Northern post-glacial fish are valuable natural systems for studying life-history responses to climate due to their recent evolutionary history, replicated spatial structure, and strong temperature dependence of physiological processes. From published data we developed matrix models for Arctic charr (Salvelinus alpinus) populations distributed across a latitudinal air temperature gradient spanning the species' full thermal range. Using elasticity analysis, which estimates the proportional change in the population growth rate for a proportional change in a vital rate, we examined the importance of reproduction, juvenile survival, and adult survival for mean fitness (population growth rate) across this gradient. Reproductive elasticity increased significantly with temperature, with regression models estimating an similar to 150% rise from -22.1 to 7.8 degrees C. This trend paralleled earlier maturation, shorter lifespan, faster juvenile growth, and more frequent breeding in warmer environments. The temperature responses of survival elasticities were less clear: in anadromous populations (N = 12), juvenile elasticity increased while adult elasticity decreased with temperature; in lake-resident populations (N = 41), juvenile elasticity showed the opposite trend and adult elasticity was unresponsive to temperature. Despite substantial variation in life-history traits, the relative ranking of life-stage elasticities-an important consideration for wildlife management-was largely consistent among populations across most of the temperature range, supporting the evolutionary conservation of elasticity rankings within species and the use of data-rich populations to inform the management of data-limited populations. Our findings indicate that as climates warm, natural selection on reproduction will probably intensify.

The South African coast exhibits high spatial and environmental variability, which supports a diverse biodiversity of fish, and other marine species, providing valuable ecosystem services, including fisheries, nutrient cycling, habitat stabilization and tourism. However, ongoing anthropogenic pressure, including climate change and land-use alterations, are contributing to coastal biodiversity loss, necessitating the need for effective conservation strategies and a deeper understanding of the environmental factors driving marine biodiversity dynamics. Environmental DNA (eDNA) offers a non-invasive means to assess marine biodiversity and is becoming widely adopted as effective means to conduct ecological and biodiversity assessments . Here we looked to determine the spatial and environmental effects on coastal fish biodiversity across the entire extent of South Africa's coast using environmental DNA (eDNA). From 31 sites we detected 310 unique amplicon sequence variants (ASVs), representing 157 genera and 89 families. Genus, family and ASV richness all significantly increased with increasing temperature (p < 0.01), aligning with the west-to-east temperature gradient. Beta-diversity also significantly increased with difference in temperature (p < 0.01) and distance (p = 0.01), with turnover having a stronger influence compared to richness difference. We identified 22 key genera as indicators of spatial biodiversity change, and with hierarchical modeling provide insights into spatial and environmental influences on specific genera distributions along the coast This study underscores the utility of eDNA as a powerful, cost-effective, and non-invasive tool for capturing biodiversity dynamics across extensive spatial scales, offering a comprehensive understanding of the factors shaping coastal biodiversity and supporting global marine biodiversity monitoring and conservation efforts.

Effective species conservation and management requires comprehensive biomonitoring, enhanced by combining traditional and newer methodologies, such as environmental DNA (eDNA) analyses. A seasonal pulse of spawning adult Atlantic salmon (Salmo salar) was detected by normalised eDNA 12S reads from metabarcoding, which facilitated estimation of spatial patterns in salmon biomass. A strong relationship was found between normalised reads in the lower section of the River Conwy (Wales, UK) and whole-river adult biomass (estimated from rod catch data and a fish counter), explaining 61% of the variation in a linear regression. Moreover, the positive linear relationship between adult biomass and partial effect on normalised reads occurred after the biomass estimate exceeded 1500 kg, indicating a threshold where normalised reads become representative of biomass. The relationship observed between normalised reads and biomass, as well as the unique profiles of normalised reads at each of the sites, supports the hypothesis of limited eDNA transport among sampling sites that were 2-4 km apart. River pH showed a significant non-linear relationship with normalised reads, with a peak in partial effect on normalised reads at pH 6.5. Partial effect on normalised reads also showed a positive linear relationship with flow (discharge), while also peaking at the highest average monthly air temperatures (14°C). These trends are contrary to what would be expected from eDNA decay, dilution or transport, demonstrating that metabarcoding is robust to such influences, reinforcing the interpretation of trends driven by Atlantic salmon ecology and physiology. For example, pH effects reflect beneficial conditions for eggs and perhaps habitat preference for spawners, flow effects reflect the annual return of salmon during higher flows which aid upstream migration, tributary entry and spawning, and, finally, temperature effects reflect higher metabolic rates and greater shedding of eDNA.

The 2024 Annual Symposium of the Fisheries Society of the British Isles reviewed the burgeoning impact of 'omics' technologies on fish ecology, management and forecasting. As with life sciences more generally, major advances in speed, cost-effectiveness and breadth of applications in 'omics' has had profound societal and environmental impacts. This article presents a synthesis of when, how and why genetics and genomics have impacted marine fisheries management and uptake by policy makers. After a brief historical perspective on genetics in fisheries and salient advances, including a critique of the traditional disjunct in approaches, three case studies are used to demonstrate impact on policy: real time management of mixed stock fisheries in demersal Atlantic cod (Gadus morhua) and anadromous sockeye salmon (Oncorhynchus nerka), and rapid estimation of population abundance in southern bluefin tuna (Thunnus maccoyii) using genetic-based tagging. Common features underpinning successful impact from these and cited studies were examined, including a consideration of the impactful population-level EU traceability programme, FishPopTrace. Among key commonalities of success were the significant role of demand-led needs, genomic automation, cost-effectiveness and speed of processing long-term collaborative programmes in enabling establishment of comprehensive spatial and temporal databases, and effective engagement with stakeholders and end-users. While current trends show a significant upsurge in applications and impacts, especially in application of environmental DNA, there remains a need to foster ongoing fundamental science with large-scale policy-led, targeted collaborative programmes, combined with enhanced visibility of exemplar case studies.

AbstractBycatch and discards, representing unwanted catches, undermine sustainable fisheries and hinder the conservation of vulnerable and endangered species. To effectively monitor bycatch and enhance the effectiveness of management measures while promoting sustainable fishing practices, reliable data is essential. Here, we explore the use of Nanopore metabarcoding to analyze the catch composition in demersal bottom fisheries. We collected eDNA samples directly from an onboard catch holding tank (catch water) for 10 fishing hauls from a fishing vessel operating in the Skagerrak (North‐East Atlantic). The approach involved sequencing a combination of long (~2 kb) and short (~170–313 bp) mitochondrial amplicons and was validated by analyzing a fishery‐related mock community sample and fishing haul replicates. Overall, the detection rate accuracy was 95% for landed species, and replicates obtained from the same fishing haul showed consistent results, validating the robustness of this approach. The detection rate accuracy for all caught species observed on board (including the non‐landed fraction) was 81%. Undetected species were always limited to species in low abundance, but may also be attributed to problems with identifying closely related species due to the impact of sequencing errors and limited diagnostic variation in the genetic regions used. In the future, such biases may be reduced by using additional markers to increase species discrimination power and applying newly available technological advantages in flow cell chemistry to improve sequencing accuracy. In conclusion, this study demonstrates the effectiveness of Nanopore eDNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries, including catches of non‐commercial and threatened and vulnerable species, without disrupting fishing activities. Incorporating eDNA analysis of catch water may therefore help facilitate effective monitoring, leading to better‐informed fisheries management, biodiversity conservation efforts, and the implementation of relevant legislation such as the EU landing obligation.

AbstractAnthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20–35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change.

Fishes are a dominant component of the macrofauna in estuaries and are important for assessing the health of these threatened ecosystems. Several studies have applied environmental DNA (eDNA) metabarcoding to assess the biodiversity of fishes in estuaries. However, none have combined measurement of physicochemical variables with a spatially extensive sampling design across the full salinity gradient. This study aimed to compare spatial fish assemblage composition detected via eDNA metabarcoding of surface water samples with conventional fishing gear surveys in a macrotidal estuary (river Dee, North Wales, UK). In addition, eDNA assemblage composition across seasons was investigated. In autumn 2018, triplicate eDNA samples were taken at 13 stations in a spatially systematic design alongside seine, fyke and beam trawl sampling. In summer 2019, eDNA samples from eight of the 13 original stations were collected again in the upper and lower estuary. DNA was extracted from samples and subjected to metabarcoding analysis using an established assay targeting teleost fishes. The key findings were that in autumn, eDNA detected 17 of the 26 (71%) species caught by fishing gears, which included the most abundant species. Overall, eDNA detected a greater species richness, per 30 samples, than seine or fyke nets (but not beam trawling). Additionally, there was a clear correlation between salinity and assemblage composition, which was consistent across seasons. Overall, the study indicates that eDNA metabarcoding could enhance existing fish sampling methods, by generating a more comprehensive picture of estuarine fish biodiversity and providing additional information for ecological inference and management actions.

Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonization, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.

The use of molecular tools to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species' range shifts. This is important when managing range shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here, we investigated the ascidian NNS Ciona robusta, Clavelina lepadiformis, Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NNS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the biodiversity survey and the COI datasets, but failed to capture the complete incidence of all NNS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing both thriving NNS and threatened species. This article is part of the theme issue 'Species' ranges in the face of changing environments (part I)'.

© 2022 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. Correction to: ‘Managing humanmediatedrange shifts: understanding spatial,temporal and genetic variation in marinenon-native species’ (2022) by Holman et al.

Sea turtle populations are under threat from an epizootic tumor disease (animal epidemic) known as fibropapillomatosis. Fibropapillomatosis continues to spread geographically, with prevalence of the disease also growing at many longer-affected sites globally. However, we do not yet understand the precise environmental, mutational and viral events driving fibropapillomatosis tumor formation and progression.Here we perform transcriptomic and immunohistochemical profiling of five fibropapillomatosis tumor types: external new, established and postsurgical regrowth tumors, and internal lung and kidney tumors. We reveal that internal tumors are molecularly distinct from the more common external tumors. However, they have a small number of conserved potentially therapeutically targetable molecular vulnerabilities in common, such as the MAPK, Wnt, TGFβ and TNF oncogenic signaling pathways. These conserved oncogenic drivers recapitulate remarkably well the core pan-cancer drivers responsible for human cancers. Fibropapillomatosis has been considered benign, but metastatic-related transcriptional signatures are strongly activated in kidney and established external tumors. Tumors in turtles with poor outcomes (died/euthanized) have genes associated with apoptosis and immune function suppressed, with these genes providing putative predictive biomarkers.Together, these results offer an improved understanding of fibropapillomatosis tumorigenesis and provide insights into the origins, inter-tumor relationships, and therapeutic treatment for this wildlife epizootic.

Rapidly assessing biodiversity is essential for environmental monitoring; however, traditional approaches are limited in the scope needed for most ecological systems. Environmental DNA (eDNA) based assessment offers enhanced scope for assessing biodiversity, while also increasing sampling efficiency and reducing processing time, compared to traditional methods. Here we investigated the effects of landuse and seasonality on headwater community richness and functional diversity, via spatio-temporal dynamics, using both eDNA and traditional sampling. We found that eDNA provided greater resolution in assessing biodiversity dynamics in time and space, compared to traditional sampling. Community richness was seasonally linked, peaking in spring and summer, with temporal turnover having a greater effect on community composition compared to localized nestedness. Overall, our assessment of ecosystem function shows that community formation is driven by regional resource availability, implying regional management requirements should be considered. Our findings show that eDNA based ecological assessment is a powerful, rapid and effective assessment strategy that enables complex spatio-temporal studies of community diversity and ecosystem function, previously infeasible using traditional methods.

Over millennia, ecological and evolutionary mechanisms have shaped macroecological patterns across the tree of life. Research describing these patterns at both regional and global scales has traditionally focused on the study of metazoan species. Consequently, there is a limited understanding of cross-phylum biogeographic structuring and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, protists and bacteria along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life despite billions of years of evolution. Analyses investigating the drivers of these patterns for each taxonomic kingdom found that environmental conditions (such as temperature) and, to a lesser extent, anthropogenic stressors (such as fishing pressure and pollution) explained some of the observed variation. Additionally, metazoans displayed biogeographic patterns that suggested regional biotic homogenization. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of biodiversity patterns across broad taxonomic, ecological and geographical scales. Despite the fact that large animals and microorganisms face different environmental and anthropogenic pressures, this study finds that marine biogeographic patterns are similar for organisms in different kingdoms.

Aquatic species throughout the world are threatened by extinction in many parts of their range, particularly in their most southerly distributions. Arctic charr ( Salvelinus alpinus ) is a Holarctic species with a distribution that includes the glacial lakes of North Wales, towards it southern limit. To date, no genetic studies have been conducted to determine the genetic health of the three remaining native Arctic charr populations in North Wales, despite exposure to stocking and adverse environmental and ecological conditions. We used seven microsatellite loci to determine whether: 1) genetic differentiation existed between native populations; 2) translocated populations from Llyn Peris were genetically similar to the historically connected Llyn Padarn population; and 3) hatchery supplementation negatively impacted genetic diversity in Llyn Padarn. All three native populations retained their genetic integrity, with Llyn Bodlyn showing high levels of divergence (F ST = 0.26 ± 0.02SD) as well as low genetic diversity (H O 0.30) compared to remaining populations (H O 0.64 ± 0.14SD). Although evidence suggests that stocking increased the effective population size of Llyn Padarn in the short term without impacting genetic diversity, the long term effects of such practices are yet to be seen. Results provide baseline data for conservation management, and highlight the need for protection of small isolated populations that are being negatively impacted by the processes of genetic drift due to escalating anthropogenic pressures. Continual monitoring of both Arctic charr and their habitats using a combination of methods will increase the likelihood that these threatened and iconic populations will persist in the future.

Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such unintentionally altered traits may reduce fitness in the wild. Atlantic salmon breeding programmes were established in the early 1970s, resulting in genetic changes in multiple traits. However, the impact of domestication on eye size has not been studied. We measured body size corrected eye size in 4000 salmon from six common garden experiments conducted under artificial and natural conditions, in freshwater and saltwater environments, in two countries. Within these common gardens, offspring of domesticated and wild parents were crossed to produce 11 strains, with varying genetic backgrounds (wild, domesticated, F1 hybrids, F2 hybrids and backcrosses). Size-adjusted eye size was influenced by both genetic and environmental factors. Domesticated fish reared under artificial conditions had smaller adjusted eye size when compared to wild fish reared under identical conditions, in both the freshwater and marine environments, and in both Irish and Norwegian experiments. However, in parr that had been introduced into a river environment shortly after hatching and sampled at the end of their first summer, differences in adjusted eye size observed among genetic groups were of a reduced magnitude and were nonsignificant in 2-year-old sea migrating smolts sampled in the river immediately prior to sea entry. Collectively, our findings could suggest that where natural selection is present, individuals with reduced eye size are maladapted and consequently have reduced fitness, building on our understanding of the mechanisms that underlie a well-documented reduction in the fitness of the progeny of domesticated salmon, including hybrid progeny, in the wild.

Rapidly assessing biodiversity is essential for environmental monitoring, however traditional approaches are limited in the scope needed for most ecological systems. Environmental DNA (eDNA) based assessment offers increased scope, while reducing cost and time, compared to traditional methods. Here we investigated the effects of landuse and seasonality on headwater community richness and functional diversity, to assess spatio-temporal dynamics between eDNA and traditional methods. Environmental DNA provided greater biodiversity resolution with both methods resulting in complementary findings. Community richness was seasonally linked, peaking in spring and summer, with temporal turnover having a greater effect on community composition compared to localized nestedness. Our assessment of ecosystem function shows community formation is driven by regional resource availability, implying regional management requirements. Our findings show that eDNA based ecological assessment is a powerful, rapid and effective assessment strategy that enables complex spatio-temporal studies of community diversity and ecosystem function previously unavailable by traditional means.

Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.

Science-based management of marine fisheries and effective ecosystem monitoring both require the analysis of large amounts of often complex and difficult to collect information. Legislation also increasingly requires the attainment of good environmental status, which again demands collection of data to enable efficient monitoring and management of biodiversity. Such data is traditionally obtained as a result of research surveys through the capture and/or visual identification of organisms. Recent years have seen significant advances in the utilisation of environmental DNA (eDNA) in the marine environment in order to develop alternative cost-effective ways to gather relevant data. Such approaches attempt to identify and/or quantify the species present at a location through the detection of extra-organismal DNA in the environment. These new eDNA based approaches have the potential to revolutionise data collection in the marine environment using non-invasive sampling methods and providing snapshots of biodiversity beyond the capacity of traditional sampling. Here we present a non-technical summary of different approaches in the field of eDNA, and emphasise the broad application of this approach, with value for the governance and management of marine aquatic ecosystems. The review focuses on identifying those tools which are now readily applicable and those which show promise but are currently in development and require further validations. The aim is to provide an understanding of techniques and concepts that can be used by managers without genetic or genomic expertise when consulting with specialists to perform joint evaluations of the utility of the approaches.

estimated marginal means and confidence intervals from linear mixed effect model for the response variable width-height residuals (WHR) between the fixed factors sex and life stage.