The FSBI holds an annual competition open to any member wishing to apply for postgraduate study leading to a PhD degree. The current and previous project reports resulting from this are available below.
PhD Student Ada Eslava (2020-2023)
(Supervisor(s): Anne Magurran (University of St Andrews), Amy Deacon (University of the West Indies, St. Augustine) and Indar Ramnarine (University of the West Indies, St. Augustine))
Biodiversity Change in Fish Communities: Integrating Taxonomic, Phylogenetic and Functional Diversity
Freshwater fish are among the most vulnerable organisms on the planet due to the ecological impacts of the multiple anthropogenic pressures that modify freshwater habitats. Despite the concern over the current state of the world’s freshwater fish faunas, little is known about how multiple facets of their diversity are changing over time.
In the tropics, the situation is particularly unclear because, historically, fewer temporal community data have been collected than in temperate locations. The tropical island of Trinidad in the Caribbean is an exception, as stream fish communities there have been monitored at different time points during the last half-century.
In my project, I will ask two main questions. First, how has the regional freshwater fish diversity in Trinidad changed since the 1950s? Second, are the spatio-temporal patterns found in this tropical island observed in other locations of the world?
In order to answer my first question, I will extend time-series surveys by re-visiting fieldwork sites throughout the geography of Trinidad and use the records from the past to establish comparisons. To tackle the second, I will use open-access, temporal data of freshwater fish communities available in repositories such as BioTIME (http://biotime.st-andrews.ac.uk/).
Since biodiversity is a multi-faceted concept, I will adopt a multi-dimensional approach in my analyses. First, I will quantify two biodiversity components: the local diversity of communities and compositional change relative to a temporal baseline (also named alpha and temporal beta diversity). Second, I will use recently developed methodologies that integrate the information contained in species traits and phylogenies to measure the functional and phylogenetic dimensions of diversity alongside their taxonomic counterpart.
I’ll carry out this research at the University of St Andrews and the fieldwork at the University of the West Indies, Trinidad.
Stirling University (supervisors: Mags Crumlish and Simon Mackenzie) 2016-19
Can the gut microbiome support fish health?
The intestinal environment of vertebrate animals is colonised by a complex microbial community, termed the microbiome. In fish, this community is extremely diverse and made up of more than one trillion bacteria/g of intestinal contents. Recent meta-analysis has revealed that many fish species share a core gut microbiome community comprised of five key bacterial phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria. Furthermore, members within this core microbiome are thought to have been selected throughout evolution to play vital roles in promoting and maintaining their host’s physiology and health status.
My PhD focuses on how this microbial community can support fish health through microbially-mediated gut functions. To investigate this, I am using next generation sequencing of the bacterial 16S rRNA gene, to profile the microbiome communities in different farmed fish species and explore how certain husbandry practices can influence these communities and their mediated functions within the fish host. In particular, my research will i) explore how antibiotic compounds influence the microbiome communities in different farmed fish and ii) investigate how manipulated microbiome communities impact on gut health in the fish host as measured by changes in immunity, metabolism and gut function.
Overall this project aims to improve our understanding of the core microbiome community composition in different fish species and help support the development of novel husbandry methods to improve the resilience of farmed fish. Data obtained from this project will be essential to the global aquaculture industry on multiple platforms – more critically addressing current attempts to reduce or find alternatives to antibiotic use in fish farming.
For further information please contact:
Institute of Aquaculture,
University of Stirling,
Email: firstname.lastname@example.orgRead More
University of Glasgow (supervisors: Kathryn Elmer and Colin Adams) 2016-19
Thesis Title: “Population Genomics and Molecular Evolution in Salmonids”
Some groups of salmonids, such as charr and whitefish, repeatedly and rapidly diversified into co-occurring ecomorphs in various lake habitats. This diversification potential has, at least to some degree, a genetic basis. Using transcriptome data from various species of salmonids, I am screening for footprints of natural selection to identify the genetic toolbox that could enable some salmonids to diversify rapidly.
Various populations of Arctic charr, which is often considered the most variable vertebrate on earth, are characterised by ongoing or recent diversification into mostly benthic and limnetic ecomorphs. To learn more about this evolution-in-progress, I am using whole-genome data to understand how adaptation to different environments shapes the genomes of diverging ecomorphs. Importantly, I am also focussing on the amount of ongoing or past gene flow between ecomorphs and among populations and its potential effects on the divergence process.
It has been shown that the demographic history of populations can influence the degree and nature of diversification. However, we know little about the interplay of demography and adaptation or selection at the genome level. With the help of in-silico simulations of large genomic elements and comparisons of the obtained genomic signatures of selection under various demographic scenarios to real-world data, I am trying to disentangle the complexities of these evolutionary processes to inform analyses of empirical data.
University of St Andrews (supervisors: Luke Rendell and Mike Webster) 2015-2018
My PhD focuses on the social behaviour of Archer fish (Toxotes spp.) and their learning. Renowned for their ability to shoot down terrestrial prey by ‘shooting’ jets of water at them archer fish may be capable of using social information from conspecifics to learn to perform specific behaviours. I am investigating this and exploring the various factors that affect their learning and social dynamics. I am supervised by Luke Rendell and Mike Webster at the University of St Andrews in collaboration with Stefan Schuster at the University of Bayreuth.Read More
University of Glasgow (supervisors: Neil Metcalfe and Kath Sloman) 2015-2018
The effects of environmental stressors on organisms have been extensively studied in a wide range of phyla, including mammals, birds and fish. It has also been shown that environmental stress experienced by mothers may affect the phenotype and behaviour of their future offspring. The questions that remain largely unanswered are whether chronic exposure of mothers to environmental stressors can cause such effects in offspring and how these are influenced by the timing and duration of stress. Untangling the relationships between these factors would give an insight into the effect that environmental changes (and the potential for increased environmental stress) may have on wild fish populations. My project aims to address these questions using an established laboratory population of three-spined sticklebacks (Gasterosteus aculeatus). Only the male three-spined stickleback provides parental care, and so the non-genetic influence of the mother on the offspring is limited to the substances deposited in her eggs or ovarian fluid at the time of egg production and spawning. This provides an opportunity to use an experimental approach to study whether environmental stressors acting upon females in the period leading up to spawning affect the growth, survival and behavioural phenotype of their offspring. This project addresses the question of transgenerational effects of chronic mild environmental stressors using a chronic, unpredictable stress protocol and non-invasive and minimally stressful method of measuring water-borne cortisol.Read More
University of Bangor & CEFAS
There are c. 1 million recreational sea anglers (RSA) in the UK, spending annually over £1.2 billion and their removals of marine fish can be quantitatively comparable to commercial landings, as revealed by landings of the European sea bass, Dicentrarchus labrax. Hence angling removals should be included in stock assessments and fisheries management, accounting for catch and release and post-release mortality rates.
RSA catch has only been included in stock assessments of Baltic cod; a gap recognised by the European Commission, and in the Common Fisheries Policy that requires members to report on catches by RSA for some species to give a clearer picture of how fishing affects stocks. RSA data on commercially significant species are also required at a local level under the Marine and Coastal Access Act to provide an evidence-base when balancing the needs of marine environment users. However, national RSA assessments are expensive and complex, especially in the UK where sea angling is unlicensed, so there is little evidence to inform the development of a policy for UK sea angling despite the sector’s importance.
My research will seek to scope, develop and validate transferable, innovative techniques in the capture of RSA data on marine fish species of recreational and commercial importance, primarily within ICES ecoregions E and F. This work will comprise three synergistic strands:
To engage with the UK RSA community to determine the extent of existing catch data recorded by anglers and to collate those data to construct time series of catches and compare against existing fisheries independent and dependant time series.
To develop, evaluate and pilot practical, reusable low cost technological solutions to complement RSA data recording, including natural language processing of social media sources; machine vision in species identification, and optical character recognition in form processing complemented with SMS, email and mobile solutions and their application to local and national angler survey programmes.
To evaluate the viability and define success criteria for a citizen science programme on the ongoing assessment of recreational sea angling, based on the outcomes of the preceding strands.
School of Ocean Sciences
University of Exeter
Supervisor(s): Eduarda Santos & Rod Wilson
For metals, extreme cases exist of fish populations that can survive in highly contaminated waters, including a brown trout population in the River Hayle, where concentrations of metals far exceed the LC50 for this species. Furthermore, even for populations of fish inhabiting relatively un- impacted waters, their toxicological responses to metals can vary significantly. This highlights the need to understand natural and exposure-induced variations in the response of fish to pollutants, in order to appropriately manage and protect fish populations in their natural environment.
My research explores three key questions, firstly to determine if wild populations of three spined sticklebacks exhibit differential susceptibility to copper and if those characteristics can be inherited under control conditions. Secondly, my research aims to determine if differential susceptibility can be induced by exposure to copper during early life. Thirdly, I plan to investigate the fitness cost associated with differential susceptibility to copper in this species.
Together, this research will allow for a greater understanding of the variation in the responses to chemical stressors in wild populations, how they are induced and maintained and what are the consequences of changes in susceptibility to a pollutant on other parameters of fundamental importance to population sustainability. The data will build on previous data generated at Exeter, and will have implications for toxicity testing and regulation and for the management of wild fish populations.
My report on my attendance at the Canadian Conference for Fisheries Research is here
Uren Webster, T. M., Laing, L. V., Florance, H. & Santos, E. M. 2014. Effects of glyphosate and its formulation, Roundup, on reproduction in zebrafish (Danio rerio). Environmental Science & Technology 48, 1271-1279.
College of Life & Environmental Sciences
University of Exeter
University of Oxford
Supervisor(s): Alex Rogers (Oxford) and Dan Exton (Operation Wallacea)
Mesophotic coral reef ecosystems (MCE) occur in tropical regions extending from 30 m to the limit of the photic zone, c. 150 m. These reefs are often connected to shallow coral reef ecosystems, where it is suggested they provide an important reservoir of recruits for coral and fish populations. Existing reef fish studies are highly depth biased mostly < 30 m, making the importance of mesophotic reefs to overall reef resilience in the face of human disturbances such as overfishing largely unknown, with a lack of evidence for whether fish populations on shallow reefs and adjacent MCEs are connected. This study addresses this important information gap by using advanced diving technologies coupled with a newly developed stereo-video system and molecular ecology techniques to better understand fish communities by examining fish biomass distributions and community structure down depth gradients from shallow reefs to MCEs and by exploring the connectivity of MCE fish populations down depth gradients with shallow reefs and between mesophotic reefs. This project is being conducted in partnership with Operation Wallacea with fieldwork principally based at their field site on Utila, Honduras where MCEs connected to shallow reefs have been identified but are unstudied. The aims of the project are twofold, first to Investigate biomass and community structure. Fisheries value and ecological service provision requires biomass to be quantified as it provides a better indication of functional pressure exerted by a fish-feeding guild than richness or abundance. Fish biomass along transects will be assessed by stereo-video surveys capturing the shallow reef to MCE gradient at various fished and protected sites. Biomass will be standardised using fish length-weight relationships, through data from local fisheries monitoring programmes to obtain local length to weight ratios, but for any fish species not caught locally, through available datasets (e.g. Fishbase). To allow patterns in fish biomass and community structure to be explained, benthic composition will be quantified using point intercept video transects, quantifying coral (genera and morphology), algal and other coverage. Physical parameters will also be recorded including temperature, light and turbidity and HOBO loggers for detailed year-round temperature and light readings. The second aim is to Investigate connectivity in MCE fish populations. Levels of population connectivity between populations of depth-generalist fish species with residents found on both shallow reefs and MCEs are not known. This has major implications for conservation and sustainable management of MCE fisheries, as well as the design and location of marine protected area networks. Many studies have demonstrated the ability of molecular techniques such as microsatellites to identify population structure; these protocols can be applied to assess connectivity down depth gradients and between MCE specialist species on small spatial scales. Non-lethal fin clippings will be collected from fish using a hand net and a clove oil anaesthetic mix. Care will be taken to return individuals to the reef where they were caught. To assess connectivity along depth gradients, samples of depth-generalist reef associated fish will be collected at different depths at several sites. To assess population connectivity between MCEs, an MCE specialist fish species will be identified samples collected at several sites. Contact: Ocean Research and Conservation Group Department of Zoology University of Oxford The Tinbergen Building South Parks Road Oxford OX1 3PS UK Email: email@example.com Twitter: @dandradibrown URL: http://www.zoo.ox.ac.uk/group/oceansRead More
Supervisor(s): Robert Britton and Demetra Andreou
My research explores this using three non-native fish parasites introduced into UK freshwaters in order to identify their consequences for individual hosts, assess how these scale up into population and community effects, and determine their modifications to the structure of the invaded food web. Three non-native parasites will be studied which represent groups with varying complexity in their lifecycles so that they can demonstrate how, for example, the number of hosts in the life cycle affects food web structure.
Ergasilus briani has a simple life cycle, involving host-to-host transmission in their preferred host species of roach Rutilus rutilus and common bream Abramis brama. Bothriocephalus acheilognathi has a complex life cycle involving intermediate hosts before their definitive fish host becomes infected, where the final host here is common carp Cyprinus carpio. Anguillicoides crassus also has a complex life cycle but it involves several paratenic hosts (in which the parasite remains immature) before being transmitted to its preferred definitive host, in UK waters the European eel Anguilla anguilla. Transmission to eels is often through predation of a paratenic host.
Using both field case studies and experimental mesocosms the consequences of these parasites for food web structure will be assessed using two principal methods: food web topology and stable isotope analysis.
My report on my attendance at the Canadian Conference For Fisheries Research 2014 is here.
Faculty of Science and Technology
Supervisor(s): Dave Hoole, Mark Skidmore and Dieter Steinhagen
Since the immune protection induced by vaccination tends to be specific to the target pathogen and there is a movement away from more traditional methods of coping with disease outbreaks, such as antibiotic treatments, there is an increased interest in the concept of improving overall health by increasing general immunity. Immunomodulants act by enhancing the general immune defence which can result in a higher rate of survival during infection. Immunomodulative compounds, such as β-glucans, are already widely used within the farming industry and are known to have a positive impact on fish health although the mechanisms behind their actions are still mostly unknown. Additionally, commercial products undergo several stages of processing before reaching the target organism therefore the physical structure of the final immunomodulative components have yet to be fully elucidated.
One of the simplest, least stressful means of exposing fish to β-glucans is to incorporate the compound into the fish feed. Upon consumption, the β-glucans come into contact with the commensal microflora population within the gut. There is an important symbiotic relationship between a host fish and its commensal bacterial population which, if disturbed, may have both positive and negative effects on gut functions and general health. In addition to having immunomodulatory properties upon the host fish, β-glucans can also be utilised as a food source by certain bacterial species. The aim of my research is therefore to establish how immunomodulants affect both the immune response of the host and the ecology of the microflora of the intestine. Whilst there are many publications related to either the host or the microflora as separate entities, there is very little on bridging the gap between the two within ichthyology. Using the common carp (Cyprinus carpio) as a model host and a range of known β-glucan structures, in vitro studies will determine the effects of β-glucans on individual bacterial species and in vivo trials will establish effects on the resident microflora population and the innate immune responses in the gut of the host fish.
Another mode of exposing fish to β-glucans is to add them as a bathing agent. This has been shown to have positive health benefits including increasing the rate of wound healing in carp, but the effect this has on the environmental microflora has not yet been studied. In order to establish the extent the inclusion of known β-glucan structures are able to alter waterborne microflora populations, molecular microbiological methods will be employed to analyse closed circulation systems both with and without the presence of the selected host fish.
This project is a development of the work undertaken under the auspices of the EU ITN “Nemo” which established the effect of MacroGard®, a commercially available β-1,3/1,6-glucan, on the immune status and health of common carp.
School of Life Sciences
LinkedIn: Sarah Harris
Supervisor(s): Nick Polunin & Steve Newman
Early work on coral reef degradation focussed largely on phase shifts from coral to algal dominated states and effects on community structure. This rather ignored the role of the physical structure of the reef sustained by corals. Structural complexity has been correlated with higher levels of diversity in both terrestrial and marine habitats, including coral reefs. However, these findings relied upon simplistic habitat measures and broad community metrics. It is necessary for this relationship to be examined in greater detail to identify which aspects of structural complexity are important to specific components of the community. Related to this, there is scarcely anything known about how mobile species interact with the reef framework. Yet the utilisation of space on reefs by fish is key to predicting how degradation will affect the ecosystem and the humans that rely on them. Such understanding will offer insight into how species, trophic groups and size classes react to loss of habitat structure.
The Caribbean has been undergoing continued losses of structurally complex Acropora spp. and Montastraea spp. of coral since the late 1970s. Stress-tolerant corals that form smaller and less complex colonies, such as Porites spp. and Agaricia spp. have now become relatively more abundant and the consequences of this shift are scarcely known. While the coral cover of Caribbean reefs has been declining for 40 years, changes in fish community structure were negligible until 10 years ago. These changes in the Caribbean fish communities are thus unlikely to be exclusively linked to live coral-cover loss. Unlike their Indo-Pacific counterparts, no Caribbean reef fish are obligately dependent on living corals for food or refuge, therefore decline in reef fish communities appears to more closely relate to generic effects of the loss of reef structure.
Temporal trends in Caribbean reef complexity and community structure have been explored through sparse existing data however, there is at present no methodologically-constrained information on spatial trends in Caribbean regional complexity, yet this is crucial for understanding the current status of reefs, the extent of ongoing changes, and the implications for environmental managers.
This study will examine the concept of structural complexity in natural systems and detail the spatial patterns of reef complexity across 10 Caribbean countries. It will then focus on the relationship between complexity and the fish community and the behavioural interactions between fish and the reef structure.
Marine Science and Technology
Newcastle University NE1 7RU
Cardiff University & Bristol University
Supervisor(s): Joanna Cable & Gabrielle Archard, & Julian Partridge
How an individual’s mate choice preferences change over time is an understudied area of evolutionary ecology. Condition-dependent variation in mate choice preferences between individual female guppies has been demonstrated. It is likely, though little tested, that there is also within-individual variation in preference because condition will change through time. One mechanism by which preferences may vary both between and within individuals is through alteration in the rank females attribute to each of the several cues used during mate choice. These cues in guppies have been well studied; in healthy females mate choice appears to be based largely on visual cues, females prefer males with intense carotenoid colouration and high display rate. The role of olfaction in guppy mate choice has received little attention and is uncertain, though it is through olfaction that animals (including fish) assess MHC compatibility. Susceptibility to parasites is linked to MHC genotype in guppies, so choosing mates based on MHC compatibility is likely to increase guppy reproductive fitness. Olfactory cues may also serve to ‘prime’ the visual system, as has been found in zebrafish. I am using a range of behavioural experiments to test hypotheses relating to condition dependent, within individual variation in the use of information from different sensory modalities in a mate choice context.
Cardiff School of Biosciences,
Biomedical Sciences Building,
University of Hull & Cefas-Lowestoft
Supervisor(s): Bernd Hänfling, Lori Lawson-Handley & Gordon Copp
Research on invasive species and invaded communities is essential to understanding and predicting biodiversity change. Furthermore, introduced species are excellent model systems with which to address fundamental questions in biology. However, biological invasions can have dramatic impacts on native species and this appears to be the case for the crucian carp Carassius carassius, which is native to northwestern Europe (including southeast England), and under threat from non-native congeners goldfish C. auratus and gibel (a.k.a. Prussian) carp C. gibelio. Conservation efforts for C. carassius are hampered by the taxonomic ambiguity which exists between C. carassius, C. auratus and C. gibelio; the problems in classifying and identifying separate Carassius spp. have introduced doubt regarding the current distributions of all Carassius spp. Consequently, impact assessment has been difficult; for example, it has only recently been demonstrated that around 70% of pure C. carassius populations in Norfolk, UK have been replaced by non-native Carassius species in the past 30 years.
In order to provide impact assessments in invasive systems, conservation geneticists have previously concentrated their studies on the lowered fitness and adaptability of native species in small populations due to the loss of genetic variability. These studies almost exclusively use near-neutral genetic markers, which cannot be a proxy for genetic variation in genes which have selectively important functions. Furthermore, neutral markers will lose genetic variation more rapidly than those under selection, with there being no correlation between molecular marker heterozygosity and heritabilities. There is likely therefore to be a difference between the impact of bottlenecks and/or climate change on genetic variation in neutral and non-neutral genes. Additionally, the study of hybridisation has been carried out previously using mainly only a small number of molecular markers, which do not have sufficient power to reveal the introgression of single genes. These limitations have left two fundamental evolutionary questions unanswered: to what extent is adaptively important genetic variation affected by bottlenecks in small, isolated populations, and, what are the genetic effects associated with environmental change (through invasive species and climate change) on fragmented populations?
With the development of next-generation sequencing, it is now feasible to address these research gaps. Next generation sequencing techniques allow for genome-wide sequencing, including selectively functional genes, thus providing a better representation of the genetic variation within individuals and populations and allowing for comparison between the behaviour of these genome regions during bottlenecks. Furthermore, these techniques allow for the identification of small regions in the genome of native species that have introgressed from non-natives or vice versa. Simultaneously, the genomic analyses of this system, in conjunction with microsatellite analyses, will shed light on the genetic structure of C. carassius populations in both the UK and continental Europe, providing the means to put forward comprehensive and much needed Biodiversity action plans for this threatened species.
Evolutionary Biology Group
University of Hull