Sofia Consuegra

Swansea University | SWAN · Department of Biosciences

Hybridisation 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 natu...

Introgression is a widespread evolutionary process leading to phylogenetic inconsistencies among distinct parts of the genomes, particularly between mitochondrial and nuclear-based phylogenetic reconstructions (e.g., mito-nuclear discordances). Here, we used mtDNA and genome-wide nuclear sites to provide the first phylogenomic-based hypothesis on t...

River barriers affect river dynamics and aquatic biota, altering the entire ecosystem. Nevertheless, dams and reservoirs provide goods like water supply and low-carbon energy that are becoming increasingly critical under current climate change. To know to what extent dams and reservoirs are important to the population, we explored social attitudes...

Identifying population structuring in highly fecund marine species with high dispersal rates is challenging, but critical for conservation and stock delimitation for fisheries management. European sea bass (Dicentrarchus labrax) is a commercial species of fisheries and aquaculture relevance whose stocks are declining in the North Atlantic, despite...

We estimate over 200,000 km or 10% of previously free-flowing river habitat length has been lost due to impoundments, an amount equivalent to the entire length of rivers in Italy. This loss strongly depends on the biogeographical location and a type of impounding barrier. European rivers are disconnected by more than one million man-made barriers t...

Different mating systems are expected to affect the extent and direction of hybridization. Due to the different levels of sexual conflict, the weak inbreeder/strong outbreeder (WISO) hypothesis predicts that gametes from self-incompatible (SI) species should outcompete gametes from self-compatible (SC) ones. However, other factors such as timing of...

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 susta...

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 aquacult...

Lumpfish (Cyclopterus lumpus L.) are increasingly being used as cleaner fish to control parasitic sea lice, one of the most important threats to salmon farming. However, lumpfish cannot survive feeding solely on sea lice, and their mortality in salmon net-pens can be high, which has welfare, ethical and economic implications. The industry is under...

Farmed fish are commonly exposed to stress in intensive aquaculture systems, often leading to immune impairment and increased susceptibility to disease. As microbial communities associated with the gut and skin are vital to host health and disease resilience, disruption of microbiome integrity could contribute to the adverse consequences of stress...

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...

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 susta...

Invasive bivalves can cause widespread ecological damage, but eradication has proved difficult. Identifying the pathways of dispersal is crucial to implementing more effective biocontainment measures. We examined the distribution of the highly invasive zebra mussel (Dreissena polymorpha) in Great Britain through Species Distribution Modelling to de...

River fragmentation caused by instream barriers is a leading cause of biodiversity loss, particularly for freshwater migratory fish, the vertebrate group that has suffered the steepest decline. However, most studies have tended to focus on the impacts of large dams on only a few taxa. We estimated the cumulative impact of both large and small barri...

Mangrove killifishes of the genus Kryptolebias have been historically classified as rare because of their small size and cryptic nature. Major gaps in distribution knowledge across mangrove areas, particularly in South America, challenge the understanding of the taxonomic status, biogeographical patterns and genetic structuring of the lineages comp...

Habitat fragmentation is a principal threat to biodiversity and artificial river barriers are a leading cause of the global decline in freshwater biota. Whilst the impact of barriers on diadromous fish is well established, impacts on river‐resident fish communities remain unclear, especially for low‐head barriers. We examined the movement of five c...

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) app...

Accurate assessment of larval community composition in spawning areas is essential for fisheries management and conservation but is often hampered by the cryptic nature of many larvae, which renders them difficult to identify morphologically. Metabarcoding is a rapid and cost‐effective method to monitor early life‐stages for management and environm...

Artificial barriers cause widespread impacts on freshwater fish. Swimming performance is often used as the key metric in assessing fishes' responses to river barriers. However, barrier mitigation is generally based on the swimming ability of salmonids and other strong swimmers because knowledge of swimming ability for most other freshwater fish is...

Rivers support some of Earth’s richest biodiversity1 and provide essential ecosystem services to society2, but they are often fragmented by barriers to free flow3. In Europe, attempts to quantify river connectivity have been hampered by the absence of a harmonized barrier database. Here we show that there are at least 1.2 million instream barriers...

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 diffic...

Sloths are notoriously slow and consequently have limited dispersal ability, which makes them particularly vulnerable to the effects of habitat fragmentation and degradation. Sloths in Costa Rica are considered of conservation concern due to habitat loss, livestock production and increasing urbanisation. Reintroductions from rescue centres are comm...

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-fertilisation should have greater population structure than outcrossed species; however, demographic dynamics may a...

Lumpfish (Cyclopterus lumpus L.) are widely used for controlling sea lice in salmon farming, but their welfare is often challenged by poor husbandry, stress, and disease outbreaks, which compromise their ability to delouse salmon and cause public concern. It is hence important to identify when the welfare of lumpfish is being compromised in a simpl...

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 af...

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 an...

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 co...

Let It Flow | Magazine produced for the EU Horizon 2020 AMBER project. The origin of this magazine stems from a project involving scientists, representatives from the hydropower industry, government agencies, and non-governmental organizations who gathered to make an impact on Europe’s water management. This EU Horizon 2020 funded project, called...

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 seas...

Infectious diseases represent an important barrier to sustainable aquaculture development. Rearing density can substantially impact fish productivity, health and welfare in aquaculture, including growth rates, behaviour and, crucially, immune activity. Given the current emphasis on aquaculture diversification, stress-related indicators broadly appl...

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 inva...

Parental effects influence offspring phenotypes through pre- and post-natal routes but little is known about their molecular basis, and therefore their adaptive significance. Epigenetic modifications, which control gene expression without changes in the DNA sequence and are influenced by the environment, may contribute to parental effects. Taking a...

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...

1. Macrophytes play important functional roles in river ecosystems, providing habitat and food, as well as influencing flow, water chemistry, and sediment dynamics. They also represent an important component of river biodiversity. 2. Artificial river barriers have the potential to disrupt macrophyte dispersal, and compromise their distribution and...

The spread of invasive, non-native species is a key threat to biodiversity. Parasites can play a significant role by influencing their invasive host"s survival or behaviour, which can subsequently alter invasion dynamics. The North American signal crayfish (Pacifastacus leniusculus) is a known carrier of Aphanomyces astaci, an oomycete pathogen tha...

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 k...

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 effe...

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 environm...

The killer shrimp (Dikerogammarus villosus) is one of the most recent and damaging aquatic invasive species in many parts of Europe, but information on how the species responds to predation pressures in recently invaded areas is very limited. We employed an open test arena to examine anti-predatory behaviour in killer shrimp exposed to either blank...

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 fa...

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 exp...

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 non‐aggressive 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 exa...

Background: Infectious diseases represent an important barrier to sustainable aquaculture development. Rearing density can substantially impact fish productivity, health and welfare in aquaculture, including growth rates, behaviour and, crucially, immune activity. Given the current emphasis on aquaculture diversification, stress-related indicators...

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 fresh...

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 re‐ spond to pathogens. DNA methylation represents a potential mechanism for gener‐ ating addit...

Artificial barriers are one of the main threats to river ecosystems, resulting in habitat fragmentation and loss of connectivity. Yet, the abundance and distribution of most artificial barriers, excluding high-head dams, is poorly documented. We provide a comprehensive assessment of the distribution and typology of artificial barriers in Great Brit...

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 f...

Artificial barriers are one of the main threats to river ecosystems, resulting in habitat fragmentation and loss of connectivity. Yet, the abundance and distribution of most artificial barriers, excluding high-head dams, is poorly documented. We provide a comprehensive assessment of the distribution and typology of artificial barriers in Great Brit...

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 re...

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 variabl...

Interbreeding between hatchery-reared and wild fish, through deliberate stocking or escapes from fish farms, can result in rapid phenotypic and gene expression changes in hybrids, but the underlying mechanisms are unknown. We assessed if one generation of captive breeding was sufficient to generate inter- and/or transgenerational epigenetic modific...

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 seas...

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 natur...

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 s...

The role of river obstacles in preventing or facilitating the dispersal and establishment of aquatic invasive species is controversial. Novel detection tools like environmental DNA (eDNA) can be used for monitoring aquatic invasive species (AIS) such as the American signal crayfish (Pacifastacus leniusculus) and the Chinese mitten crab (Eriocheir s...

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 faci...

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 tradeoffs and its success n...

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 inva...

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 host's ability to respond to pathogens. DNA methylation represents a potential mechanism for gener...

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 k...