussel, Rosabal, et al., 2016; Morrison et al., 2023; Spear et al., 2021; Wood et al., 2021).…”

Beyond species detection—leveraging environmental DNA and environmental RNA to push beyond presence/absence applications

“…Bourque et al (2023),Morrison et al (2023), andGaudet-Boulay et al (2023) demonstrate the importance of the effect of temperature when relating quantitative eDNA signals to metrics of organism abundance (see discussion below), andJo et al (2023) similarly highlight the effect of temperature on eDNA and eRNA degradation, particularly when comparing the ratio of eDNA to eRNA.3 | INFERRING ORG ANIS M ABUNDAN CE FROM QUANTITATIVE eDNA DATAEstimating abundance from quantitative eDNA signals remains a major goal at the forefront of eDNA research. While studies in natural ecosystems have consistently demonstrated positive correlations between quantitative eDNA data and metrics of organism abundance(Lamb et al, 2019;Rourke et al, 2021;Yates et al, 2019),controlled laboratory experiments are critical to understanding the functional links between organism abundance and eDNA concentrations.…”