Accurate detection of hybridization and introgression is critical for both evolutionary research and applied conservation. In many systems, however, hybrid ancestry is difficult to detect beyond the F1 generation, especially when based on limited genetic markers. In European waters, hybridization between the native Homarus gammarus and the invasive H. americanus poses a direct risk to the integrity of native stocks and effective fishery management, yet detection methods are often limited to morphological traits or first-generation hybrids. A set of 79 SNPs previously developed to distinguish species between American and European lobsters and F1 individuals has shown promise, but its capacity to resolve later-generation backcrosses remains untested. Here, we present a resampling-based evaluation of this panels performance under realistic introgression scenarios, using individual-based population genetic models informed by empirical data. We show that the panel retains discriminatory power across multiple hybrid classes, with diminishing accuracy in second-generation backcrosses. These findings validate the panels utility for applied monitoring and highlight the broader potential of resumpling-anchored frameworks to benchmark hybrid detection tools in a wide range of species.

Wrasse species are widely used as cleaner fish in salmon aquaculture but their performance as cleaner fish may be impacted by thermal and ontogenetic changes. Understanding the conditions in which each species of wrasse is most productive as cleaner fish is hugely valuable to make informed decisions on the management of fisheries. To do this, we use a novel geochemical proxy to reconstruct ontogenetic trends in thermal habitat and field metabolic rate for six species of wrasse from two sampling locations from the Isle of Skye (Scotland) and Dorset (southern England). We describe consistent ontogenetic transitions from warmer to cooler thermal habitats across all species, and demonstrate reductions in activity levels associated with ontogenetic habitat shifts after accounting for body size and temperature effects. Field metabolic rates were not significantly different between Dorset and Skye after accounting for body size and temperature. Ontogenetic shifts in thermal habitat and activity level have implications for the effectiveness of wrasse as cleanerfish, as well as providing evidence to support size-based harvesting rules. More broadly, this work highlights the potential of otolith isotope analyses to recover field-based, context-specific data on physiology and thermal ecology, advancing fisheries conservation and management strategies.

Brown trout (Salmo trutta L.) exhibit a variety of life-history strategies. The two physiological and phenotypic extremes are represented by freshwater residents that remain in freshwater for their entire life and anadromous sea trout that migrate to sea to grow. The cue to initiate anadromy appears to be a combination of environmental factors, genetics, and non-genetic parental effects. We currently lack a systematic understanding of the interplay between these two life-history strategies, in particular their relative importance in the recruitment of populations displaying facultative migration. We assessed the importance of anadromous females in the recruitment of S. trutta at sampling locations 16-44 river km upstream of the tidal limit in a productive chalk stream using a combination of tissue stable isotope ratios and SNP genotyping of newly emerged fry, with a primary goal of understanding the migratory strategy of their mother and hence the relative contribution of the two strategies to recruitment. A secondary goal was to test a new method of assessing maternal strategy using the delta 13C of the core of the eye lens. By combining information from muscle tissue and eye lens core stable isotope ratios, and SNP genotyping, we were able to allocate 97.5% of fry to either anadromous or freshwater-resident mothers. In most cases, the delta 13C of the core of the eye lens appeared to provide greater discrimination among maternal strategies than muscle tissue. Given the inert nature of this archival structure, lens core chemistry represents a promising approach to assess maternal strategy in any aged fish. Anadromous females contributed disproportionately to recruitment throughout the catchment, where the proportion of fry with anadromous mothers followed a non-linear decline with increasing distance from the tidal limit. Close to the tidal limit (16 river km upstream) 100% of fry had anadromous mothers, declining to 43% at the site furthest from the tidal limit (44 river km upstream). As well as a disproportionate contribution of anadromous fish to young-of-the-year, the number of full-sibling family groups involving anadromous mothers was higher than for freshwater resident mothers at all sites. Anadromous S. trutta mothers contribute disproportionately to recruitment even in the headwaters of a productive chalk stream. Whilst we do not know how the contribution of anadromous mothers influences the balance of the two life history strategies, recruitment appears highly dependent on unobstructed migration pathways to and from the marine environment.

As coral populations decline under climate change and other stressors, surviving corals will become increasingly isolated. While Allee effects that reduce gamete encounters and fertilisation success may lead to reproductive and recruitment failure, the critical population densities and distances between individuals required to maintain viable populations remains uncertain. Here, we investigate the links between colony isolation and fertilisation patterns using an experimentally manipulated patch of the broadcast spawning tabular coral, Acropora hyacinthus. Corals were arranged in a clustered radial design, with colonies arranged at increasing distances radiating downstream from a central spawning aggregation. Fertilisation and paternity assignment analyses were used to examine the influence of parental distance, current alignment, colony size, and genetic relatedness. Fertilisation success declined sharply with increasing distance among corals, and paternity assignments indicated most parents were located within 3 m of each other, underscoring the importance of colony proximity. Additionally, fertilisation success was highest for colonies positioned downstream of the central cluster, and 84% of sequenced progeny were sired by colonies located directly upstream. Simulations of natural reef spatial population distributions projected onto a virtual grid, incorporating empirically derived parentage distances, indicated that populations remained well-mixed at typical adult densities in nearby reefs. However, as densities decreased to 1 colony per 100 m-2 (i.e. 0.01 colonieslllm-2), reproductive isolation and the formation of patchy breeding units became prevalent. Overall, our findings highlight that the spatial arrangement and isolation of corals on reefs, and subsequent Allee effects on fertilisation, can jeopardise the reproductive success of broadcast spawning corals. Conservation efforts are needed to help maintain viable coral populations and successful reproductive aggregations for degraded reef systems. ### Competing Interest Statement The authors have declared no competing interest.

Anadromous salmonids migrate seaward to exploit feeding and growth opportunities in marine habitats, yet how smolt biological characteristics influence their marine migratory behavior remains poorly understood. This study used 9 years of trout (Salmo trutta) population monitoring data from 15,595 tagged age-0+ parr, 1033 smolts detected migrating downstream in spring, and 99 adults detected returning from their first marine migration to the River Frome (Dorset, UK) to investigate the influence of smolt biological characteristics on their migration timing and maiden marine sojourn duration. Age-specific differences in the influence of smolt length on migration timing were found, with longer 1-year-old smolts emigrating later than their shorter counterparts within the same age class, but the opposite association existed for 2-year-old smolts. A bespoke integrated statistical model quantified the effects of smolt emigration day of year, age, sex, and length on the probability of first-time migrants returning to the river after one or more sea winters. Younger, later migrating smolts had a longer marine sojourn duration than their older, earlier migrating counterparts, and females remained at sea for longer periods than males. Although the statistical model was designed to maximize the use of information available in the data, it revealed only weak effects of smolt biological characteristics on the maiden marine sojourn duration. A complementary simulation study suggested that detecting more spring migrating smolts and analyzing longer time series of trout population monitoring data would increase the ability to detect statistically significant effects. Therefore, a strategic review of the trout population monitoring program, including more long-term biological data collection, is recommended. The modelling work presented here can provide guidance on the size of the required dataset and how to maximize the power of imperfect data.

Aim The British Isles have been worked for millennia to extract metal ores to feed industrial development, leaving a legacy of mine water pollution that continues to impact freshwater communities in many regions. Brown trout (Salmo trutta L.) have long been observed to persist in these metal-impacted systems as apex predators, with previous studies showing a small number of impacted populations to be highly genetically divergent. We sought to understand the scale of genetic diversity across regions and the repeatability of genetic divergence in trout populations affected by metal pollution. Location We examined four mine water-impacted regions across the British Isles: west Wales, northeast England, southwest England and southeast Ireland. Methods We employed a panel of 95 SNP loci to screen 1236 individuals from 71 sites representing paired metal-impacted and clean sites from across the four regions. From these, we obtained diversity statistics, assessed genetic structuring of populations and modelled historical demographic scenarios to understand which factors most credibly explain genetic variation in divergent populations. Results We evidenced hierarchical population structure in the regions studied, in line with expectations from phylogeographic history. However, in a hierarchical analysis of genetic structuring the first level of differentiation was driven by the divergence of the metal-impacted trout of Cornwall in southwest England. Within regions we observed reduced genetic diversity and repeated patterns of local genetic sub-structuring between paired samples from metal-impacted and relatively clean sites. Demographic history analyses suggested the timing of these splits to be relatively recent and to be associated with periods of peak mining activity. Main conclusions Our findings demonstrate distinct patterns of genetic isolation and reduced diversity arising from legacy pollution in freshwater ecosystems, with impacts being most apparent where both chemical pollution and physical barriers are present. Management should focus on the amelioration of mine water wash-out and the removal of barriers to fish movement to safeguard genetic diversity in impacted populations.

Understanding gene flow can help biodiversity to mitigate habitat changes by contributing to inform and design protected areas. The brown trout, Salmo trutta, displays a multitude of life-history strategies and represents an ideal model for applications in conservation genetics. Using a panel of 185-single nucleotide polymorphism markers, the present study aimed to explore the population structure of the brown trout and in the English Channel. The genotypes of 2,729 individual trout from 88 rivers were obtained across England and France. Population structure revealed the presence of genetic clusters following an east/west gradient. The maximum threshold distance between genetic distance and geographic distance was 344 km. The measure appeared relative to the studied spatial environment and reflected Salmo trutta capacity to achieve long migration distances. A machine-learning framework derived from a gradient forest analysis was used to generate a resistance surface using changes in allelic frequencies and environmental predicators. The resulting surface identified areas limiting gene flow. On the British coast, a genetic break was observed along the Jurassic coast, whereas the Cotentin peninsula acted as a physical barrier among French coastal populations. Salmo trutta populations appeared to be differently affected by environmental factors reflecting demes preference to specific breeding ground. Using our resistance map, the distance of maximum correlation using cost distance were computed allowing the pruning of our genetic graph. The resulting least cost path connections were mapped to reveal the main dispersal routes. Finally, a prioritization analysis using connectivity surface was implemented to design potential protected areas.

Identifying isolated populations is a key step towards enacting effective conservation management. European lobsters (Homarus gammarus) from Oosterschelde in the Netherlands are subject to fishery pressure and have previously been reported as genetically differentiated. They are also putatively of transplanted origin and have subsequently endured recent bottlenecking and environmental change. We assessed Oosterschelde lobsters to evaluate their demographic independence and appraise potential founder effects and evolutionary responses to isolation. Using restriction-site associated DNA sequencing, we genotyped 6185 single nucleotide polymorphisms across 188 individuals from 27 sites across the Atlantic range of H. gammarus to investigate population genetic diversity, structure, and potential adaptation. Our results show that Oosterschelde lobsters are genetically divergent from other stocks. We evidence extensive differentiation via both neutral and outlier loci, indicative of strong biophysical and demographic isolation, and detect signatures of reduced genetic diversity that may reflect weak founder effects or subsequent population contractions. Among outlier loci, we identify candidates for range-wide local adaptation via variants in genes of important biological functionality and link a private allele of Oosterschelde to a locus potentially conveying adaptive tolerance to environmental hypoxia. Given our findings, we advise proactive monitoring of Oosterschelde lobsters to explore whether existing management measures effectively conserve this discrete, self-recruiting population.

The Norway lobster (Nephrops norvegicus) is one of the most important decapod crustacean seafood species in the Adriatic Sea. Previous research has identified significant differences in growth rates and maturation timing of Nephrops in the Pomo/Jabuka Pits area compared to other subpopulations in Adriatic fishing grounds. Here, we use 1,623 genome-wide single nucleotide polymorphisms (SNPs) to investigate whether the Pomo Pits subpopulation is genetically different from other sites in the Adriatic and neighbouring seas. We found no genetic differentiation among all sampled Adriatic sites, suggesting high gene flow between Pomo Pits Nephrops and those of surrounding areas. We also found genetic homogeneity between the Adriatic sites and single-site samples from the Aegean and Tyrrhenian Seas. However, we detected distinct genetic differentiation between all Mediterranean sites and an Atlantic site in western Scotland, which provides evidence for a phylogenetic break between the Atlantic and the Mediterranean. Our results indicate that Pomo Pits Nephrops are not genetically different from others sampled in the Adriatic and that key biological parameters in Pomo Pits Nephrops could be driven by spatial variation in fishing pressure and/or environmental factors rather than geographic isolation.

Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species' marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed high-confidence assignment of known-origin individuals to region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long-distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.

Within the UK, allis shad (Alosa alosa) are classified as Critically Endangered and are known to breed in only a single river, the Tamar. Despite evidence of spawning within the lower freshwater reaches of the river and at the tidal limit within the estuary, juvenile allis shad have never been found. Genetic analysis, based on mitochondrial DNA haplotype and nuclear Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) data, confirmed that juvenile shad found within the lower Tamar estuary in autumn 2022 were A. alosa.

Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.

AbstractCharacterizing patterns of genetic connectivity in marine species is of critical importance given the anthropogenic pressures placed on the marine environment. For sessile species, population connectivity can be shaped by many processes, such as pelagic larval duration, oceanographic boundaries and currents. This study combines restriction‐site associated DNA sequencing (RADseq) and passive particle dispersal modelling to delineate patterns of population connectivity in the pink sea fan, Eunicella verrucosa, a temperate octocoral. Individuals were sampled from 20 sites covering most of the species' northeast Atlantic range, and a site in the northwest Mediterranean Sea to inform on connectivity across the Atlantic‐Mediterranean transition. Using 7510 neutral SNPs, a geographic cline of genetic clusters was detected, partitioning into Ireland, Britain, France, Spain (Atlantic), and Portugal and Spain (Mediterranean). Evidence of significant inbreeding was detected at all sites, a finding not detected in a previous study of this species based on microsatellite loci. Genetic connectivity was characterized by an isolation by distance pattern (IBD) (r2 = 0.78, p < 0.001), which persisted across the Mediterranean‐Atlantic boundary. In contrast, exploration of ancestral population assignment using the program ADMIXTURE indicated genetic partitioning across the Bay of Biscay, which we suggest represents a natural break in the species' range, possibly linked to a lack of suitable habitat. As the pelagic larval duration (PLD) is unknown, passive particle dispersal simulations were run for 14 and 21 days. For both modelled PLDs, inter‐annual variations in particle trajectories suggested that in a long‐lived, sessile species, range‐wide IBD is driven by rare, longer dispersal events that act to maintain gene flow. These results suggest that oceanographic patterns may facilitate range‐wide stepping‐stone genetic connectivity in E. verrucosa and highlight that both oceanography and natural breaks in a species' range should be considered in the designation of ecologically coherent MPA networks.

Effective management of Atlantic salmon requires a suite of metrics that are fed into stock assessment models to assess stock compliance within individual rivers in relation to estimated conservation limits. Key among metrics required to assess compliance are the number of adult female spawners within each adult sea age class and their corresponding egg deposition rates. Owing to the current need to conserve salmon stocks, adult sex ratios used to calculate egg deposition estimates often depend on data derived from historic lethal sampling. Using non-invasive sampling and an accurate genetic sex test, we determined the proportion of female fish in two adult life history stages (one sea winter and two sea winter) of Atlantic salmon from the River Tamar, an Environment Agency (England) Monitored River. Our results suggested that phenotypic-based sexing of Tamar salmon was unreliable, especially for early run fish and that the proportion of female salmon has been under-estimated, thereby leading to consistent under-estimation of egg deposition rates.

This study provides a regional picture of long-term changes in Atlantic salmon growth at the southern edge of their distribution, using a multi-population approach spanning 49 years and five populations. We provide empirical evidence of salmon life history being influenced by a combination of common signals in the marine environment and population-specific signals. We identified an abrupt decline in growth from 1976 and a more recent decline after 2005. As these declines have also been recorded in northern European populations, our study significantly expands a pattern of declining marine growth to include southern European populations, thereby revealing a large-scale synchrony in marine growth patterns for almost five decades. Growth increments during their sea sojourn were characterized by distinct temporal dynamics. At a coarse temporal resolution, growth during the first winter at sea seemed to gradually improve over the study period. However, the analysis of finer seasonal growth patterns revealed ecological bottlenecks of salmon life histories at sea in time and space. Our study reinforces existing evidence of an impact of early marine growth on maturation decision, with small-sized individuals at the end of the first summer at sea being more likely to delay maturation. However, each population was characterized by a specific probabilistic maturation reaction norm, and a local component of growth at sea in which some populations have better growth in some years might further amplify differences in maturation rate. Differences between populations were smaller than those between sexes, suggesting that the sex-specific growth threshold for maturation is a well-conserved evolutionary phenomenon in salmon. Finally, our results illustrate that although most of the gain in length occurs during the first summer at sea, the temporal variability in body length at return is buffered against the decrease in post-smolt growth conditions. The intricate combination of growth over successive seasons, and its interplay with the maturation decision, could be regulating body length by maintaining diversity in early growth trajectories, life histories, and the composition of salmon populations.

Cold-water corals form an important part of temperate benthic ecosystems by increasing three-dimensionality and providing an important ecological substrate for other benthic fauna. However, the fragile three-dimensional structure and life-history characteristics of cold-water corals can leave populations vulnerable to anthropogenic disturbance. Meanwhile, the ability of temperate octocorals, particularly shallow-water species, to respond to adjustments in their environment linked to climate change has not been studied. This study reports the first genome assembly of the pink sea fan (Eunicella verrucosa), a temperate shallow-water octocoral species. We produced an assembly of 467 Mb, comprising 4,277 contigs and an N50 of 250,417 bp. In total, 213 Mb (45.96% of the genome) comprised repetitive sequences. Annotation of the genome using RNA-seq data derived from polyp tissue and gorgonin skeleton resulted in 36,099 protein-coding genes after 90% similarity clustering, capturing 92.2% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) ortholog benchmark genes. Functional annotation of the proteome using orthology inference identified 25,419 annotated genes. This genome adds to the very few genomic resources currently available in the octocoral community and represents a key step in allowing scientists to investigate the genomic and transcriptomic responses of octocorals to climate change.

Aim: Comparing genetic structure in species with shared spatial ranges and ecological niches can help identify how dissimilar aspects of biology can shape differences in population connectivity. Similarly, where species are widely distributed across heterogeneous environments and major topographic barriers, knowledge of the structuring of populations can help reveal the impacts of factors which limit dispersal and/or drive divergence, aiding conservation management.Location: European seas of the northeast Atlantic and Mediterranean.Taxa: European clawed lobster (Homarus gammarus) and European crawfish (Palinurus elephas), two sympatric, heavily fished decapods with extensive dispersal potential.Methods: By RAD-sequencing 214 H. gammarus from 32 locations and 349 P. elephas from 15 locations, we isolated 6340 and 7681 SNP loci, respectively. Using these data to characterise contemporary population structuring, we investigate potential spatial and environmental drivers of genomic heterogeneity.Results: We found higher levels of differentiation among clawed lobsters than crawfish, both globally and within basins, and demonstrate where known hydrographic and topographic barriers generate shared patterns of divergence, such as a genetic break between the Atlantic and Mediterranean basins. Genetic structure not common to both species is principally apparent in the Atlantic portions of their range, where clawed lobster exhibits a genetic cline and increased differentiation towards range margins, while crawfish appear effectively panmictic throughout this region.Main Conclusions: We attribute the comparative lack of crawfish population structuring to their greater dispersal tendencies via a longer pelagic larval duration and sporadic adult movements. In contrast, genetic connectivity in clawed lobster is relatively restricted, with the correlation of site of origin and temperature to geographical heterogeneity at many divergent loci indicative of both neutral and adaptive processes. Our results help inform how contemporary management can account for likely demographic connectivity and marry the conservation of genomic variation with sustainable fisheries in these ecologically and economically important crustaceans.

A juvenile American lobster, Homarus americanus, H. Milne Edwards, 1837, was recorded for the first time in European waters in August 2019, with the capture of a single early benthic phase specimen during surveys along the North East England coast. Identification was determined by a combination of morphological and molecular approaches. The record raises serious questions of whether the species is now breeding in the region, with associated implications for its invasiveness. The mechanisms of introduction, invasion status, risks to native shellfisheries, and directions of future study are discussed.

Species distribution models have become a valuable tool to predict the distribution of species across geographic space and time. In this study, maximum entropy models were constructed for two temperate shallow-water octocoral species, the pink sea fan (Eunicella verrucosa) and dead man’s fingers (Alcyonium digitatum), to investigate and compare habitat suitability. The study area covered the north-east Atlantic from the Bay of Biscay to the British Isles and southern Norway; this area includes both the northern range of E. verrucosa and the middle-northern range of A. digitatum. The optimal models for each species showed that, overall, slope, temperature at the seafloor and wave orbital velocity were important predictors of distribution in both species. Predictions of habitat suitability showed areas of present-day (1951–2000) suitable habitat where colonies have not yet been observed, particularly for E. verrucosa, where areas beyond its known northern range limit were identified. Moreover, analysis with future layers (2081–2100) of temperature and oxygen concentration predicted a sizable increase in habitat suitability for E. verrucosa beyond these current range limits under the Representative Concentration Pathway 8.5 scenario. This suggests that projected climate change may induce a potential range expansion northward for E. verrucosa, although successful colonisation would also be conditional on other factors such as dispersal and interspecific competition. For A. digitatum, this scenario of projected climate change may result in more suitable habitat in higher latitudes, but, as with E. verrucosa, there is a degree of uncertainty in the model predictions. Importantly, the results from this study highlight present-day areas of high habitat suitability which, if combined with knowledge on population density, could be used to identify priority areas to enhance protection and ensure the long-term survival of these octocoral species in the region.

The rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e., southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.