Sofia Consuegra

Institute of Marine Research (IIM-CSIC) · Department of Biosciences

Background The gut microbiota influences human and animal cognition and behaviour through its effects on the endocrine and immune systems, but the relationship between host genetics, environmental factors and the microbiota, and their joint effect on the host cognitive behaviour has not been determined. The microbiome-behaviour relationship may be...

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 th...

In marine species with large populations and high dispersal potential, large-scale genetic differences and clinal trends in allele frequency can provide insight into the evolutionary processes that shape diversity. Lumpfish, Cyclopterus lumpus, is found throughout the North Atlantic and has traditionally been harvested for roe and more recently use...

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‐...

Alien species constitute one of the main threats to freshwater ecosystems, negatively impacting biodiversity, economy, biosecurity and ecosystem services. Predicting the arrival and spread of alien species is of paramount importance to prevent new introductions and control the expansion and establishment of already introduced species. We modelled t...

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...

Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms—a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure an...

The killifish genus Kryptolebias currently contains seven recognized species found in freshwater and mangrove microhabitats in South and Central America, the Caribbean, and Florida. Kryptolebias species have several unique features. Beyond its amphibious nature, two of the Kryptolebias species ( K. marmoratus and K. hermaphroditus sensu Costa 2011)...

Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important sources of adaptive variation for species with low genetic diversity, but little is known about the complex interaction between them and the genetic diversity of the host, particularly in wild populations. We examined the skin microbiome compos...

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 Nile tilapia fed wi...

Use of microalgae in fish nutrition can relieve pressure on wild fish stocks, but there is no systematic quantitative evaluation of microalgae benefits. We conducted a metanalysis on the nutritional benefits of Spirulina and Schizochytrium as replacements of fishmeal and fish or plant oil, respectively. We reviewed 50 peer-reviewed studies involvin...

Non-native salmonids are protected in the Southern hemisphere where they sustain aquaculture and lucrative sport fisheries, but also impact many native 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 introd...

Use of microalgae in fish nutrition can relieve pressure on wild fish stocks, but there is no systematic quantitative evaluation of microalgae benefits. We conducted a metanalysis on the nutritional benefits of Spirulina and Schizochytrium as replacements of fishmeal and fish or plant oil, respectively. We reviewed 50 peer-reviewed studies involvin...

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...

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...

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...

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...

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...

Habitat fragmentation is a principal threat to biodiversity and artificial river barriers are a leading cause of the global decline in freshwater biota. Although 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...

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...

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 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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...