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.

Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, and present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have shown mixed results in detecting the presence of these animals under field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored non-avian reptile eDNA quantification by sampling four lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months to detect differences in eDNA using a qPCR assay amplifying the COI gene of the mtDNA genome. Only one sample of the highest-density pond amplified eDNA for a positive detection. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present the “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—as a potential challenge for eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

Analysis of environmental DNA (eDNA) has gained widespread usage for taxonomically based biodiversity assessment. While interest in applying noninvasive eDNA monitoring for population genetic assessments has grown, its usage in this sphere remains limited. One barrier to uptake is that the effectiveness of eDNA detection below the species level remains to be determined for multiple species and environments. Here, we test the utility of this emergent technology to obtain within‐species haplotypic variation of New Zealand (NZ) blackfoot pāua (Haliotis iris). We compare mitochondrial haplotype diversity recovered from marine eDNA samples against traditional tissue samples of blackfoot pāua collected at the same NZ coastal site. Targeting the ATP8‐ATP6 region, we recovered four mitochondrial haplotypes from eDNA versus six haplotypes from tissue samples. Three common haplotypes were recovered with both eDNA and tissue samples, while only one out of three rare haplotypes – represented in tissue samples by one individual each – was recovered with our eDNA methods. We demonstrate that eDNA monitoring is an effective tool for recovering common genetic diversity from pāua, although rare (<5%) haplotypes are seldom recovered. Our results show the potential of eDNA to identify population‐level haplotypic diversity for gastropods in the marine environment below the species level. This work demonstrates that eDNA methods can be an effective, noninvasive tool for genetic monitoring. Noninvasive eDNA sampling could minimize target organism stress and human interaction enabling population genetic research for hard‐to‐sample, delicate, or sensitive species.

Biofilms are formed by communities of microorganisms living in a self-produced extracellular polymeric matrix attached to a surface. When living in a biofilm microorganisms change phenotype and thus are less susceptible to antibiotic treatment and biofilm infections can become severe. The aim of this study was to determine if the presence of multikingdom microorganisms alters the virulence of a biofilm infection in a host organism. The coexistence of Candida albicans and Staphylococcus epidermidis in biofilm was examined in the nematode model Caenorhabditis elegans. It was evaluated if the hyphal form of C. albicans and extracellular polymeric substances (EPS) formed by S. epidermidis increases biofilm virulence. Survival assays were performed, where C. elegans nematodes were exposed to S. epidermidis and C. albicans. Single inoculation assays showed a decreased survival rate after 2 days following exposure, while dual inoculation assays showed that a clinical S. epidermidis strain together with C. albicans significantly increased the virulence and decreased nematode survival. EPS seem to interfere with the bacterial attachment to hyphae, since the EPS overproducing S. epidermidis strain was most virulent. The clinical S. epidermidis paired with C. albicans led to a severe infection in the nematodes resulting in reduced survival.

In response to climate change, biodiversity patterns in the oceans are predicted to shift rapidly, thus increasing the need for efficient monitoring methods. Environmental DNA (eDNA) metabarcoding recently emerged as a potent and cost-effective candidate to answer this challenge. We targeted three molecular markers to determine multicellular metazoan communities from two timepoints across a long-standing transect in the Southern Hemisphere, the Munida Observational Time Series. We detected four community types across the successive water masses—neritic, sub-tropical, frontal, and sub-Antarctic—crossed by the transect, together with important community differences between the two sampling points. From indicator species analysis, we found diversity patterns were mostly driven by planktonic organisms. Mesopelagic communities differed from surface-water communities in the sub-Antarctic water mass, with at-depth communities dominated by single-cellular organisms. We evaluate the ability of eDNA to detect species-compositional changes across surface and depth gradients and lay the foundations for using this technique in multi-trophic environmental monitoring efforts across long time series. We observed community differences across time and space. More intensive sampling will be critical to fully capture diversity across marine gradients, but this multi-trophic method represents an invaluable opportunity to understand shifts in marine biota.

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.