Environmental DNA (eDNA) is transforming the ways in which scientists and resource managers assess the diversity and distribution of organisms. While eDNA approaches are well established for detecting species and communities in aquatic environments, far less is known about the ability to use eDNA to obtain population-level genetic information. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population-level genetic diversity and estimates of species abundance. Using a panel of multiallelic microsatellite markers, we evaluated intraspecific genetic diversity in the round goby (Neogobius melanostomus) from eDNA samples. We tested the similarity between eDNA and individual genotype-based estimates of allele frequencies in experimental mesocosms. We then used a likelihood-based DNA mixture framework to estimate absolute round goby abundance using eDNA-based allele frequencies.
Results/Conclusions
Allele frequencies from eDNA showed high similarity to allele frequencies from genotyped round goby tissue samples (Pearson’s correlation coefficient r = 0.95), indicating nuclear DNA may be reliably amplified from water samples. DNA mixture analyses resulted in accurate estimates of the number of round goby individuals in mesocosms using eDNA samples, with the degree of bias dependent on the filtering scheme of low-frequency alleles. This study is the first to document the application of eDNA approaches to obtain intraspecific nuclear genetic information and estimate absolute abundance of a species in environmental samples using eDNA-derived allele frequencies. This novel approach broadens the application of eDNA to inform population-level management objectives, with potential to transform the ways in which we obtain population-level genetic information on species or conservation or management concern.