Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

Abstract

Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.

Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

“…The promising applications of eDNA for monitoring aquatic biodiversity including fishes or their communities have been extensively reviewed [1,2,5,8,[12][13][14][15][16][17][18][19][20][21][22][23]. With respect to eDNA, fish are currently the most studied group of macro-organisms in aquatic ecosystems [24].…”

Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation

“…This problem is especially true for non-model organisms for which many functional pathways are unknown, or gene annotation is based on phylogenetically distant taxa. Furthermore, while palaeogenomics can provide evidence for community changes over time, there is rarely sufficient resolution for population-level analysis (although this might change, see a recent perspective paper 90 ), and it cannot provide a direct link to specific changes at the phenotype level and the organisms' fitness. Resurrection studies can address these limitations.…”

HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves

“…First, it is not immediately clear how the argument N , is to be handled since multiple reads could be associated with single individuals. That is, unlike in traditional Sanger-based sequencing, there is not a one-to-one correspondence between specimen and sequence (Wares & Pappalardo, 2015;Adams et al, 2019). Second, obtaining reliable haplotype information from noisy HTS datasets is challenging without first having strict quality filtering criteria in place to minimize the occurrence of rare, low-copy sequence variants which may reflect artifacts stemming from the Polymerase Chain Reaction (PCR) amplification step or sequencing process (Elbrecht et al, 2018;Braukmann et al, 2019;Turon et al, 2019).…”

“…Second, obtaining reliable haplotype information from noisy HTS datasets is challenging without first having strict quality filtering criteria in place to minimize the occurrence of rare, low-copy sequence variants which may reflect artifacts stemming from the Polymerase Chain Reaction (PCR) amplification step or sequencing process (Elbrecht et al, 2018;Braukmann et al, 2019;Turon et al, 2019). Turning to molecular population genetics theory might be the answer (Adams et al, 2019). Wares & Pappalardo (2015) suggest three different approaches to estimating the number of specimens of a species that may have contributed to a metabarcoding sample: (1) use of prior estimates of haplotype diversity, together with observed number of haplotypes;…”