Biology subjects

Lawson Handley, L.

Publications and source records attributed to Lawson Handley, L..

11 recordsLinked to original sources

bioRxiv2026

Pumping stations negatively affect the distribution of critically endangered European eel (Anguilla anguilla); a landscape-scale study using environmental DNA metabarcoding

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).

ecology↗

bioRxiv2026

Species-specific versus community-wide assays in eDNA monitoring of European eel Anguilla anguilla: Trade-offs between detection sensitivity and the value of additional community data

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.

ecology↗

bioRxiv2025

Multi-tool monitoring: integrating non-invasive methods to assess vertebrate diversity and trophic complexity in terrestrial rewilding

O_LIRewilding, 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. C_LIO_LIWe 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. C_LIO_LIIn 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. C_LIO_LITree 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. C_LIO_LISynthesis 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. C_LI

ecology↗

bioRxiv2025

eDNA sampling reveals no negative effects of beaver recolonisation on the catchment-scale distribution of migratory fish

O_LIReintroduction 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. C_LIO_LISequencing 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 UKs 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. C_LIO_LIUsing 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. C_LIO_LIThis 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. C_LI

ecology↗

bioRxiv2023

Mussels on the move: new records of the invasive non-native quagga mussel (Dreissena rostriformis bugensis) in Great Britain using eDNA and a new probe-based qPCR assay

Invasive non-native species (INNS) pose a worldwide environmental threat, negatively impacting invaded ecosystems on an ecological and economical scale. In recent decades, quagga mussels (Dreissena rostriformis bugensis) have successfully invaded several countries in Western Europe from the Ponto-Caspian region, being recorded for the first time in Great Britain (GB) in 2014, in Wraysbury, near London. In recent years, environmental DNA (eDNA) analysis has proven to be a sensitive and effective method for early detection and monitoring of a number of INNS. Previously, a dye-based quantitative PCR (qPCR) assay was developed for the detection of quagga mussels from eDNA samples. Here, a target-specific probe was designed to further increase the specificity of this assay and used to obtain an updated distribution of this species in GB. Twenty-four sites were sampled, including sites with established populations near London and sites spread across the East Midlands and East Anglia regions. Positive detections were obtained for 11 of the 24 sites, and these were widely spread, as far as Nottingham (East Midlands) and Norfolk (East Anglia). Detection rates were 100% at the three sites with known established populations, while rates were lower (3-50% of positive replicates) in the eight newly-identified sites, consistent with an early stage of invasion. Of particular concern was the detection of quagga mussels in major waterways and in popular recreational sites, highlighting urgent measures are needed to control pathways and spread. Our study demonstrates that quagga mussels are considerably more widespread in GB than previously thought and provides a much-needed step towards operational use of eDNA for monitoring quagga mussels.

ecology↗

bioRxiv2020

Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity - a comparison of conventional and molecular tools

Fishes stocked for recreation and angling can damage freshwater habitats and negatively impact biodiversity. The pond-associated crucian carp (Carassius carassius) is rare across Europe and stocked for conservation management in England, but impacts on pond biota are understudied. Freshwater invertebrates contribute substantially to aquatic biodiversity, encompassing many rare and endemic species, but their small size and high abundance complicates their assessment. Practitioners have employed sweep-netting and kick-sampling with microscopy (morphotaxonomy), but specimen size/quality and experience can bias identification. DNA and eDNA metabarcoding offer alternative means of invertebrate assessment. We compared invertebrate diversity in ponds (N = 18) with and without crucian carp using morphotaxonomic identification, DNA metabarcoding, and eDNA metabarcoding. Five 2-L water samples and 3-minute sweep-net samples were collected at each pond. Inventories produced by morphotaxonomic identification of netted samples, DNA metabarcoding of bulk tissue samples, and eDNA metabarcoding of water samples were compared. Alpha diversity was greatest with DNA or eDNA metabarcoding, depending on whether standard or unbiased methods were considered. DNA metabarcoding reflected morphotaxonomic identification, whereas eDNA metabarcoding produced markedly different communities. These complementary tools should be combined for comprehensive invertebrate assessment. Crucian carp presence minimally reduced alpha diversity in ponds, but positively influenced beta diversity through taxon turnover (i.e. ponds with crucian carp contained different invertebrates to fishless ponds). Crucian carp presence contributes to landscape-scale invertebrate diversity, supporting continued conservation management in England. Our results show that molecular tools can enhance freshwater invertebrate assessment and facilitate development of more accurate and ecologically effective pond management strategies.

ecology↗

bioRxiv2019

Fishing for mammals: landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from lotic ecosystems

O_LIEnvironmental DNA (eDNA) metabarcoding has revolutionised biomonitoring in both marine and freshwater ecosystems. However, for semi-aquatic and terrestrial animals, the application of this technique remains relatively untested.\nC_LIO_LIWe first assess the efficiency of eDNA metabarcoding in detecting semi-aquatic and terrestrial mammals in natural lotic ecosystems in the UK by comparing sequence data recovered from water and sediment samples to the mammalian communities expected from historical data. Secondly, we evaluate the detection efficiency of eDNA samples compared to multiple conventional non-invasive survey methods (latrine surveys and camera trapping) using occupancy modelling.\nC_LIO_LIeDNA metabarcoding detected a large proportion of the expected mammalian community within each area. Common species in the areas were detected at the majority of sites. Several key species of conservation concern in the UK were detected by eDNA in areas where authenticated records do not currently exist, but potential false positives were also identified for several non-native species.\nC_LIO_LIWater-based eDNA samples provided comparable results to conventional survey methods in per unit of survey effort for three species (water vole, field vole, and red deer) using occupancy models. The comparison between survey effort to reach a detection probability of [≥]0.95 revealed that 3-6 water replicates would be equivalent to 3-5 latrine surveys and 5-30 weeks of single camera deployment, depending on the species.\nC_LIO_LISynthesis and Applications. eDNA metabarcoding represents an extremely promising tool for monitoring mammals, allowing for the detection of multiple species simultaneously, and provides comparable results to widely-used conventional survey methods. eDNA from freshwater systems delivers a terrestrial dividend by detecting both semi-aquatic and terrestrial mammalian communities, and provides a basis for future monitoring at a landscape level over larger spatial and temporal scales (i.e. long-term monitoring at national levels).\nC_LI

ecology↗

bioRxiv2019

Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals

O_LIEnvironmental DNA (eDNA) metabarcoding is largely used to survey aquatic communities, but can also provide data on terrestrial taxa utilising aquatic habitats. However, the entry, dispersal, and detection of terrestrial species DNA within waterbodies is understudied. C_LIO_LIWe evaluated eDNA metabarcoding of pond water for monitoring semi-aquatic, ground-dwelling, and arboreal mammals, and examined spatiotemporal variation in mammal eDNA signals using experiments in captive and wild conditions. C_LIO_LIWe selected nine focal species of conservation and management concern: European water vole, European otter, Eurasian beaver, European hedgehog, European badger, red deer, Eurasian lynx, red squirrel, and European pine marten. We hypothesised that eDNA signals (i.e. proportional read counts) would be stronger for semi-aquatic than terrestrial species, and at sites where mammals exhibited behaviours (e.g. swimming, urination). We tested this by sampling waterbodies in enclosures of captive focal species at specific sites where behaviours had been observed ( directed sampling) and at equidistant intervals along the shoreline ( stratified sampling). We then surveyed natural ponds (N = 6) where focal species were present using stratified water sampling, camera traps, and field signs. eDNA samples were metabarcoded using vertebrate-specific primers. C_LIO_LIAll focal species were detected in captivity. eDNA signal strength did not differ between directed and stratified samples across or within species, between species lifestyles (i.e. semi-aquatic, ground-dwelling, arboreal), or according to behaviours. Therefore, eDNA was evenly distributed within artificial waterbodies. Conversely, eDNA was unevenly distributed in natural ponds. eDNA metabarcoding, camera trapping, and field signs detected beaver, red deer, and roe deer. Badger and red fox were recorded with cameras and field signs, but not eDNA metabarcoding. However, eDNA metabarcoding detected small mammals missed by cameras and field signs, e.g. water vole. Terrestrial mammal eDNA signals were weaker and detected in fewer samples than semi-aquatic mammal eDNA signals. C_LIO_LIeDNA metabarcoding has potential for inclusion in mammal monitoring schemes by enabling large-scale, multi-species distribution assessment for priority and difficult to survey species, and could provide early indication of range expansions or contractions. However, eDNA surveys need high spatiotemporal resolution and metabarcoding biases require further investigation before this tool is routinely implemented. C_LI

molecular biology↗

bioRxiv2018

Development of environmental DNA surveillance for the threatened crucian carp (Carassius carassius)

O_LIThe crucian carp (Carassius carassius) is one of few fish species associated with small ponds in the UK. These populations contain genetic diversity not found in Europe and are important to conservation efforts for the species, which has declined across its range. Detection and monitoring of extant crucian carp populations are crucial for conservation success. Environmental DNA (eDNA) analysis could be very useful in this respect as a rapid, cost-efficient monitoring tool.\nC_LIO_LIWe developed a species-specific quantitative PCR (qPCR) assay for eDNA surveillance of crucian carp to enable non-invasive, large-scale distribution monitoring. We compared fyke netting and eDNA at ponds with (N = 10) and without (N = 10) crucian carp for presence-absence detection and relative abundance estimation, specifically whether DNA copy number reflected catch-per-unit-effort (CPUE) estimate. We examined biotic and abiotic influences on eDNA detection and quantification, and compared qPCR to standard PCR. Notably, eDNA occurrence and detection probabilities in relation to biotic and abiotic factors were estimated using a hierarchical occupancy model.\nC_LIO_LIeDNA analysis achieved 90% detection for crucian carp (N = 10), failing in only one pond where presence was known. We observed an overall positive trend between DNA copy number and CPUE estimate, but this was not significant. Macrophyte cover decreased the probability of eDNA occurrence at ponds, whereas CPUE and conductivity had positive and negative influences on eDNA detection probability in qPCR replicates respectively. Conductivity also had a negative effect on DNA copy number, but copy number increased with temperature and percentage of macrophyte cover. PCR was comparable to qPCR for species detection and may provide semi-quantitative information.\nC_LIO_LIOur results demonstrate that eDNA could enable detection of crucian carp populations in ponds and benefit ongoing conservation efforts, but imperfect species detection in relation to biotic and abiotic factors and eDNA workflow requires further investigation. Nonetheless, we have established an eDNA framework for crucian carp and sources of imperfect detection which future investigations can build upon.\nC_LI

molecular biology↗

bioRxiv2018

Understanding biodiversity at the pondscape using environmental DNA: a focus on great crested newts

Environmental DNA (eDNA) metabarcoding is revolutionising biodiversity monitoring, but has unrealised potential for ecological hypothesis generation and testing. Here, we validate this potential in a large-scale analysis of vertebrate community data generated by eDNA metabarcoding of 532 UK ponds. We test biotic associations between the threatened great crested newt (Triturus cristatus) and other vertebrates as well as abiotic factors influencing T. cristatus detection at the pondscape. Furthermore, we test the status of T. cristatus as an umbrella species for pond conservation by assessing whether vertebrate species richness is greater in ponds with T. cristatus and higher T. cristatus Habitat Suitability Index (HSI) scores. T. cristatus detection was positively correlated with amphibian and waterfowl species richness. Specifically, T. cristatus was positively associated with smooth newt (Lissotriton vulgaris), common coot (Fulica atra), and common moorhen (Gallinula chloropus), but negatively associated with common toad (Bufo bufo). T. cristatus detection did not significantly decrease as fish species richness increased, but negative associations with common carp (Cyprinus carpio), three-spined stickleback (Gasterosteus aculeatus) and ninespine stickleback (Pungitius pungitius) were identified. T. cristatus detection was negatively correlated with mammal species richness, and T. cristatus was negatively associated with grey squirrel (Sciurus carolinensis). T. cristatus detection was negatively correlated with larger pond area, presence of inflow, and higher percentage of shading, but positively correlated with HSI score, supporting its application to T. cristatus survey. Vertebrate species richness was significantly higher in T. cristatus ponds and broadly increased as T. cristatus HSI scores increased. We reaffirm reported associations (e.g. T. cristatus preference for smaller ponds) but also provide novel insights, including a negative effect of pond inflow on T. cristatus. Our findings demonstrate the prospects of eDNA metabarcoding for ecological hypothesis generation and testing at landscape scale, and dramatic enhancement of freshwater conservation, management, monitoring and research.

ecology↗

bioRxiv2017

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of great crested newt (Triturus cristatus)

Environmental DNA (eDNA) analysis is a rapid, cost-effective, non-invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and metabarcoding have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA. We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real-time quantitative PCR (qPCR) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using High-Throughput Sequencing technology. With qPCR and a detection threshold of 1/12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4/12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species-specific surveys.

molecular biology↗