Louise Archer
Louise Claire Archer

Project Title: The effects of proximate factors on alternative migratory tactics in brown trout.

Brown trout show dramatic differences in life history tactics, in particular, the phenomenon of partial migration. Populations can be comprised of solely anadromous individuals (that move to sea and grow to a large size, returning to spawn in freshwater), purely freshwater residents or a mixture of the two ecotypes. If a physiological condition cue exceeds an inherited threshold, a resident life history is triggered, alternatively, anadromy occurs.

I aim to analyse how genes and environment interactively determine anadromous life histories. Experimental families created from one anadromous and one freshwater resident population have been reared in a controlled laboratory setting, where environmental conditions are manipulated: food and temperature. Smolting rates will be measured within each treatment. If energy requirements exceed energy acquisition (through increased temperatures or reduced food), higher rates of anadromy are expected as individuals are energy constrained and move to more productive feeding areas at sea. Life history will be related back to metabolism to determine if differences in energy usage underpin life history decisions. This “common-garden” experiment will help establish whether differences in energy usage (and resulting life history tactics) have a genetic basis, and whether genes and environment interactively determine life history.

PhD Completed 2019


Project Title: Genetic basis of alternative migratory tactics in brown trout.

My research aims to gain further insight into how and why sympatric individuals of the same species can develop strikingly different life histories. Although many alternative life history (ALH) traits have been well documented and described in a physiological and behavioural sense, the genomic basis of this phenotypic variation remains poorly understood, despite advances in genomic technology.  

My PhD project will focus on understanding the relative roles of genes and environment in shaping facultative anadromy in brown trout (Salmo trutta).  One goal of the study is to establish whether phenotypic differences among trout populations, with ALH traits, reflect genetic divergence.  To do this we will conduct a common garden experiment involving two populations of S. trutta (one that naturally exhibits high rates of anadromy, the other low). Offspring of pure and hybrid crosses will be reared under fully wild conditions, the environment is equipped with downstream traps to capture migrants.  Furthermore, two complimentary genomic approaches will be applied to investigate the genomic basis of ALH tactics and their plasticity: (1) a genome wide association study (GWAS) to identify single nucleotide polymorphisms statistically associated with discrete phenotypic variation within populations, and (2) gene expression profiling to quantify “genomic reaction norms”.  Gene expression differences among cross types within a single common environment should provide information on genetic variation in reaction norm elevations, while cross-specific expression differences among environments provides information on reaction norm slopes (i.e. genetic variation in plasticity).

Robert Wynne
Ronan O'Sullivan


Project Title: Adaptive capacity and resilience of hybridised populations in a changing world: interactions between wild and domesticated Atlantic salmon.

Farming of Atlantic Salmon, Salmo salar, occurs throughout the species’ natural range and escapes from fish farms are an annual occurrence. Farmed strains of salmon have been bred for traits such as increased growth rate and size relative to their wild conspecifics, with all strains of farmed Irish salmon coming from limited Norwegian founding stock. Previous work has shown that the F1 and F2 hybrids between wild and farm salmon have reduced lifetime fitness compared to pure wild salmon stock.

My research shall focus on developing an eco-genetic model to predict what specific adaptive phenotypes are divergent between wild and farmed salmon and how such divergence depresses the overall fitness of hybrid progeny. The model will utilise quantitative traits to examine the phenology mismatch and will also incorporate various predicted future climate scenarios, in order to quantify how climate change is likely to impact upon hybrid populations’ fitness and persistence.


Project Title:  The biology of farmed Atlantic salmon (Salmo salar) in the wild.

Farmed Atlantic salmon (Salmo salar) represent a group of individuals extracted from the wild and selected for commercially viable traits. This selection has resulted in a suite of genetic and trait specific differences between farmed salmon and wild conspecifics. When these farmed salmon escape, they often swim upstream to spawning habitat and if mature they can breed with local wild populations, thus introducing their genes to the natural spawning pool.  Their hybridised progeny show reduced survival and fitness in natural environments, therefore continuous or large scale escape events may have evolutionary consequences for wild populations through introgression and gene flow. 
The aim of my PhD is to understand the energetic mechanisms of this reduced fitness. A number of experimental families of pure farm, pure wild, F1 hybrids and captive-bred origin have been placed under common environment conditions in the wild. Through seasonal sampling, I am monitoring the comparative energy phenotypes of these experimental fish with an aim to reveal the underlying physiological, behavioural and genomic determinants of fitness in the wild. My research is particularly relevant for climate change models and will provide insight into projected impacts that farm escapes pose for wild populations in a changing world.
Sarah Ryan
Michele De Noia

My core interests are marine conservation, genomics and microbiome. I am a passionate advocate for the sustainable exploitation of marine resources and for biodiversity conservation with a special interest in endangered species.

The focus of my PhD will be the difference in microbiome and host-parasite interaction between the two different yellow eels ecomorph: broad and narrow head. I will try to understand if ecomorph diversity have stable and predictable consequences on energetics including maximal metabolic rate, standard metabolic rate and lipid content and rate of lipid accumulation. How the diet and the ecomorph diversity predicts gut microbial complement and biochemistry more robustly than salinity preference. I will try to characterise the immune genes and immune gene expression involved in the differentiation of the ecomorph and the difference between eels parasitise with A. crassus or not. I will try to define declining A. crassus abundance in infected catchments using adaptive immunity and clearance rather than swim bladder destruction with a definition of a new vaccine targets. To understand the parasite dynamic, A. crassus, I will conduct also a second host survey to understand the epidemiology and the principal vector taxa.

Project Title:  Genotype and phenotype mapping of the three-spined sticklebacks in the Burrishoole system
My work is focused on the three-spined stickleback (Gasterosteus aculeatus), a well-studied species in many research areas. Previous studies have shown that three-spined sticklebacks have recolonized freshwater environments from the sea after the last glacial maximum. This event induced an adaptive radiation resulting in several ecotypes. In the Burrishoole catchment, previous studies have highlighted three different ecotypes living in distinct habitats: fresh, brackish and marine environments. No proof of hybridization have been observed despite some connected areas.
The goal of my PhD is to study the biological and ecological characteristics of these three ecotypes to understand the population dynamic in the wild and the potential barriers between them. For that, I will use a multidisciplinary approach including morphometric traits, diet analysis, parasites communities, gut microbiota, behaviour and aerobic scope. I will also run a common garden to get some F1 and potentially F2 generations to study the genetic and genomic architecture. My research aims to study the evolution in action under divergent ecological pressures and more broadly, to monitor adaptation in a context of global changes. It is a part of the Beyond2020 project whose main goals are to understand, predict and communicate the role and responses of aquatic ecosystems in a global changing environment.
Floriane Leseur
Raminta Kazlauskaite

Project Title SalmoSim: Exploring the microbial basis of Atlantic Salmon energetics via a synthetic intestinal system.

I’ve just graduated from The University of Edinburgh, where I finished BSc Hons Cell Biology. I am interested in bioengineering and molecular biology.  Currently my PhD focuses on creating an in vitro system replicating the Atlantic Salmon gut, which can be later used as a test-bed to analyse salmon microbial fermentation of novel feeds as well as the effectiveness of pro, pre and symbiotic. 

Currently my PhD focuses on the gut microbiota of Atlantic salmon and its link with host metabolism, physiology and behaviour via microbiological methods.  By amplifying bacterial 16S rRNA, I aim to explore the Atlantic salmon gut microbiota in the hope of improving aquaculture sustainability.  I am interested in links between the gut microbiota and host behaviour and the mechanisms behind this and is therefore hoping to explore this further.








Eleanor Lindsay
Patrick Schaal

My PhD focuses on the microbiota in the gut of Atlantic salmon.

Currently I am working with three different cohorts of salmon; wild, farmed and hybrid.  My research aims to disentangle the genetic and environmental effects on host microbiomes and also to monitor bacterial impacts on phenotypic traits (e.g. metabolism, immune response).