Biology subjects

Consuegra, S.

Publications and source records attributed to Consuegra, S..

At least 19 recordsLinked to original sources

bioRxiv2021

Conservation of endangered galaxiid fishes in the Falkland Islands requires urgent action on invasive brown trout

Non-native salmonids are protected in the Southern hemisphere where they sustain aquaculture and valuable sport fisheries, but also impact on native galaxiid fishes, which poses a conservation conundrum. Legal protection and human-assisted secondary releases may have helped salmonids to spread, but this has seldom been tested. We reconstructed the introduction of brown trout (Salmo trutta) to the Falkland Islands using historical records and modelled its dispersal. Our results indicate that establishment success was [~]88%, and that dispersal was facilitated by proximity to introduction sites and density of stream-road crossings, suggesting it was human assisted. Brown trout has already invaded 54% of Falkland rivers, which are 2.9-4.5 times less likely to contain native galaxiids than uninvaded streams. Without strong containment we predict brown trout will invade nearly all suitable freshwater habitats in the Falklands within the next [~]70 years, which might put native freshwater fishes at a high risk of extinction.

ecology↗

bioRxiv2021

Personality profiling may help select better cleaner fish for sea-lice control in salmon farming

Lumpfish (Cyclopterus lumpus) are increasingly being used as cleaner fish to control parasitic sea-lice in salmon farming, but cleaning rates are very variable and not all individuals eat sea-lice, which increases the risk of emaciation and has ethical and practical implications. Selecting good cleaners is a priority to make the industry more sustainable, but there is little information on what behaviours make cleaner fish effective under a commercial setting. We examined variation in lumpfish personalities according to the five-factor personality model that takes into account differences in activity, anxiety (shelter use, thigmotaxis), aggression, sociality, and boldness (neophobia). We then quantified how variation in lumpfish personalities influenced interactions with naive Atlantic salmon (Salmo salar), without the confounding effects of variation in sea-lice loads. Variation in activity, sociality, aggression and neophobia, but not in anxiety, was repeatable, which is consistent with a heritable basis. Neophilic, non-aggressive lumpfish spent more time inspecting salmon than neophobic and aggressive individuals, but salmon fled in the presence of the most active and social individuals, suggesting there may be an optimal cleaner fish personality amenable to artificial selection. The personality screening protocols developed in this study could inform a more efficient use of cleaner fish in salmon farming and reduce the number of individuals required to control sea-lice.

animal behavior and cognition↗

bioRxiv2020

More than meets the eye: syntopic and morphologically similar mangrove killifish species show different mating systems and patterns of genetic structure along the Brazilian coast

Different mating systems can strongly affect the extent of genetic diversity and population structure among species. Given the increased effects of genetic drift on reduced population size, theory predicts that species undergoing self-fertilization should have greater population structure than outcrossed species, however demographic dynamics may affect this scenario. The mangrove killifish clade is composed of the two only known examples of self-fertilising species among vertebrates (Kryptolebias marmoratus and K. hermaphroditus). A third species in this clade, K. ocellatus, inhabits mangrove forests in southeast Brazil, however its mating system and patterns of genetic structure have been rarely explored. Here, we examined the genetic structure and phylogeographic patterns of K. ocellatus along its distribution, using mitochondrial DNA and microsatellites to compare its patterns of genetic structure with the predominantly selfing and often syntopic, K. hermaphroditus. Our results indicate that K. ocellatus reproduces mainly by outcrossing across much of its known range, with no current evidence of selfing, despite being an androdioecious species. Our results also reveal a stronger population subdivision in K. ocellatus compared to K. hermaphroditus, contrary to the theoretical predictions based on reproductive biology of the two species Our findings indicate that, although morphologically similar, K. ocellatus and K. hermaphroditus had remarkably different evolutionary histories when colonising the same mangrove areas in south-eastern Brazil, with other factors (e. g. time of colonisation, dispersal/establishment capacity) having more profound effects on the current population structuring of those species than differences in mating systems.

evolutionary biology↗

bioRxiv2020

Additive and non-additive epigenetic signatures of hybridisation between fish species with different mating systems

Hybridisation is a major source of evolutionary innovation. However, several prezygotic and postzygotic factors influence its likelihood and evolutionary outcomes. Differences in mating systems can have a major effect on the extent and direction of hybridisation and introgression. In plants, epigenetic mechanisms 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 extent of a unique case of natural hybridisation between two genetically distant mangrove killifish species with different mating systems, Kryptolebias hermaphroditus (self-fertilising) and K. ocellatus (outcrossing), and the methylation patterns of their hybrids. Hybridisation rate between the species ranged between 14% and 26%. Although co-existing parental species displayed highly distinct genetic (microsatellites and SNPs) and methylation patterns (37,000 differentially methylated cytosines), our results indicate that F1 hybrids are viable and able to backcross with parental species. Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridisation between genetically distant species. Differentially methylated cytosines between hybrids and both parental species (5,800) suggest that introgressive hybridisation may play a role in generating novel genetic and epigenetic variation which could lead to species diversification. We also found a small percentage of non-additive epigenetic effects which might act as an evolutionary bet-hedging strategy and increase fitness under environmental change.

evolutionary biology↗

bioRxiv2020

Early life stress causes persistent impacts on the microbiome of Atlantic salmon

Intensively farmed fish are commonly stressed, often leading to immune impairment and increased susceptibility to disease. Microbial communities associated with the gut and skin are vital to host immune function, but little is known about how stress affects the fish microbiome, especially during the sensitive early life stages. We compared the effects of two aquaculture-relevant stressors on the gut and skin microbiome of Atlantic salmon fry: an acute cold stress during late embryogenesis, and a chronic environmental stress during the larval stage. Acute cold stress had a lasting effect on the structure of both the gut and the skin microbiome, likely due to disruption of the egg shell microbial communities which seed the initial colonisation of the teleost microbiome upon hatching. In contrast, chronic post hatch stress altered the structure of the gut microbiome, but not that of the skin. Both types of stressors promoted similar Gammaproteobacteria ASVs, particularly within the genera Acinetobacter and Aeromonas which include several important fish pathogens and, in the gut, reduced the abundance of Lactobacillales. This suggests that there may be common signatures of stress in the salmon microbiome, which may represent useful stress biomarkers in aquaculture.

microbiology↗

bioRxiv2020

Rapid quantitative assessment of fish larvae community composition using metabarcoding

Climate change stressors greatly impact the early life-stages of many organisms but their cryptic morphology often renders them difficult to monitor using morphological identification. High-throughput sequencing of DNA amplicons (metabarcoding) is potentially a rapid and cost-effective method to monitor early life-stages for management and environmental impact assessment purposes. Yet, there is conflicting information about the quantitative capability of metabarcoding. We compared metabarcoding with traditional morphological identification to evaluate taxonomic precision and reliability of abundance estimates, using 332 fish larvae from multinet hauls (0-50m depth) collected at 14 offshore sampling sites in the Irish and Celtic seas. To improve relative abundance estimates, the amount of tissue for each specimen was standardised and mitochondrial primers with conserved binding sites were used. Family level correction factors for amplification bias and back-calculations were applied to estimate numbers of individuals of a given taxon in a sample. Estimates from metabarcoding reads and morphological assessment were positively correlated for relative family abundances as well as taxon richness (Rs=0.81, P=0.007) and diversity (Rs=0.88, P=0.003). After applying family level correction, back-estimates of the number of individuals per family within a sample were accurate to {+/-} 2 individuals. Spatial patterns of community composition did not differ significantly between metabarcoding and morphological assessments. Our results show that DNA metabarcoding of bulk tissue samples can be used to monitor changes in fish larvae abundance and community composition. This represents a feasible, efficient and faster alternative to morphological identification that can be applied to terrestrial and aquatic habitats.

ecology↗

bioRxiv2019

Cortisol-induced signatures of stress in the fish microbiome

Stress experienced in intensive aquaculture can compromise fish growth, condition and immunity. Microbiome disruption may contribute to these adverse health effects, but little is known about how stress affects fish microbial communities. Here, we specifically examined the effects of stress-induced cortisol production on the fish microbiome. We exposed juvenile Atlantic salmon to a mild confinement stressor for two weeks. We then measured cortisol in the plasma, skin-mucus and faeces, and characterised the skin and faecal microbiome. Faecal and skin cortisol concentrations increased in fish exposed to confinement stress, and were positively correlated with plasma cortisol. Elevated faecal cortisol was associated with pronounced changes in the diversity and structure of the faecal microbiome. In particular, we identified a marked decline in probiotic Lactobacillales (Carnobacterium sp.) and an increase in pro-inflammatory and pathogenic taxa within the classes Clostridia and Gammaproteobacteria. In contrast, skin-mucus cortisol concentrations were lower and not associated with any detectable changes in the skin microbiome. Our results demonstrate that cortisol disrupts 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 faecal samples to monitor stress, including simultaneous determination of cortisol and stress-responsive bacteria.

microbiology↗

bioRxiv2019

Seasonal and spatial variation in growth and abundance of zebra mussel (Dreissena polymorpha) in a recently invaded lake: implications for management

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 one year in Cardiff Bay (UK), an artificial amenity lake invaded by zebra mussels in 2003 and where the species is rapidly expanding. Mean settling 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, with growth taking place during the summer and ceasing during winter and spring. Mixture analysis reveals the existence of multiple cohorts displaying different growth and settling rates and 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 taken into account 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.

ecology↗

bioRxiv2019

Predator recognition and anti-predatory behaviour in a recent aquatic invader, the killer shrimp (Dikerogammarus villosus)

The killer shrimp (Dikerogammarus villosus) is one of the most recent, but also most damaging, aquatic invasive species in Europe, but information on how the species responds to novel predation pressures in recently invaded areas is very limited. We employed an open test arena to examine predator recognition and anti-predatory behaviour in killer shrimp exposed to either blank water or water conditioned with fish kairomones to simulate a predator threat. Within five years after their introduction, killer shrimp spent much more time hiding in the presence of fish kairomones than when they were exposed to blank water. However, no significant difference was found in aggregation behaviour, and killer shrimp were strongly attracted to the scent of conspecifics regardless of predator threat. Given the strong selective pressures that fish predators can exert on native and invasive gammarids, our findings highlight the need to consider prey-predator interactions to better predict the dispersal and likely impact of killer shrimp into invaded ecosystems.

ecology↗

bioRxiv2019

Experimental evidence of invasion facilitation in the zebra mussel-killer shrimp system

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 mussels scent did not differ between sympatric and allopatric populations of killer shrimp, suggesting that chemical facilitation is not an acquired or learned trait. Our results have implications for managing the spread of killer shrimp, and perhaps other freshwater invasive species, because invasion facilitation could significantly increase establishment success. Failure to consider invasion facilitation may underestimate the risk of establishment and likely impact of some aquatic invaders.

ecology↗

bioRxiv2019

Trophic plasticity of the highly invasive topmouth gudgeon (Pseudorasbora parva) inferred from stable isotope analysis

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 four contrasting ponds and reservoirs in South Wales. Marked differences in diet and trophic position were found among neighbouring systems only a few kilometres 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 {delta}13C and {delta}15N 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 empty stomachs 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 neighbouring 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.

ecology↗

bioRxiv2019

Local parasite pressures and host genotype may modulate epigenetic diversity in a mixed-mating fish

Parasite-mediated selection is one of the main drivers of genetic variation in natural populations. The persistence of asexual reproduction and self-fertilization, however, challenges the notion that low genetic variation and inbreeding compromise the hosts 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 (MSAFLPs), and parasite loads in three populations of Kryptolebias hermaphroditus, a unique mixed-mating (partially self-fertilising) fish, to analyse 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.

zoology↗

bioRxiv2019

Environmental plasticity and colonisation history in the Atlantic salmon microbiome: a translocation experiment

Microbial communities associated with the gut and the skin are strongly influenced by environmental factors, and can rapidly adapt to change. Historical processes may also affect the microbiome. In particular, variation in microbial colonisation in early life has the potential to induce lasting effects on microbial assemblages. However, little is known about the relative extent of microbiome plasticity or the importance of historical colonisation effects following environmental change, especially for non-mammalian species. To investigate this we performed a reciprocal translocation of Atlantic salmon between captive and semi-natural conditions. Wild and hatchery-reared fry were transferred to three common garden experimental environments for six weeks: standard hatchery conditions, hatchery conditions with an enriched diet, and simulated wild conditions. We characterised the faecal and skin microbiome of individual fish before and after the environmental translocation, using a BACI (before-after-control-impact) design. We found evidence of extensive plasticity in both gut and skin microbiota, with the greatest changes in alpha and beta diversity associated with the largest changes in environment and diet. Microbiome richness and diversity were entirely determined by environment, with no detectable historical effects of fish origin. Microbiome structure was also strongly influenced by current environmental conditions but, for the first time in fish, we also found evidence of colonisation history, including a number of OTUs characteristic of captive rearing. These results may have important implications for host adaptation to local selective pressures, and also highlight how conditions during early life can have a long-term influence on the microbiome and, potentially, host health.

microbiology↗

bioRxiv2018

Monitoring the eradication of the highly invasive topmouth gudgeon (Pseudorasbora parva) using a novel eDNA assay

Aquatic Invasive Species (AIS) represent an important threat for Biodiversity and are one of the factors determining the ecological integrity of water bodies under the Water Framework Directive. Eradication is one of the most effective tools for the management of invasive species but has important economic and ecological trade-offs and its success needs to be carefully monitored. We assessed the eradication success of the topmouth gudgeon (Pseudorasbora parva), an invasive fish that poses significant risks to endemic aquatic fauna, in four ponds previously treated with the piscicide Rotenone using a novel environmental DNA (eDNA)-qPCR assay. Topmouth gudgeon was detected in all four treated ponds using 750 mL water samples and in three of the ponds using 15 mL samples, despite the eradication treatment. The highly sensitive qPCR assay detected topmouth gudgeon in a significantly greater proportion of sites (77.5%) than eDNA detection methods based on conventional PCR (35%). Our results highlight the difficulties of eradicating invasive fish and the need to incorporate reliable monitoring methods as part of a risk management strategy under the Water Framework Directive.

ecology↗

bioRxiv2018

Density-dependent changes in neophobia and stress-coping styles in the worlds oldest farmed fish

Farmed fish are typically reared at densities much higher than those observed in the wild, but to what extent crowding results in abnormal behaviours that can impact welfare and stress coping styles is subject to debate. Neophobia (i.e. fear of the new) is thought to be adaptive under natural conditions by limiting risks, but it is potentially maladapted in captivity, where there are no predators or novel foods. We reared juvenile Nile tilapia (Oreochromis niloticus) for six weeks at either high (50g/L) or low density (14g/L), assessed the extent of skin and eye darkening (two proxies of chronic stress), and exposed them to a novel object in an open-test arena, with and without cover, to assess the effects of density on neophobia and stress coping styles. Fish reared at high density were darker, more neophobic, less aggressive, less mobile and less likely to take risks than those reared at low density, and these effects were exacerbated when no cover was available. Thus, the reactive coping style shown by fish at high density was very different from the proactive coping style shown by fish at low density. Our findings provide novel insights into the plasticity of fish behaviour and the effects of aquaculture intensification on one of the worlds oldest farmed and most invasive fish, and highlight the importance of considering context. Crowding could have a positive effect on the welfare of tilapia by reducing aggressive behaviour, but it can also make fish chronically stressed and more fearful, which could make them less invasive.

animal behavior and cognition↗

bioRxiv2018

Genetic and phenotypic differentiation of lumpfish (Cyclopterus lumpus) across the North Atlantic: implications for conservation and aquaculture

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 UICN 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 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 NE Atlantic (Iceland, Faroe Islands, 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.

genetics↗

bioRxiv2018

Contrasting effects of acute and chronic stress on the transcriptome, epigenome, and immune response of Atlantic salmon

Early-life stress can have long-lasting effects on immunity, but the underlying molecular mechanisms are unclear. We examined the effects of acute stress (cold-shock during embryogenesis) and chronic stress (absence of tank enrichment during larval-stage) on the gill transcriptome and methylome of Atlantic salmon four months after hatching. While only chronic stress induced pronounced transcriptional effects, both acute and chronic stress caused lasting, and contrasting, changes in the methylome. Crucially, we found that acute stress enhanced immune response to a pathogenic challenge (lipopolysaccharide), while chronic stress suppressed it. We identified stress-induced changes in promoter or gene-body methylation that were associated with altered expression for a small proportion of genes, and also evidence of wider epigenetic regulation within signalling pathways involved in immune response. Our study suggests that early-life stress can affect immuno-competence through epigenetic mechanisms, a finding that could open the way for improved stress and disease management of farmed fish.

genomics↗

bioRxiv2018

Simultaneous detection of invasive signal crayfish, endangered white-clawed crayfish and the crayfish plague pathogen using environmental DNA

Aquatic Invasive Species (AIS) are important vectors for the introduction of novel pathogens which can, in turn, become drivers of rapid ecological and evolutionary change, compromising the persistence of native species. Conservation strategies rely on accurate information regarding presence and distribution of AIS and their associated pathogens to prevent or mitigate negative impacts, such as predation, displacement or competition with native species for food, space or breeding sites. Environmental DNA is increasingly used as a conservation tool for early detection and monitoring of AIS. We used a novel eDNA high-resolution melt curve (HRM) approach to simultaneously detect the UK endangered native crayfish (Austropotamobius pallipes), the highly invasive signal crayfish (Pacifastacus leniusculus) and their dominant pathogen, Aphanomyces astaci, (causative agent of crayfish plague). We validated the approach with laboratory and field samples in areas with known presence or absence of both crayfish species as well as the pathogen, prior to the monitoring of areas where their presence was unknown. We identified the presence of infected signal crayfish further upstream than previously detected in an area where previous intensive eradication attempts had taken place, and the coexistence of both species in plague free catchments. We also detected the endangered native crayfish in an area where trapping had failed. With this method, we could estimate the distribution of native and invasive crayfish and their infection status in a rapid, cost effective and highly sensitive way, providing essential information for the development of conservation strategies in catchments with populations of endangered native crayfish.

ecology↗