Lori Lawson Handley

Context: Pumping stations pose a threat to fish globally through land use change, habitat fragmentation and entrainment risk, with the catadromous and critically endangered European eel particularly impacted. Objectives/methods: Establish, model, assess and understand the present-day distribution of European eel and resident fishes in 152 pumping station catchments in a once extensive wetland (The Fens) using eDNA metabarcoding (855 samples over two and half years), with specific focus on anthropogenic influences on hydrological connectivity and habitat quality. A removal survey design maximised confidence in negative results while minimising time and consumable costs. Results: Eel occurrence upstream of pumping stations was low (occupancy = 28.3%) and positively associated with catchment area, fish species richness and natural hydrological connectivity (gravity drainage or flooding) and negatively associated with distance from the tidal limit. Fish species richness replaced catchment area and improved model performance, potentially acting as a biotic indicator of habitat quality and connectivity. Pumped catchments with manually operated upstream water transfers had reduced eel presence, potentially linked to the direction of water flow or the timing of operation. By contrast, fish species richness increased in these catchments during summer, suggesting displacement into unsuitable long-term habitats. Physical habitat maintenance had no detectable effect on eel occurrence or fish species richness. Conclusions: This study provides the first landscape-scale assessment of European eel distribution and drivers of occurrence in pumped river catchments. The highly novel and comprehensive insights have implications for European eel conservation as well as infrastructure and catchment management, including compliance with legislation (EC Regulation No. 1100/2007).

Reintroduction of keystone species is considered part of the solution to the current biodiversity crisis. The Eurasian beaver ( Castor fiber ) is one such species, shaping its habitat by felling trees, building dams and creating wetlands. However, whilst the potential benefits to aquatic biodiversity and ecological functioning have been studied on a local scale, the impacts of beavers on catchment‐scale processes such as fish migration remain understudied. Sequencing of environmental DNA (eDNA metabarcoding) from water samples is a cost‐effective method to study species distributions across large geographical scales. Here, eDNA samples ( n = 426) were collected from 142 sites across Britain's oldest and largest established wild beaver population, located on Tayside, East Scotland and analysed using a vertebrate‐specific metabarcoding assay. We combined detection/non‐detection data from eDNA results with other environmental and anthropogenic variables to model the effects of beaver eDNA detections on the distribution of three migratory fish species. Using generalised linear models, we found no effects of the current beaver eDNA detections on the distribution of Atlantic salmon or lamprey, but a positive co‐occurrence with European eel at the catchment scale. Model outputs also reinforced previous findings on the impact of barriers to migration and other abiotic and biotic factors on fish species, demonstrating the effectiveness of eDNA sampling in rivers for understanding species distributions at a catchment scale. Synthesis and applications . This study provides novel insights into the catchment‐scale co‐distribution of beavers and migratory fish, and there was no evidence of negative effects on the catchment‐scale distribution of migratory fish species. More generally, this study highlights how catchment‐wide eDNA monitoring can be applied by environmental managers to aid decision‐making and impact assessment of multiple priority species at the catchment scale.

Effective biodiversity monitoring is essential for understanding taxonomic, functional and trophic dynamics in changing ecosystems. Non‐invasive tools such as environmental DNA (eDNA) metabarcoding, passive acoustic monitoring (PAM) and camera trapping offer complementary strengths, yet their relative effectiveness for assessing biodiversity, in particular functional diversity and trophic structure, remains underexplored. These approaches are particularly valuable in rewilding landscapes, where restoration actions create heterogeneous, rapidly changing habitats that require scalable monitoring solutions. We applied an integrated monitoring approach at a rewilding site in Scotland, comparing vertebrate diversity detected by metabarcoding four eDNA sample types (water, soil, tree rolling and scat) with PAM and camera traps. Each method was evaluated for taxonomic richness, community composition, functional diversity via trait‐based analyses and trophic complexity through co‐occurrence networks, metrics rarely assessed together across methods. In total, 79 vertebrate taxa were detected: PAM captured 52 taxa, eDNA 44 and camera traps 12. Of the eDNA substrates, water and tree‐rolling samples had the highest richness. Each method detected unique species, with birds and bats best covered by PAM, and small mammals by eDNA. Community composition varied between methods, with eDNA substrates capturing broader communities. PAM revealed the strongest community differences between wooded and open habitats. Tree rolling and water eDNA captured the greatest functional diversity, while PAM showed higher redundancy. No single method captured all functional traits. Integrating eDNA methods with PAM produced the most complete trophic network. PAM provided the most complete network but missed key terrestrial interactions that were filled by eDNA. Practical implication . Rewilding and restoration programmes require an integrated multi‐method ‘toolkit’ to comprehensively capture vertebrate richness, functional diversity and trophic complexity. We recommend combining PAM with either tree rolling or water eDNA sampling as an optimal monitoring strategy, balancing their complementary strengths in taxonomic and functional coverage.

Environmental DNA (eDNA) sequencing from water samples has emerged as a promising and cost-effective approach to collect comprehensive freshwater biodiversity data. However, critics might highlight potential shortcomings, such as the possibility of false positives (detection of absent species) and false negatives (failing to detect a species that is present). Misconceptions and misunderstandings may also stem from the complexity of the scientific approach and technical language, with implications for decision-makers and potentially hindering conservation. In the present article, we propose an analogy of eating a pizza to simplify messaging and increase understanding of detection probability within typical eDNA metabarcoding workflows. The pizza represents a site, slices represent water samples, bites represent PCR replicates, toppings represent species and olives represent a low-abundance species. Overall, the pizza analogy provides a novel, lighthearted and memorable way to communicate complex eDNA workflows to a broad spectrum of biological scientists and practitioners.

Effective monitoring of the critically endangered European eel ( Anguilla anguilla ) is essential for conservation planning and regulatory decision-making, particularly in heavily fragmented rivers. Environmental DNA (eDNA) methods offer sensitive alternatives to traditional surveys, but there is uncertainty around whether targeted assays or community-wide approaches are better suited to achieve monitoring objectives. We compared eDNA metabarcoding and species-specific quantitative PCR (qPCR) for detecting A. anguilla across 145 pumped catchments in the Fens, East Anglia, England. All sites were sampled once initially, and sites negative for A. anguilla were re-sampled based on metabarcoding results. This allowed comparison of detection rates from a single water sample and site-level retrospective identification of sites where qPCR could have identified A. anguilla in earlier samples. The findings were also set in the context of the wider biodiversity information generated by metabarcoding. From the initial (single) water sample, qPCR detected A. anguilla at seven more sites than metabarcoding (17 versus 10). With repeated sampling, metabarcoding detected A. anguilla at 43 sites, including all but one of the sites where qPCR detected A. anguilla , and ten sites where qPCR did not detect A. anguilla within the same number of samples. Indeed, the additional sampling effort required to detect A. anguilla with metabarcoding at sites also positive with qPCR was small relative to the overall sampling effort. Furthermore, metabarcoding additionally detected 28 non-target fish species alongside fish, amphibian and mammal species of conservation concern. Our results highlight trade-offs between target-species sensitivity and the broader ecological information provided by each method, and support metabarcoding as an effective tool for a holistic conservation approach, with the additional community data outweighing the marginally increased sensitivity of qPCR.

Rewilding, the restoration of natural processes to create self-sustaining and resilient ecosystems, is an increasingly popular conservation approach. However, outcomes are often unpredictable, and effective ecological monitoring is critical for understanding impacts. Integrating environmental DNA (eDNA) metabarcoding with other non-invasive tools may help provide more comprehensive assessments of taxonomic and functional diversity and trophic complexity. We applied an integrated monitoring approach at a rewilding site in Scotland, comparing vertebrate diversity detected by metabarcoding four eDNA sample types (water, soil, tree rolling, scat) with passive acoustic monitoring (PAM) and camera trapping. Each method was evaluated for taxonomic richness, community composition, functional diversity using trait-based analyses, and trophic complexity through co-occurrence networks. The comparative effectiveness of these methods is rarely explored beyond basic taxonomic diversity metrics. In total, 79 vertebrate taxa were detected: PAM captured 52 taxa, eDNA 44, and camera traps 17. Of the eDNA substrates, water and tree-rolling samples had the highest richness. Each method detected unique species, with birds and bats best covered by PAM, and small mammals by eDNA. Community composition varied between methods, with eDNA substrates capturing broader communities. PAM revealed the most pronounced community differences between wooded and open habitats. Tree rolling and water eDNA captured the greatest functional diversity, while PAM showed higher redundancy, detecting species with similar ecological roles. No single method captured all functional traits. Integrating eDNA methods with PAM produced the most complete trophic network. PAM provided the most complete network but missed key terrestrial interactions that were filled by eDNA. Synthesis and applications: Our findings highlight the necessity of an integrated multi-method ‘toolkit’ for practitioners to comprehensively capture vertebrate richness, functional diversity, and trophic complexity, particularly in rewilding contexts. We recommend combining PAM with either tree rolling or water eDNA sampling as an optimal monitoring strategy, balancing their complementary strengths in taxonomic and functional coverage.

Reintroduction of keystone species is considered part of the solution to the current biodiversity crisis. The Eurasian beaver ( Castor fiber ) is one such species, shaping its habitat by felling trees, building dams and creating wetlands. However, while the potential benefits to aquatic biodiversity and ecological functioning have been studied on a local scale, the impacts of beavers on catchment-scale processes such as fish migration remain understudied. Sequencing of environmental DNA (eDNA metabarcoding) from water samples is a cost-effective method to study species distributions across large geographical scales. Here, eDNA samples ( n =426) were collected from 142 sites across the UK’s oldest and largest established wild beaver population, located on Tayside, East Scotland, and analysed using a vertebrate specific metabarcoding assay. We combined presence/absence data from eDNA results with other environmental and anthropogenic variables to model the effects of beaver presence on the distribution of three migratory fish species. Using generalised linear models, we found no effects of the current beaver presence on the distribution of Atlantic salmon or lamprey, but a positive co-occurrence with European eel at the catchment scale. Model outputs also reinforced previous findings on the impact of barriers to migration and other abiotic and biotic factors on fish species, demonstrating the effectiveness of eDNA sampling in rivers for understanding species distributions at a catchment scale. This case study provides novel insights into the co-distribution of beavers and migratory fish, and highlights how catchment-wide eDNA monitoring can be applied by environmental managers to aid decision-making and impact assessment more generally.

Hybridization plays a pivotal role in evolution, influencing local adaptation and speciation. However, it can also reduce biodiversity, which is especially damaging when native and non-native species meet. Hybridization can threaten native species via competition (with vigorous hybrids), reproductive resource wastage, and gene introgression. The latter, in particular, could result in increased fitness in invasive species, decreased fitness of natives, and compromise reintroduction or recovery conservation practices. In this study, we use a combination of RAD sequencing and microsatellites for a range-wide sample set of 1366 fish to evaluate the potential for hybridisation and introgression between native crucian carp ( Carassius carassius ) and three non-native species ( Carassius auratus auratus , Carassius auratus gibelio , and Cyprinus carpio ) in European water bodies. We found hybridization between native and non-native species in 82% of populations with non-natives present, highlighting the potential for substantial ecological impacts from hybrids on crucian carp populations. However, despite such high rates of hybridization, we could find no evidence of introgression between these species. The presence of triploid backcrosses in at least two populations points suggests that the lack of introgression among these species is likely due to meiotic dysfunction in hybrids, leading to production of polyploid offspring which are unable to reproduce sexually. This result is promising for crucian reintroduction programs, as it implies limited risk to the genetic integrity of source populations. Future research should investigate the reproductive potential of triploid hybrids and the ecological pressures hybrids impose on C. carassius .

Hybridization plays a pivotal role in evolution, influencing local adaptation and speciation. However, it can also reduce biodiversity, which is especially damaging when native and non‐native species meet. Hybridization can threaten native species via competition (with vigorous hybrids), reproductive resource wastage and gene introgression. The latter, in particular, could result in increased fitness in invasive species, decreased fitness of natives and compromise reintroduction or recovery conservation practices. In this study, we use a combination of RAD sequencing and microsatellites for a range‐wide sample set of 1366 fish to evaluate the potential for hybridization and introgression between native crucian carp (Carassius carassius) and three non‐native taxa (Carassius auratus auratus, Carassius auratus gibelio and Cyprinus carpio) in European water bodies. We found hybridization between native and non‐native taxa in 82% of populations with non‐natives present, highlighting the potential for substantial ecological impacts from hybrids on crucian carp populations. However, despite such high rates of hybridization, we could find no evidence of introgression between these taxa. The presence of triploid backcrosses in at least two populations suggests that the lack of introgression among these taxa is likely due to meiotic dysfunction in hybrids, leading to the production of polyploid offspring which are unable to reproduce sexually. This result is promising for crucian reintroduction programs, as it implies limited risk to the genetic integrity of source populations. Future research should investigate the reproductive potential of triploid hybrids and the ecological pressures hybrids impose on C. carassius.