Report

Teaser, summary, work performed and final results

Periodic Reporting for period 3 - ALH (Alternative life histories: linking genes to phenotypes to demography)

Teaser

\"Understanding how and why individuals develop strikingly different phenotypes, or follow alternative life history pathways, is a major goal in evolutionary biology. It is also a prerequisite for conserving important biodiversity within species and predicting the impacts of...

Summary

\"Understanding how and why individuals develop strikingly different phenotypes, or follow alternative life history pathways, is a major goal in evolutionary biology. It is also a prerequisite for conserving important biodiversity within species and predicting the impacts of environmental change on wildlife populations. The aim of this ERC project is to examine alternative migratory and life history tactics in fish using brown trout (Salmo trutta) as a model system. This species exhibits \"\"facultative anadromy\"\", a phenomenon where some trout (known as anadromous individuals) migrate to sea for part of their lives, while others from the same population remain resident in freshwater and never go to sea. The two forms are known to interbreed on returning to shared freshwater spawning areas and anadromous parents are capable of producing non-anadromous offspring, and vice versa. Many important questions remain, however, regarding the relative importance of genetic versus environmental factors in shaping migratory phenotypes, the genetic architecture of facultative anadromy and associated traits such as age and size at first reproduction, and the speed with which tactic frequency can evolve or respond to ecological changes via phenotypic plasticity.

Our team are examining these and other questions using a combination of large-scale laboratory and field experiments, integrating several previously independent perspectives from evolutionary ecology, ecophysiology and genomics. Recent advances in molecular parentage assignment, quantitative genetics and genomics (next generation sequencing and bioinformatics) will allow novel insights into how complex phenotypes are moulded by the interaction between genes and environment. To provide additional mechanistic understanding of these processes, the balance between metabolic requirements during growth and available extrinsic resources will be investigated as the major physiological driver of migratory behaviour. Together these results will be used to develop a predictive model to explore the consequences of rapid environmental change for trout populations, accounting for both ecological and evolutionary processes.

The results of this project will generate general insights into facultative migration, a phenomenon not limited to trout (e.g. many fish, bird and insect species exhibit co-existing migratory and non-migratory forms). Migration is a crucial aspect of biological responses to climate change and better understanding of how (and the speed with which) populations can shift their migratory tactics will inform conservation and adaptive management strategies. Salmonid fishes are iconic and economically important species in European freshwaters and coastal seas, and this project strives to increase knowledge of their basic biology. Our goal is to create a predictive model informed by empirical data that can eventually be used to explore how facultatively anadromous salmonid populations might respond to human-induced changes in their environments.

More generally, humans may value certain phenotypes over others (e.g. so-called trophy specimens, such as the biggest fish in a population, or animals with the largest horns or antlers), but often our actions lead unintentionally to the demise of the very thing we value more. For example, fishing activities may preferentially target the larger sea-going trout in a population, effectively selecting against any genes involved in anadromy or large body size. Harvested fish populations may therefore evolve changes in migration behaviours, or in age and size at maturation, with potential consequences for their resilience in the face of environmental change, and/or knock-on impacts on other species and the wider ecosystem. By improving our understanding of eco-evolutionary processes in wild or semi-wild populations, the insights from this project may help to guard against such unintended consequences.
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Work performed

This project (code name ALH, for “alternative life histories”) has four interlinked goals:
1. To analyse how genes and environment interactively determine ALH tactics, using two large-scale experiments (one laboratory-based, the other field-based);
2. To relate ALH tactics to variation in how fish acquire and utilise energy;
3. To advance understanding of the genomic basis of ALH tactics in variable environments;
4. To explore how environmental change might lead to rapid life history shifts in facultatively migratory populations using an eco-genetic simulation model.

Here follows a brief summary of progress to-date on each goal:

Goal 1:
Two large-scale experiments were planned as part of Goal 1 (note that the data and samples generated by these experiments also feed into Goals 2-4). The first of these experiments is a lab-based study, where trout sourced from different populations in the West of Ireland are being reared in tanks in an indoor recirculating aquaculture system (RAS). Our primary objective in the first 18 months of this project has been to set up this RAS and to get this crucial experiment up-and-running. This required a considerable amount of work, as while there was some existing equipment already in place at the Host Institute, much of it was old and needed replacing, and we also decided to change the original experimental design slightly in order to increase the chances of success. Originally, the plan was to have two separate recirculation systems running simultaneously, each on a different temperature regime (because a major aspect of this experiment is to explore the effects of temperature on trout life history decisions and associated metabolic mechanisms). That original design had one major limitation, however, in that there would have been no replication – i.e. there would be one set of inter-linked tanks in the “normal temperature” treatment, and another set of inter-linked tanks in the “high temperature” treatment. While we would have strived to keep all other factors constant across these treatments, we could not have guaranteed this.

Thus we decided to instead build a single, large RAS that contains 18 tanks all connected to the same filtration systems. Once the water that drains from these tanks has passed through mechanical and biological filters, it then flows into two separate sumps. The temperature in each sump is controlled by separate conditioning units, and thus one can be set to “normal temperature” and the other to “high temperature”). The water is then pumped from both sumps around to the tanks, but each tank then has a “tap” that can be either set to “warm” (i.e. water from warm sump flows into tank) or “cold” (i.e. water from cold sump flows in). This gives us full tank-level control over water temperature and allows for replication across tanks of a given water temperature treatment. Moreover, the water from all tanks remixes as it drains out and goes through the same filtration processes, plus the light-levels and oxygen levels for each tank are carefully controlled and standardised. Hence the only thing that varies between tanks is water temperature and/or food supply (each tank has its own automatic feeder, and food is the second variable of interest that we are manipulating in this experiment), which is a more robust experimental design than the original plan.

The construction of this system required both the re-use of old components from the pre-existing systems, and the purchasing of new components, new tanks and automatic feeders and lights. This system is now fully up-and-running and the experiment is underway.

A PhD student (Ms Louise Archer) was taken on to work specifically on this lab-based fish rearing experiment, and a Research Assistant (Mr Stephen Hutton) was also hired to oversee the construction of the system and the day-to-day running of the equipment, fish husbandry and health, and data recording. After careful d

Final results

The main progress made so far on this ERC project has been:

* To set up a large-scale, challenging laboratory (aquaculture) experiment. Here we are exploring how food quantity and temperature interactively affect life history decisions, which has never before been tested in the context of facultative anadromy in salmonids. Moreover, we have fish from different genetic backgrounds in this experiment, allowing us to tease apart the relative roles of genes versus environment (i.e. G x E interactions). G x E is a fundamental topic in modern evolutionary biology that remains poorly understood, particularly in non-model organisms, and hence we aspire to break new ground here.

This laboratory (aquaculture) experiment, pertaining to Goal 1 of the ALH project, is now nearing completion (as of 1 June 2018). This experiment was always risky, in that many things can go wrong in recirculating aquaculture systems (RAS) such as technical equipment failures, or fish disease etc. However, we successfully took the experiment to full completion, with no major problems along the way, and we intend to publish a series of papers in the coming months based on the data from this experiment.

* A common garden experiment has been initiated in a wild river system in the West of Ireland, and data collection, analysis efforts and paper writing associated with experiment are ongoing (experiment will continue through to the end of the overall ALH project). This experiment involves rearing trout from different genetic backgrounds (including population-hybrids) within a fully wild, experimental river system. Common garden experiments allow inferences to made regarding the extent to which phenotypic differences among populations (in this case related to migratory, life history and associated energetic traits) have a genetic basis versus being shaped by phenotypic plasticity. Additionally, this common garden experiment doubles as a local adaptation experiment – and again, such experiments are few-and-far-between in fishes, or vertebrates in general, owing to the logistical difficulties involved. We expect the results to therefore generate one or more high-impact publications. Data collection, analysis efforts and paper writing associated with this experiment are ongoing (experiment will continue through to the end of the overall ALH project).

* A pilot genome-wide association study (GWAS) has been successfully undertaken, where the aim is to identify chromosomal regions associated with anadromy and migration in Salmo trutta. The results have highlighted several candidate genomic regions, into which we are now looking further. This pilot study has formed the basis for a much larger genomic study of broader geographic scope we are currently implementing, which we hope will identify, with greater precision and power, genes underlying anadromy. While recent work on steelhead/rainbow trout in North America has made substantial advances in this area, studies on brown trout in Europe have lagged far behind. The “holy grail” of this aspect of the project is identity actual genes involved in alternative life histories, which would represent a major scientific advance of both fundamental and applied relevance (e.g. for the aquaculture, fish farming and fishing industries).

* Significant progress has been made in developing a modelling framework to address Goal 4 of the ALH project (“To explore how environmental change might lead to rapid life history shifts in facultatively migratory populations using an eco-genetic simulation model”.)

* By drawing attention to fundamentally important biological questions in an iconic species of major economic importance in Europe, this ALH project aspires to enhance the wider societal impacts of evolutionary ecology research and ultimately to generate results that will be of practical utility to fisheries managers and conservation biologists.

* An important element of the ALH project is also the training of the n

Website & more info

More info: http://fisheye.ucc.ie/.