DOI: 10.5061/dryad.mw6m9067j
title: Monitoring Atlantic salmon (Salmo salar) smolt migration in a large river system using environmental DNA

description: Effective monitoring strategies are key for aquatic species conservation,
 but traditional methods often require significant resources, especially in
 large aquatic systems. The emergence of quantitative environmental DNA
 (eDNA) is a promising alternative. Yet, few studies have evaluated the
 possibility of quantifying Atlantic salmon abundance with eDNA when
 individuals are at low abundance and occur in large river systems. In this
 study, we tested the efficacy of eDNA to monitor and quantify daily
 variation in smolts counts during their downstream migration in a large
 river system with low abundance of smolts. During the 2021 and 2022
 downstream migrations, trap nets were used to conduct a daily census of
 smolts in the Romaine and Puyjalon rivers (Québec, Canada) while eDNA
 samples were collected daily over a transect perpendicular to the
 riverbank. Using quantitative real-time qPCR, we showed that
 discharge-corrected eDNA concentrations were positively correlated with
 daily smolt counts for both years. In addition, we found that controlling
 for temperature and precipitation improved model transferability between
 years, showing the importance of considering environmental correlates when
 using eDNA for abundance quantification. Finally, smolt counts were
 correlated with eDNA concentrations on the same day, but not with eDNA
 concentrations one or two days prior, highlighting the capacity of the
 model to track daily fluctuations in smolt abundance. Our results
 underscore the potential of using eDNA to monitor Atlantic salmon in large
 river systems with low smolt abundance when the river hydrology and
 environmental conditions are documented.
description: # Monitoring Atlantic salmon (Salmo salar) smolt migration in a large
 river system using environmental DNA Dataset DOI:
 [10.5061/dryad.mw6m9067j](10.5061/dryad.mw6m9067j) ## Description of the
 data and file structure We provide here the complete data set we used in
 our article : Monitoring Atlantic Salmon (*Salmo salar*) Smolt Migration
 in a Large River System Using Environmental DNA. You will find three
 sheets in the excel. The first one describe all variable present in the
 study along with their unit and transformation. Second sheet is the
 dataset we used to predict capture with eDNA modified concentration.
 Finally, the third one is the complete capture of smolts before, during
 and after eDNA sampling used for Figure 2 in the article. ### Files and
 variables #### File: modelling\_data.xlsx **Description:** Data used for
 the study. Variables are describe below with unit in bracket. #####
 Variables | Variable | Unit | Description | | | | :-------- | :----- |
 :-------------------------------------------------------------------------------------------------- | :- | :- | | Date | none | Date of sampling of smolts and eDNA  | | | | Jour | none | Date without the year | | | | Year | none | Year of sampling | | | | Caughts | none | Number of smolts caught each day | | | | Discharge | m3/s | Mean Flowate for the Day | | | | T | °C  | Mean Temperature for the Day | | | | Precip | mm | Mean Precipitation for the Day | | | | C\_cover | % | Mean Cloud Cover for the Day | | | | S\_energy | MJ/m2 | Mean Solar Energy for the Day | | | | eDNA | copy/L | Mean eDNA concentration calculated from each eDNA sampling from one day (see Materials and Methods) | | | | C\_eDNA | copy/s | Corrected eDNA concentration with the flowrate (eDNAc = (log10(eDNA)\*Discharge)/1000 | | | ## Code/software All analysis were performed in R software (version 4.2) and are described in the materials and methods section of the article.