Optimization of eDNA Surveys for Evaluating Freshwater Biodiversity and Invasive Species Populations
Date of Award
8-23-2024
Publication Type
Thesis
Degree Name
M.Sc.
Department
Great Lakes Institute for Environmental Research
Keywords
Abundance;Concentration;eDNA;Goldfish;Metabarcoding;Pond
Supervisor
Hugh MacIsaac
Supervisor
Nicholas Mandrak
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Abstract
Stormwater management ponds are both vital infrastructure to any large city and an understudied urban aquatic environment. As interconnected waterbodies, these ponds have the capacity to serve as reservoirs for potential invasive species (e.g., Goldfish (Carassius auratus). If invasive species can tolerate conditions in stormwater management ponds, they may invade connected natural waterbodies. In this study I surveyed fish community biodiversity in 26 stormwater ponds in Hamilton, ON, using novel eDNA techniques. eDNA has many features that make it more appealing to use for fisheries surveys, as it is generally more sensitive and can cause less stress to some species. The limits of eDNA surveys are not yet understood and work needs to be done to determine when these methods should be utilized. The goal of this thesis was to both demonstrate the use of eDNA to detect and quantify freshwater fish species as well as to optimize eDNA survey methods by determining sampling requirements and effects of sampling locations. In the first chapter, I used metabarcoding to determine species composition of whole ecosystems and compared these results to those of conventional surveys. I hypothesized that detections and relative abundance estimates for eDNA would be not significantly different than those produced by conventional methods. I detected an average of 4.19 species using eDNA, whereas electrofishing and seine netting detected 3.71 and 2.65 species, respectively, highlighting the similarities of the methods. A power analysis was performed and I found that to estimate species richness a survey would require 11 samples which is an achievable number for future surveys. Models to compare the nearshore and offshore locations of the ponds were created and I found no significant difference on species richness. I found that relative abundances positively correlated with the relative catch per unit effort for the conventional techniques (Pseudo R2 = 0.601, 0.402). For the second chapter, I used a Goldfish specific qPCR assay to assess the effectiveness of eDNA concentrations estimates in ponds inhabited by Goldfish. I hypothesized that the estimates of goldfish populations would have high correlations with true population values determined through live counts following whole pond draining. By comparing eDNA concentration to these true population metrics, I determined that there was a positive correlation, with the relationship being the strongest after accounting for allometric scaling in eDNA production (R2 = 0.762). To determine the number of samples needed to detect Goldfish I compared the LoD of the species-specific primer to the minimum abundance and biomass values for the ponds and found the most conservative estimates at 535 fish/ha and 4251 g/ha respectively. I then determined the number of samples needed to accurately estimate eDNA concentration for hypothetical surveys and found that 112 and 28 samples to be within 10% and 20% of the true eDNA concentration respectively. Models were created to compare the effects of sampling location on eDNA concentrations and I found no significant of location alone, however a conditional term was significant indicating that there were bias towards near or offshore location in some of the ponds. This thesis has demonstrated the usage of eDNA to both effectively detect and quantify fish species compared to conventional methods. The optimizations determined here should be applied to future eDNA surveys to decrease the required efforts.
Recommended Citation
Smith, Ian, "Optimization of eDNA Surveys for Evaluating Freshwater Biodiversity and Invasive Species Populations" (2024). Electronic Theses and Dissertations. 9427.
https://scholar.uwindsor.ca/etd/9427