Population‐level inferences from environmental DNA—Current status and future perspectives

Abstract

Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms.This approach offers several potential advantages compared with conventional tissuebased methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances.However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.

Environmental DNA captures the genetic diversity of bowhead whales (Balaena mysticetus) in West Greenland

“…Numerous studies have successfully demonstrated the use of eDNA for monitoring the presence of marine species (Carroll et al., 2019; Foote et al., 2012; Miya et al., 2015; Sigsgaard, Torquato, et al., 2020; Thomsen et al., 2012; Valsecchi et al., 2020). However, the applicability of eDNA for population genetic inference has not been extensively investigated, although a few studies have indicated a promising potential for large marine vertebrates (Baker et al., 2018; Parsons et al., 2018; Sigsgaard, Jensen, et al., 2020; Sigsgaard et al., 2016). Cetaceans are known to slough skin regularly while passing through the water column, which may favor their detection by eDNA sampling (Foote et al., 2012).…”

Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

“…These limitations also complicate standardization across space and personnel. Biomonitoring and habitat characterization based on environmental DNA (eDNA) extracted from seawater samples could overcome some of these challenges (Thomsen & Willerslev ; Sigsgaard et al ). Analyses of eDNA in seawater can cover a broad range of taxonomic groups simultaneously (e.g., Stat et al.…”

Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples

“…Estimating the genetic diversity and abundance of a species provides insights into a wide range of ecological and evolutionary processes and may have important implications for conservation management opportunities. While analysis of eDNA is a well‐established approach for detecting species, it also holds potential to detect genetic diversity within species (Adams et al, 2019; Sigsgaard et al, 2020). With this study, we use eDNA and NGS methods to detect intraspecific genetic diversity of an aquatic invasive species by recovering microsatellite allele frequencies that are similar to those derived from genotyped tissue samples in experimental mesocosms and in field‐based eDNA collections.…”

“…Indeed, even with targeted eDNA sampling in areas of high expected round goby densities, read depths in eDNA samples from the field trial averaged 4,305 reads per sample, which is much lower than reported in other eDNA studies using targeted field sampling and markers in the mitochondrial genome (e.g., average 263,111 reads per sample at sites where whale sharks were reported, Sigsgaard et al, 2017; average 237,434.5 reads per sample taken from harbour porpoise fluke prints, Parsons et al, 2018). To ensure genetic data obtained from eDNA samples sufficiently reflects the genetic diversity of the population of interest when targeting loci in the nuclear genome, efforts to evaluate the limit of detection and optimize field and laboratory strategies to achieve sufficient eDNA copy numbers may be required (Adams et al, 2019; Sigsgaard et al, 2020).…”