Combining environmental DNA and species distribution modeling to evaluate reintroduction success of a freshwater fish

From genomic threat assessment to conservation action

Genomic approaches have the potential to play a pivotal role in conservation, both to detect threats to species and populations and to restore biodiversity through actions. We here separate these approaches into two subdisciplines, vulnerability and restoration genomics, and discuss current applications, outstanding questions, and future potential.

Environmental DNA metabarcoding of water samples as a tool for monitoring Iberian freshwater fish composition

Environmental DNA (eDNA) metabarcoding has been increasingly used to monitor the community assemblages of a wide variety of organisms. Here, we test the efficacy of eDNA metabarcoding to assess the composition of Iberian freshwater fishes, one of the most endangered groups of vertebrates in Spain. For this purpose, we sampled 12 sampling sites throughout one of Spain's largest basins, the Duero, which is home to approximately 70% of the genera and 30% of the primary freshwater fish in Spain. We sampled these sampling sites in the summer by using electrofishing, a traditional sampling method, and eDNA metabarcoding of river water samples using the mitochondrial 12S rRNA gene (12S) as a marker. We also resampled four of these sampling sites in autumn by eDNA. We compared the results obtained through eDNA metabarcoding with those of electrofishing surveys (ones conducted for the present study and past ones) and assessed the suitability of 12S as an eDNA metabarcoding marker for this group of freshwater fishes. We found that the 12S fragment, analysed for 25 Iberian species, showed sufficient taxonomic resolution to be useful for eDNA approaches, and even showed population-level differences in the studied populations across the tissue samples for Achondrostoma arcasii. In most cases, a greater number of species was detected through eDNA metabarcoding than through electrofishing. Based on our results, eDNA metabarcoding is a powerful tool to study the freshwater fish composition in the Iberian Peninsula and to unmask cryptic diversity. However, we highlight the need to generate a local genetic database for 12S gene for such studies and to interpret the results with caution when studying only mitochondrial DNA. Finally, our survey shows that the high detection sensitivity of eDNA metabarcoding and the non-invasiveness of this method allows it to act as a detection system for species of low abundance, such as early invasive species or species in population decline, two key aspects of conservation management of Spanish freshwater fishes.

Using eDNA to understand predator-prey interactions influenced by invasive species

Invasive predatory species may alter population dynamic processes of their prey and impact biological communities and ecosystem processes. Revealing biotic interactions, however, including the relationship between predator and prey, is a difficult task, in particular for species that are hard to monitor. Here, we present a case study that documents the utility of environmental DNA analysis (eDNA) to assess predator-prey interactions between two invasive fishes (Lepomis gibbosus, Pseudorasbora parva) and two potential amphibian prey species, (Triturus cristatus, Pelobates fuscus). We used species-specific TaqMan assays for quantitative assessment of eDNA concentrations from water samples collected from 89 sites across 31 ponds during three consecutive months from a local amphibian hotspot in Germany. We found a negative relationship between eDNA concentrations of the predators (fishes) and prey (amphibians) using Monte-Carlo tests. Our study highlights the potential of eDNA application to reveal predator-prey interactions and confirms the hypothesis that the observed local declines of amphibian species may be at least partly caused by recently introduced invasive fishes. Our findings have important consequences for local conservation management and highlight the usefulness of eDNA approaches to assess ecological interactions and guide targeted conservation action.

Broad-scale eDNA sampling for describing aquatic species distributions in running waters: Pacific lamprey Entosphenus tridentatus in the upper Snake River, USA

One of the most fundamental yet challenging tasks for aquatic ecologists is to precisely delineate the range of species, particularly those that are broadly distributed, require specialized sampling methods, and may be simultaneously declining and increasing in different portions of their range. An exemplar is the Pacific lamprey Entosphenus tridentatus, a jawless anadromous fish of conservation concern that is actively managed in many coastal basins in western North America. To efficiently determine its distribution across the accessible 56,168 km of the upper Snake River basin in the north-western United States, we first delimited potential habitat by using predictions from a species distribution model based on conventionally collected historical data and from the distribution of a potential surrogate, Chinook salmon Oncorhynchus tshawytscha, which yielded a potential habitat network of 10,615 km. Within this area, we conducted a two-stage environmental DNA survey involving 394 new samples and 187 archived samples collected by professional biologists and citizen scientists using a single, standardized method from 2015 to 2021. We estimated that Pacific lamprey occupied 1875 km of lotic habitat in this basin, of which 1444 km may have been influenced by recent translocation efforts. Pacific lamprey DNA was consistently present throughout most river main stems, although detections became weaker or less frequent in the largest and warmest downstream channels and near their headwater extent. Pacific lamprey were detected in nearly all stocked tributaries, but there was no evidence of indigenous populations in such habitats. There was evidence of post-stocking movement because detections were 1.8-36.0 km upstream from release sites. By crafting a model-driven spatial sampling template and executing an eDNA-based sampling campaign led by professionals and volunteers, supplemented by previously collected samples, we established a benchmark for understanding the current range of Pacific lamprey across a large portion of its range in the interior Columbia River basin. This approach could be tailored to refine range estimates for other wide-ranging aquatic species of conservation concern.

Methodology of fish eDNA and its applications in ecology and environment

Fish environmental DNA (eDNA) studies have made substantial progress during the past decade, and significant advances in monitoring fishes have been gained by taking advantage of this technology. Although a number of reviews concerning eDNA are available and some recent fish eDNA reviews focused on fisheries or standard method have been published, a systematic review of methodology of fish eDNA and its applications in ecology and environment has not yet been published. To our knowledge, this is the first review of fish eDNA for solving ecological and environmental issues. First, the most comprehensive literature analysis of fish eDNA was presented and analyzed. Then, we systematically discuss the relevant experiments and analyses of fish eDNA, and infers that standard workflow is on the way to consensus. We additionally provide reference sequence databases and the primers used to amplify the reference sequences or detecting fish eDNA. The abiotic and biotic conditions affecting fish eDNA persistence are also summarized in a schematic diagram. Subsequently, we focus on the major achievements of fish eDNA in ecology and environment. We additionally highlight the exciting new tools, including in situ autonomous monitoring devices, CRISPR nucleic acid detection technology, and meta-omics technology for fish eDNA detection in future. Ultimately, methodology of fish eDNA will provide a wholly new paradigm for conservation actions of fishes, ecological and environmental management at a global scale.