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Abstract There are millions of river barriers worldwide, ranging from wooden locks to concrete dams, many of which form associated impoundments to store water in small ponds or large reservoirs. Besides their benefits, there is growing recognition of important environmental and social trade-offs related to these artificial structures. However, global datasets describing their characteristics and geographical distribution are often biased towards particular regions or specific applications, such as hydropower dams affecting fish migration, and are thus not globally consistent. Here, we present a new river barrier and reservoir database developed by the Global Dam Watch (GDW) consortium that integrates, harmonizes, and augments existing global datasets to support large-scale analyses. Data curation involved extensive quality control processes to create a single, globally consistent data repository of instream barriers and reservoirs that are co-registered to a digital river network. Version 1.0 of the GDW database contains 41,145 barrier locations and 35,295 associated reservoir polygons representing a cumulative storage capacity of 7,420 km3 and an artificial terrestrial surface water area of 304,600 km2.

Abstract Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.

Abstract Microalgae offer a sustainable source of omega − 3 fatty acids that can replace fish oil in aquafeeds, but the nutritional benefits are not always clear, particularly when microalgae are used as complete oil replacements in starter feeds. We compared the survival, growth, omega − 3 deposition and composition of the gut microbiota of juvenile mixed‐sex Nile tilapia (Oreochromis niloticus) that had been fed over a 3‐month period on six isonitrogenous, isolipidic and isocaloric aquafeeds that varied only on the contribution of fish oil, soya oil and microalgae (Schizochytrium) oil as lipid sources. Survival was not affected by diet, but fish fed a diet where the entire oil component (5%) was replaced by microalgae oil grew twice as fast as fish fed plant oil or a mixture of plant and fish oil. Dietary omega − 3 content was strongly correlated with omega − 3 deposition in the fish fillet. Complete replacement of fish oil by plant oil caused a significant decrease in the abundance of Peptostreptococcaceae and an increase in the abundance of Aeromonadaceae which is often associated with an inflammatory response in the fish gut. In contrast, when fish and soya oil in the reference diet were replaced by 100% microalgae oil, an increase in Mycobacteriaceae was observed. Our study indicates that Schizochytrium oil can be used to improve the growth of Nile tilapia and increase its omega − 3 content without any of the detrimental effects on the gut microbiome typically associated with some plant oil replacements.

Abstract European rivers are disconnected by more than one million man-made barriers that physically limit aquatic species migration and contribute to modification of freshwater habitats. Here, a Conceptual Habitat Alteration Model for Ponding is developed to aid in evaluating the effects of impoundments on fish habitats. Fish communities present in rivers with low human impact and their broad environmental settings enable classification of European rivers into 15 macrohabitat types. These classifications, together with the estimated fish sensitivity to alteration of their habitat are used for assessing the impacts of six main barrier types (dams, weirs, sluices, culverts, fords, and ramps). Our results indicate that over 200,000 km or 10% of previously free-flowing river habitat has been altered due to impoundments. Although they appear less frequently, dams, weirs and sluices cause much more habitat alteration than the other types. Their impact is regionally diverse, which is a function of barrier height, type and density, as well as biogeographical location. This work allows us to foresee what potential environmental gain or loss can be expected with planned barrier management actions in rivers, and to prioritize management actions.

Hybridization is a major source of evolutionary innovation. In plants, epigenetic mechanisms can help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the relationship between genetic background and methylation patterns in natural hybrids of two genetically divergent fish species with different mating systems, Kryptolebias hermaphroditus (self-fertilizing) and K. ocellatus (outcrossing). Co-existing parental species displayed highly distinct genetic (SNPs) and methylation patterns (37,000 differentially methylated cytosines). Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridization between genetically distant species. The large number of differentially methylated cytosines between hybrids and parental species (n = 5,800) suggests that hybridization may play a role in increasing genetic and epigenetic variation. Although most of the observed epigenetic variation was additive and had a strong genetic component, we also found a small percentage of non-additive, potentially stochastic, methylation differences that might act as an evolutionary bet-hedging strategy and increase fitness under environmental instability.

Fragmentation caused by artificial barriers is one of the main stressors of rivers worldwide. However, many barrier inventories only record large barriers, which underestimates barrier numbers, and hence fragmentation. Corrected barrier numbers can be obtained via river walkovers, but these are costly and time consuming. We assessed the performance of remote sensing as an alternative to river walkovers for barrier discovery by comparing the number and location of barriers detected in the field with those detected using Google Earth imagery. Only 56% of known barriers could be detected remotely, but machine learning models predicted the likelihood of remote detection with 62%–65% accuracy. Barriers located downstream were twice as likely to be detected remotely than those in the headwaters, the probability of detection diminishing by 3%–4% for every decrease in Strahler stream order and for every 10 km increase in distance from the river mouth. Barriers located in forested reaches were 35% less likely to be detected than those in open reaches. Observer skills also affected the ability to locate barriers remotely and detection rate varied by 11% between experienced and less experienced observers, suggesting that training might improve barrier detection. Our findings have implications for estimates of river fragmentation because they show that the most under-represented structures in barrier inventories, i.e. small barriers located in forested headwaters, are unlikely to be detected remotely. Although remote sensing cannot fully replace ‘boots on the ground’ field surveys for filling barrier data gaps, it can reduce the field work necessary to improve barrier inventories and help inform optimal strategies for barrier removal under data-poor scenarios.

Abstract Biological invasions are important causes of biodiversity loss, particularly in remote islands. Brown trout (Salmo trutta) have been widely introduced throughout the Southern Hemisphere, impacting endangered native fauna, particularly galaxiid fishes, through predation and competition. However, due to their importance for sport fishing and aquaculture farming, attempts to curtail the impacts of invasive salmonids have generally been met with limited support and the best prospects for protecting native galaxiids is to predict where and how salmonids might disperse. We analysed 266 invasive brown trout from 14 rivers and ponds across the Falkland Islands as well as 32 trout from three potential source populations, using a panel of 592 single nucleotide polymorphisms (SNPs) and acoustic tagging, to ascertain their origins and current patterns of dispersal. We identified four genetically distinct clusters with high levels of genetic diversity and low admixture, likely reflecting the different origins of the invasive brown trout populations. Our analysis suggests that many trout populations in the Falklands may have originated from one of the donor populations analysed (River Wey). The highest genetic diversity was observed in the rivers with the greatest number of introductions and diverse origins, while the lowest diversity corresponded to a location without documented introductions, likely colonized by natural dispersal. High levels of gene flow indicated widespread migration of brown trout across the Falkland Islands, likely aided by anadromous dispersal. This is supported by data from acoustically tagged fish, three of which were detected frequently moving between two rivers ~26 km apart. Our results suggest that, without containment measures, brown trout may invade the last remaining refuges for the native endangered Aplochiton spp. We provide new insights into the origin and dispersal of invasive brown trout in the Falkland Islands that can pave the way for a targeted approach to limit their impact on native fish fauna.

Abstract Brown trout are highly invasive in the Southern Hemisphere where they support important sport fisheries and aquaculture activities, which may impact endangered native galaxiid fishes and cause conflicts. To protect native galaxiids it is essential to monitor changes in species distributions, but this can be difficult when species are rare or difficult to sample. We developed and validated, both in the laboratory and in the field, a new assay using a high‐resolution melt curve (HRM)‐eDNA approach to simultaneously detect the presence of two threatened native galaxiids (Aplochiton zebra and Aplochiton taeniatus) and the invasive brown trout (Salmo trutta). Using this method, we found brown trout in 30% of the sampled waterbodies and Aplochiton sp. in 15% of them. Galaxiids were solely identified as being present in rivers that lacked brown trout, with both native species coexisting in two of the three rivers where they were detected, despite their different niche preferences. These assays can be used to monitor threatened zebra trout as well as invasive brown trout populations, allowing conservation managers to target areas for intervention.

Abstract Early life stages of aquatic organisms are particularly vulnerable to climatic stressors; however, they are difficult to monitor due to challenges in sampling and morphological identification. Environmental DNA (eDNA) from water samples represents an opportunity for rapid, nondestructive monitoring of aquatic community composition as well as single species monitoring. eDNA can also detect spawning events, although has not been yet tested in offshore spawning grounds. Here, we used metabarcoding of water samples to detect the presence of key fish taxa in spawning areas that are difficult to monitor using traditional means. We analyzed DNA from water samples and fish larvae samples at 14 offshore sites, using 12S mitochondrial metabarcoding and compared taxa detections, diversity, and community structure estimated by both sample types. Species richness and diversity did not differ between water and larvae samples. Both sample types detected a core of 12 taxa across the survey, with an average agreement in detections of 75% at sampling site level. Water samples detected two of the three most abundant taxa, the sandeel, Ammodytes marinus, and clupeids, Clupea harengus/Sprattus sprattus, at 31% and 38% more sites than larvae samples respectively, while Callionymus sp. was more prevalent in larvae samples. Mackerel (Scomber scombrus) and blue whiting (Micromestius poutassou) were only detected in water samples despite sampling taking place at peak spawning times for these species. Our results demonstrate that eDNA metabarcoding provides a rapid and feasible monitoring method for the management of key taxa, such as sandeel, that cannot be easily monitored using traditional capture surveys.

The impact of fish escaping from fish farms may depend on the extent to which escapees adapt to the natural environment, resemble wild conspecifics, and become feral. Yet, little is known about the process of feralization in marine fish. We examined phenotypic changes in body shape, body condition, and scale growth profiles of sea bass escaping from fish farms in the Canary Islands and quantified the extent to which escapees had diverged from farmed conspecifics. Most feral sea bass had sizes that overlapped with those of farmed fish, indicating that they had escaped throughout the production cycle. However, 29% of escapees were larger than the maximum size at harvesting, indicating growth in the wild. Analysis of scale growth profiles showed that some escapees had grown in the wild as fast as cultured fish, albeit at more variable growth rates. Feral sea bass tended to converge towards a similar body shape, having more streamlined bodies, lower body condition, and lower hepatosomatic indices (HSI) than fish in cages. Although our study cannot discriminate between phenotypic plasticity and differential mortality of escapees, we interpret phenotypic convergence as the likely result of a period of initial starvation, phenotypic plasticity, and selection against maladapted phenotypes. Our results warn against the risks of rearing sea bass in open-net cages and suggest that sea bass escapees could pose a threat to shallow coastal assemblages, particularly in areas where the species is not naturally found.

Epigenetic mechanisms generate plastic phenotypes that can become locally adapted across environments. Disentangling genomic from epigenomic variation is challenging in sexual species due to genetic variation among individuals, but it is easier in self-fertilizing species. We analysed DNA methylation patterns of two highly inbred strains of a naturally self-fertilizing fish reared in two contrasting environments to investigate the obligatory (genotype-dependent), facilitated (partially depend on the genotype) or pure (genotype-independent) nature of the epigenetic variation. We found higher methylation differentiation between genotypes than between environments. Most methylation differences between environments common to both strains followed a pattern where the two genotypes (inbred lines) responded to the same environmental context with contrasting DNA methylation levels (facilitated epialleles). Our findings suggest that, at least in part, DNA methylation could depend on the dynamic interaction between the genotype and the environment, which could explain the plasticity of epigenetically mediated phenotypes.

Abstract To meet future global demand for fish protein, more fish will need to be farmed using fewer resources, and this will require the selection of nonaggressive individuals that perform well at high densities. Yet, the genetic changes underlying loss of aggression and adaptation to crowding during aquaculture intensification are largely unknown. We examined the transcriptomic response to aggression and crowding in Nile tilapia, one of the oldest and most widespread farmed fish, whose social structure shifts from social hierarchies to shoaling with increasing density. A mirror test was used to quantify aggression and skin darkening (a proxy for stress) of fish reared at low and high densities, and gene expression in the hypothalamus was analysed among the most and least aggressive fish at each density. Fish reared at high density were darker, had larger brains, were less active and less aggressive than those reared at low density and had differentially expressed genes consistent with a reactive stress‐coping style and activation of the hypothalamus–pituitary–interrenal (HPI) axis. Differences in gene expression among aggressive fish were accounted for by density and the interaction between density and aggression levels, whereas for nonaggressive fish differences in gene expression were associated with individual variation in skin brightness and social stress. Thus, the response to crowding in Nile tilapia is context dependent and involves different neuroendocrine pathways, depending on social status. Knowledge of genes associated with the response to crowding may pave the way for more efficient fish domestication, based on the selection of nonaggressive individuals with increasing tolerance to chronic stress necessary for aquaculture intensification.

Abstract Parasite‐mediated selection is one of the main drivers of genetic variation in natural populations. The persistence of long‐term self‐fertilization, however, challenges the notion that low genetic variation and inbreeding compromise the host's ability to respond to pathogens. DNA methylation represents a potential mechanism for generating additional adaptive variation under low genetic diversity. We compared genetic diversity (microsatellites and AFLPs), variation in DNA methylation (MS‐AFLPs), and parasite loads in three populations of Kryptolebias hermaphroditus, a predomintanly self‐fertilizing fish, to analyze the potential adaptive value of DNA methylation in relation to genetic diversity and parasite loads. We found strong genetic population structuring, as well as differences in parasite loads and methylation levels among sampling sites and selfing lineages. Globally, the interaction between parasites and inbreeding with selfing lineages influenced DNA methylation, but parasites seemed more important in determining methylation levels at the local scale.

Abstract Aim Codium fragile, an invasive seaweed, has spread widely during the last century, impacting on local seaweed communities through competition and disturbance. Early detection of C. fragile can help on its control and management. Environmental DNA (eDNA) has proved successful for early detection of aquatic invasive species but its potential use for seaweed remains understudied. We used a species‐specific eDNA qPCR approach to investigate the spatial distribution, abundance, and coexistence of the invasive C. fragile and three native Codium species (Codium vermilara, Codium tomentosum, and Codium decorticatum) in the Cantabrian Sea. Location Bay of Biscay, Northern Atlantic Coast of the Iberian Peninsula; two ports, a beach and a rocky cliff. Methods We designed species‐specific primers in barcoding regions targeting short fragments of the rbcL gene for the invasive Codium species, and the elongation factor Tu (tufA) gene for the native species, to assess their spatial and seasonal distributions using quantitative real‐time PCR in samples collected during summer, autumn, and winter. Results We found seasonal differences in the presence of the invasive Codium fragile and two of the native Codium species, but did not detect C. decorticatum at any point. Species distribution patterns produced with qPCR targeting species‐specific eDNA coincided with the known distribution based on previous conventional sampling, with a seasonal alternance of C. fragile and C. vermilara, and a marked dominance of invasive C. fragile in ports, which are known hotspots for invasive species. Main conclusions Our results demonstrate the utility of using eDNA for early detection and monitoring of invasive seaweed. Native and invasive Codium spp. displayed significant seasonal and spatial differentiation that needs to be taken into account in risk management. Regular monitoring of ports and adjacent areas using eDNA should help to assess the potential expansion of invasive Codium and the need for management interventions to avoid the displacement of native seaweed.

Stress experienced during early life may have lasting effects on the immune system, with impacts on health and disease dependent on the nature and duration of the stressor. The epigenome is especially sensitive to environmental stimuli during early life and represents a potential mechanism through which stress may cause long-lasting health effects. However, the extent to which the epigenome responds differently to chronic vs acute stressors is unclear, especially for non-mammalian species. We examined the effects of acute stress (cold-shock during embryogenesis) and chronic stress (absence of tank enrichment during larval-stage) on global gene expression (using RNA-seq) and DNA methylation (using RRBS) in the gills of Atlantic salmon (Salmo salar) four months after hatching. Chronic stress induced pronounced transcriptional differences, while acute stress caused few lasting transcriptional effects. However, both acute and chronic stress caused lasting and contrasting changes in the methylome. Crucially, we found that acute stress enhanced transcriptional immune response to a pathogenic challenge (bacterial lipopolysaccharide, LPS), while chronic stress suppressed it. We identified stress-induced changes in promoter and gene-body methylation that were associated with altered expression for a small proportion of immune-related genes, and evidence of wider epigenetic regulation within signalling pathways involved in immune response. Our results suggest that stress can affect immuno-competence through epigenetic mechanisms, and highlight the markedly different effects of chronic larval and acute embryonic stress. This knowledge could be used to harness the stimulatory effects of acute stress on immunity, paving the way for improved stress and disease management through epigenetic conditioning.

Aquatic invasive species (AIS) are one of the principal threats to freshwater biodiversity. Exclusion barriers are increasingly being used as a management strategy to control the spread of AIS. However, exclusion barriers can also impact native organisms and their effectiveness is likely to be context dependent. We conducted a quantitative literature review to evaluate the use of barriers to control animal AIS in freshwater ecosystems worldwide. The quantitative aspect of the review was supplemented by case studies that describe some of the challenges, successes, and opportunities for the use of the use of AIS exclusion barriers globally. Barriers have been used since the 1950s to control the spread of AIS, but effort has been increasing since 2005 (80% of studies) and an increasingly diverse range of AIS taxa are now targeted in a wide range of habitat types. The global use of AIS barriers has been concentrated in North America (74% of studies), Australasia (11%), and Europe (10%). Physical barriers (e.g., weirs, exclusion screens, and velocity barriers) have been most widely used (47%), followed by electric (27%) and chemical barriers (12%). Fish were the most targeted taxa (86%), followed by crustaceans (10%), molluscs (3%) and amphibians (1%). Most studies have been moderately successful in limiting the passage of AIS, with 86% of the barriers tested deterring >70% of individuals. However, only 25% of studies evaluated barrier impacts on native species, and development of selective passage is still in its infancy. Most studies have been too short (47% < 1 year, 87% < 5 years) to detect ecological impacts or have failed to use robust before-after-control-impact (BACI) study designs (only 5%). Hence, more effective monitoring is required to assess the long-term effectiveness of exclusion barriers as an AIS management tool. Our global case studies highlight the pressing need for AIS control in many ecoregions, and exclusion barriers have the potential to become an effective tool in some situations. However, the design and operation of exclusion barriers must be refined to deliver selective passage of native fauna, and exclusion barriers should only be used sparingly as part of a wider integrated management strategy.

Artificial instream barriers are a major cause of habitat fragmentation that reduce population connectivity and gene flow by limiting fish movements. To mitigate their impacts, obsolete barriers are increasingly been removed worldwide, but few barrier removal projects are monitored. We employed a powerful Before-After-Downstream-Upstream (BADU) approach using environmental DNA (eDNA) metabarcoding to examine the effects on fish community composition of removing a weir in the river Lugg (England) that had been suggested to have a detrimental effect on salmonid migration. We found no change in fish community diversity or relative abundance after the removal above or below the weir, but detected an important effect of sampling season, likely related to the species' life cycles. eDNA detected nine fish species that were also identified by electrofishing sampling and one additional species (Anguilla anguilla) that was missed by traditional surveys. Our results suggest that monitoring of barrier removal projects should be carried out to ensure that any ecological benefits are properly documented and that eDNA metabarcoding is a sensitive technique to monitor the effects of barrier removal.

Exposure to environmental stressors can compromise fish health and fitness. Little is known about how stress-induced microbiome disruption may contribute to these adverse health effects, including how cortisol influences fish microbial communities. We exposed juvenile Atlantic salmon to a mild confinement stressor for two weeks. We then measured cortisol in the plasma, skin-mucus, and feces, and characterized the skin and fecal microbiome. Fecal and skin cortisol concentrations increased in fish exposed to confinement stress, and were positively correlated with plasma cortisol. Elevated fecal cortisol was associated with pronounced changes in the diversity and structure of the fecal microbiome. In particular, we identified a marked decline in the lactic acid bacteria Carnobacterium sp. and an increase in the abundance of operational taxonomic units within the classes Clostridia and Gammaproteobacteria. In contrast, cortisol concentrations in skin-mucus were lower than in the feces, and were not related to any detectable changes in the skin microbiome. Our results demonstrate that stressor-induced cortisol production is associated with disruption of the gut microbiome, which may, in turn, contribute to the adverse effects of stress on fish health. They also highlight the value of using non-invasive fecal samples to monitor stress, including simultaneous determination of cortisol and stress-responsive bacteria.

A wide trophic niche and high trophic plasticity are often invoked to explain the successful establishment of many aquatic invaders, but there is little information regarding the diet of most invasive fish in European waters. We combined stomach content and stable isotope analysis (SIA) of 13C and 15N to examine the trophic niche of the highly invasive topmouth gudgeon (Pseudorasbora parva) in three contrasting ponds and a reservoir in South Wales. Marked differences in diet and trophic position were found among neighboring systems only a few kilometers apart. The most diverse diet was found in ponds with the fewest number of inter-specific competitors, and resulted in topmouth gudgeon having the highest condition factor, the widest variation in δ13C and δ15N values, and the highest carbon content, typical of generalist feeders. In contrast, topmouth gudgeon that coexisted with other cyprinids, were much more likely to have an empty stomach and relied almost exclusively on plant seeds, resulting in fish having a poor condition factor and low trophic position. Comparisons with other trophic studies indicate that variation in isotope values among neighboring sites can exceed variation across continents, making it difficult to predict the diet or trophic impacts of the invasive topmouth gudgeon. Given the importance of obtaining reliable data on trophic position for risk assessment, our study shows that the use of SIA could be used to prioritize control and eradication measures that take into account trophic plasticity.

The control of the highly invasive zebra mussel (Dreissena polymorpha) has been flagged as a priority but success has been variable. A better understanding of the growth and drivers of settlement of zebra mussel is necessary for a more efficient management of this invasive species, but seasonal data are still relatively scant. We monitored the seasonal changes in settlement rates, density, and growth of zebra mussel in artificial substrates over 1 year in Cardiff Bay (United Kingdom), an artificial amenity lake invaded by zebra mussels in 2004, where the species is rapidly expanding. Mean settlement rates varied from 4,200 to 6,200 mussel m–2 over June to September mirroring changes in water temperature, and peaked at 17,960 mussels m–2, the highest density reported in Britain. Density was highest at the deepest panels (3 m). Growth varied significantly among sampling stations, taking place during the summer and ceasing during winter and spring. Mixture analysis reveals the existence of multiple cohorts displaying different growth and settlement rates that follow different density dependent mechanisms, being positive density-dependent at low densities, and negative density-dependent at high densities. We suggest this creates the conditions necessary for source and sink metapopulations to develop which may need to be considered in management. Targeting mussels for removal in deep waters during the summer and early autumn might prove beneficial, but the existence of contrasting density-dependent mechanisms suggests that removal may be beneficial or counterproductive depending on local conditions.

Abstract Background Captive animal populations, be it for food production or conservation programmes, are often maintained at densities far beyond those in natural environments, which can have profound effects on behaviour, immune and stress levels, and ultimately welfare. How such alterations impact transcriptional responses to pathogen infection is a ‘different kettle of fish’ and remains poorly understood. Here, we assessed survival and gene expression profiles of infected fish reared at two different densities to elucidate potential functional genomic mechanisms for density-related differences in disease susceptibility. Results Utilising a whole-transcriptome sequencing (RNAseq) approach, we demonstrate that rearing density in tilapia (Oreochromis niloticus) significantly impacts susceptibility to the oomycete Saprolegnia parasitica, via altered transcriptional infection responses. Tilapia held at low densities have increased expression of genes related to stress, likely due to increased aggressive interactions. When challenged with Saprolegnia, low-density fish exhibit altered expression of inflammatory gene responses and enhanced levels of adaptive immune gene suppression compared to fish reared at higher density, resulting in significantly increased mortality rates. In addition, Saprolegnia infection substantially perturbs expression of circadian clock genes, with fish reared at low-density having higher levels of molecular clock dysregulation. Conclusions Our results reveal the wide-scale impact of stocking density on transcriptional responses to infection and highlight the need to incorporate circadian biology into our understanding of disease dynamics in managed animals.

Invasion facilitation, whereby one species has a positive effect on the establishment of another species, could help explain the rapid colonisation shown by some freshwater invasive species, but the underlying mechanisms remain unclear. We employed two-choice test arenas to test whether the presence of zebra mussel (Dreissena polymorpha) could facilitate the establishment of the killer shrimp (Dikerogammarus villosus). Killer shrimp preferred to settle on mats of zebra mussel, but this was unrelated to mat size, and was not different from attraction shown to artificial grass, suggesting that zebra mussel primarily provides substrate and refuge to the killer shrimp. Killer shrimp were strongly attracted to water scented by zebra mussel, but not to water scented by fish. Chemical attraction to the zebra mussel’s scent did not differ between sympatric and allopatric populations of killer shrimp, suggesting that chemical attraction is not an acquired or learned trait. Our study shows, for the first time, chemical attraction between two highly invasive freshwater species, thereby providing a plausible mechanism for invasion facilitation. This has implications for managing the spread of killer shrimp, and perhaps other freshwater invasive species, because chemical attraction could significantly increase establishment success in mutualistic systems. Failure to consider invasion facilitation may underestimate the risk of establishment, and likely also the impact of some aquatic invaders.

Many animal species rely on changes in body coloration to signal social dominance, mating readiness and health status to conspecifics, which can in turn influence reproductive success, social dynamics and pathogen avoidance in natural populations. Such colour changes are thought to be controlled by genetic and environmental conditions, but their relative importance is difficult to measure in natural populations, where individual genetic variability complicates data interpretation. Here, we studied shifts in melanin-related body coloration in response to social context and parasitic infection in two naturally inbred lines of a self-fertilizing fish to disentangle the relative roles of genetic background and individual variation. We found that social context and parasitic infection had a significant effect on body coloration that varied between genetic lines, suggesting the existence of genotype by environment interactions. In addition, individual variation was also important for some of the colour attributes. We suggest that the genetic background drives colour plasticity and that this can maintain phenotypic variation in inbred lines, an adaptive mechanism that may be particularly important when genetic diversity is low.

Freshwater ecosystems rank among the most endangered ecosystems in the world and are under increasing threat from aquatic invasive species (AIS). Understanding the range expansion of AIS is key for mitigating their impacts. Most approaches rely on Species Distribution Models (SDMs) to predict the expansion of AIS, using mainly environmental variables, yet ignore the role of human activities in favouring the introduction and range expansion of AIS. In this study, we use five SDM algorithms (independently and in ensemble) and two accuracy measures (TSS, AUC), combined with a null modelling approach, to assess the predictive performance of the models and to quantify which predictors (environmental and anthropogenic from the native and introduced regions) best explain the distribution of nine freshwater invasive species (including fish, arthropods, molluscs, amphibians and reptiles) in a large island (Great Britain), and which species characteristics affect model performance. Our results show that the distribution of invasive species is difficult to predict by SDMs, even in cases when TSS and AUC model accuracy values are high. Our study strongly advocates the use of null models for testing SDMs performance and the inclusion of information from the native area and a variety of both human-related and environmental predictors for a more accurate modelling of the range expansion of AIS. Otherwise, models that only include climatic variables, or rely only on standard accuracy measures or a single algorithm, might result in mismanagement of AIS.

Environmental DNA is increasingly being used for assessing the presence and relative abundance of fish in freshwater, but existing protocols typically rely on filtering large volumes of water which is not always practical. We compared the effects of water volume, filtration type and eDNA extraction procedures in the detection of fish in three freshwater bodies (pond, lake and river) using a short fragment of the 12s rRNA mtDNA gene. Quantification of eDNA capture efficiency after DNA extraction, as well as amplification efficiency, were evaluated by conventional PCR and quantitative PCR. No significant differences on eDNA capture yield were found among freshwater bodies, but increasing water volume had a positive effect on eDNA capture and amplification efficiency. Although highest eDNA capture rates were obtained using 2 L of filtered water, 100 mL syringe filtration in combination with ethanol- sodium acetate precipitation proved to be more practical and increased quantitative PCR amplification efficiency by 6.4%. Our results indicate that such method may be optimal to detect fish species effectively across both lotic and lentic freshwater environments.

Demand for lumpfish (Cyclopterus lumpus) has increased exponentially over the last decade, both for their roe, which is used as a caviar substitute, and increasingly also as cleaner fish to control sea lice in salmon farming. The species is classified as Near Threatened by the IUCN and there are growing concerns that over-exploitation of wild stocks and translocation of hatchery-reared lumpfish may compromise the genetic diversity of native populations. We carried out a comparative analysis of genetic and phenotypic variation across the species’ range to estimate the level of genetic and phenotypic differentiation, and determined patterns of gene flow at spatial scales relevant to management. We found five genetically distinct groups located in the West Atlantic (USA and Canada), Mid Atlantic (Iceland), East Atlantic (Faroe Islands, Ireland, Scotland, Norway and Denmark), English Channel (England) and Baltic Sea (Sweden). Significant phenotypic differences were also found, with Baltic lumpfish growing more slowly, attaining a higher condition factor and maturing at a smaller size than North Atlantic lumpfish. Estimates of effective population size were consistently low across the North East Atlantic (Iceland, Faroe Islands and Norway), the area where most wild lumpfish are fished for their roe, and also for the aquaculture industry. Our study suggests that some lumpfish populations are very small and have low genetic diversity, which makes them particularly vulnerable to over-exploitation and genetic introgression. To protect them we advocate curtailing fishing effort, closing the breeding cycle of the species in captivity to reduce dependence on wild stocks, restricting the translocation of genetically distinct populations, and limiting the risk of farm escapes.

Knowledge of length-weight relationships for commercially exploited fish is an important tool for assessing and managing of fish stocks. However, analyses of length-weight relationship fisheries data typically do not consider the inherent differences in length-weight relationships for fish caught from different habitats, seasons, or years, and this can affect the utility of these data for developing condition indices or calculating fisheries biomass. Here, we investigated length-weight relationships for ribbonfish Trichiurus lepturus in the waters of the Arabian Sea off Oman collected during three periods (2001-02, 2007-08, and 2014-15) and showed that a multivariate modelling approach that considers the areas and seasons in which ribbonfish were caught improved estimation of length-weight relationships. We used the outputs of these models to explore spatio-temporal variations in condition indices and relative weights among ribbonfish, revealing fish of 85-125 cm were in the best overall condition. We also found that condition differed according to where and when fish were caught, with condition lowest during spring and pre-south-west monsoon periods and highest during and after the south-west monsoons. We interpret these differences to be a consequence of variability in temperature and food availability. Based on our findings, we suggest fishing during seasons that have the lowest impact on fish condition and which are commercially most viable; such fishery management would enhance fisheries conservation and economic revenue in the region.

A comparison of Upper Palaeolithic and contemporary salmonid vertebrae from the Iberian Peninsula indicates that there has been a significant decrease in the mean body size for a given age among Atlantic salmon and brown trout inhabiting the southernmost range of their endemic distribution. Mean size at age was greater in prehistoric specimens for all age classes during the freshwater phase of their life histories. Fisheries-induced evolution (selection for smaller sizes) is an obvious explanation for the observed reduction in fish body size, but recent changes in the aquatic habitat affecting density-dependent growth cannot be ruled out.

Fish growth is commonly used as a proxy for fitness but this is only valid if individual growth variation can be interpreted in relation to conspecifics' performance. Unfortunately, assessing individual variation in growth rates is problematic under natural conditions because subjects typically need to be marked, repeated measurements of body size are difficult to obtain in the field, and recaptures may be limited to a few time events which will generally vary among individuals. The analysis of consecutive growth rings (circuli) found on scales and other hard structures offers an alternative to mark and recapture for examining individual growth variation in fish and other aquatic vertebrates where growth rings can be visualized, but accounting for autocorrelations and seasonal growth stanzas has proved challenging. Here we show how mixed-effects modelling of scale growth increments (inter-circuli spacing) can be used to reconstruct the growth trajectories of sea trout (Salmo trutta) and correctly classify 89% of individuals into early or late seaward migrants (smolts). Early migrants grew faster than late migrants during their first year of life in freshwater in two natural populations, suggesting that migration into the sea was triggered by ontogenetic (intrinsic) drivers, rather than by competition with conspecifics. Our study highlights the profound effects that early growth can have on age at migration of a paradigmatic fish migrant and illustrates how the analysis of inter-circuli spacing can be used to reconstruct the detailed growth of individuals when these cannot be marked or are only caught once.

Early juvenile growth is a good indicator of growth later in life in many species because larger than average juveniles tend to have a competitive advantage. However, for migratory species the relationship between juvenile and adult growth remains obscure. We used scale analysis to reconstruct growth trajectories of migratory sea trout (Salmo trutta) from six neighbouring populations, and compared the size individuals attained in freshwater (before migration) with their subsequent growth at sea (after migration). We also calculated the coefficient of variation (CV) to examine how much body size varied across populations and life stages. Specifically, we tested the hypothesis that the CV on body size would differ between freshwater and marine environment, perhaps reflecting different trade-offs during ontogeny. Neighbouring sea trout populations differed significantly in time spent at sea and in age-adjusted size of returning adults, but not on size of seaward migration, which was surprisingly uniform and may be indicative of strong selection pressures. The CV on body size decreased significantly over time and was highest during the first 8 months of life (when juvenile mortality is highest) and lowest during the marine phase. Size attained in freshwater was negatively related to growth during the first marine growing season, suggesting the existence of compensatory growth, whereby individuals that grow poorly in freshwater are able to catch up later at sea. Analysis of 61 datasets indicates that negative or no associations between pre- and post-migratory growth are common amongst migratory salmonids. We suggest that despite a widespread selective advantage of large body size in freshwater, freshwater growth is a poor predictor of final body size amongst migratory fish because selection may favour growth heterochrony during transitions to a novel environment, and marine compensatory growth may negate any initial size advantage acquired in freshwater.

The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty.