Project Description
Understanding how marine organisms respond to acute environmental stressors such as pollution and chronic stressors such as climate change is essential for managing and conserving coastal marine ecosystems. A major knowledge gap is the extent to which individuals vary in responding to stress, what mechanisms underly these differences and how this variation then affects resilience at a population-, species- and ecosystem level.
Functional genomics tools provide a wealth of opportunity for identifying and monitoring short-term and long-term molecular responses to stress in the form of changes in gene expression, RNA splicing or epigenetic information such as DNA methylation. This information offers novel and innovative approaches for monitoring and predicting physiological and evolutionary responses to stress, that can then be used in conservation and management to understand population vulnerability or resilience to environmental change.
This project will use the common intertidal beadlet anemone Actinia equina as a powerful model system for examining these issues. In this species, environmental stressors such as temperature and oil pollution disrupt feeding, reproduction and social behaviour, leading to population perturbation and knock-on effects on intertidal communities. Intriguingly, these responses vary distinctly between two colour morphs that differ markedly in ecology and physiology and have been proposed to be, in fact, separate species [1-3]. However, we do not know the functional genomic basis of this physio-ecological divergence and how this may affect capacity for resilience to enduring environmental stress.
In this project you will combine extensive fieldwork along Scottish and Irish coasts with controlled microcosm experiments in the lab and state-of-the-art molecular tools to identify functional genomic differences between Actinia equina morphs. You will address questions such as:
- What genes change expression, splicing or methylation in response to environmental stress?
- What are the differences in these molecular responses between the colour morphs?
- How is genetic diversity at important stress-response genes structured in populations and between colour morphs?
- Do genome-wide patterns of divergence between colour morphs suggest additional cryptic species divergence?
You will gain comprehensive training in a range of functional ‘omics technologies including the very latest DNA/RNA sequencing approaches, coupled with extensive training in bioinformatics and biostatistics analyses. The QUADRAT DTP further provides an extensive training programme for developing transferable professional skills. You will be part of vibrant postgraduate communities at the University of Aberdeen and Queen’s University Belfast. Both institutions provide extensive state-of-the-art research facilities for molecular work, experimental work in microcosms, and high-performance bioinformatics computing.
The project provides an exciting opportunity to address a fundamental issue in marine evolutionary biology using cutting-edge genomics approaches and will also contribute to a much broader understanding of the evolutionary resilience that will allow organisms to persist and adapt in the face of environmental change. You should have strong interest and ambition in evolutionary biology, genomics and bioinformatics. Previous experience in working with genomics data is desirable but not essential because full training will be provided. You will have the opportunity to develop the project in directions to suit your interests.
Essential & desirable candidate skills
Essential: Background in evolution, genetics and marine ecology. Clean driving license for fieldwork. Experience in molecular lab techniques (e.g., DNA/RNA extraction, PCR). Experience in statistical data analysis in R or similar.
Desirable: Experience in fieldwork. Experience in handling large high-throughput sequencing datasets. Experience in Linux-based bioinformatics computing.
Supervisors
Marius WenzelPrimary Supervisor: | Profile: Marius Wenzel Email: marius.wenzel@abdn.ac.uk Institution: University of Aberdeen Department/School: School of Biological Sciences |
Sarah HelyarSecondary Supervisor: | Profile: Sarah Helyar Email: s.helyar@qub.ac.uk Institution: Queen's University, Belfast Department/School: School of Biological Sciences |
Stuart PiertneyAdditional Supervisor: | Profile: Stuart Piertney Email: s.piertney@abdn.ac.uk Institution: University of Aberdeen Department/School: School of Biological Sciences |
Additional Supervisor: | Dr Craig Wilding Liverpool John Moores University, School of Biological and Environmental Sciences Email: C.S.Wilding@ljmu.ac.uk |
References
[1] https://doi.org/10.1016/j.jembe.2017.07.011
[2] https://doi.org/10.1111/1365-2656.13301
[3] https://doi.org/10.1016/j.jembe.2018.10.001
Research Methods
The project will involve a significant amount of intertidal fieldwork to collect samples for DNA extraction, and live anemones for experimentation in microcosms. A driving licence for standard cars is required. The fieldwork will take place primarily in Scotland and Ireland; there might be scope for additional sampling beyond these localities. The fieldwork will take place primarily in the first year, though additional field trips may be undertaken later in the project.
Experimental work will be carried out in dedicated microcosms allowing for manipulating environmental factors such as temperature, salinity or pollution. The project will use DNA and RNA sequencing to identify genomic regions that 1) are diverged between Actinia equina morphs; 2) change gene expression, splicing and/or DNA methylation in response to environmental stress; and 3) show spatial structure on a landscape scale. It is anticipated that Illumina sequencing will be used to identify candidate genes in a relatively small sample set, which will then be examined using targeted PCR-based approaches to characterise a much more extensive sample set across many populations. The project also provides scope for using the latest Oxford NanoPore sequencing technology to characterise alternative splicing patterns or nucleotide modification associated with experimental intervention.
Impact
This research will contribute to both academic and broader socio-economic impact. First, identifying the genomic basis of species divergence in a group of sessile marine organisms with highly diverse reproductive strategies will help our understanding of the fundamental mechanisms through which marine biodiversity is generated and maintained. Such knowledge is instrumental in predicting how biodiversity may be disrupted or promoted by global change.
Second, identifying the molecular basis of physiological responses of Actinia to environmental stressors will provide a better understanding of how anthropogenic disruption to marine ecosystems elicits adaptive responses from populations through to community-level effects. Actinia is particularly sensitive to environmental disturbance and is an important component of the intertidal ecosystem. Its sessility and rapid behavioural response to stress makes Actinia a particularly well-suited species for studying intertidal ecosystem resilience. Insight gained from this project will promote the development of Actinia as an ecotoxicological bioindicator species and will inform costal conservation management in light of decommissioning, pollution and climate change.
Finally, this research will lay foundational work for characterising the physio-biochemical repertoire of Actinia, which will help identify potential bioactive compounds of pharmaceutical and biotechnological interest. Marine organisms such as anemones are underexplored sources of such compounds and hold great potential in discovering novel therapeutics, toxins and other resources. Insight obtained from the functional genomics component of this project will directly inform further work in biochemistry and biotechnology.
Proposed Supervision
The project is supervised by a strong team of evolutionary geneticists, ecologists and bioinformaticians from three institutions. Dr Marius Wenzel is a research fellow in functional evolutionary genomics and bioinformatics at the University of Aberdeen. He will lead supervision on all aspects of the project, with a particular focus on navigating the landscape of high-throughput sequencing approaches, bioinformatics and biostatistics analyses. Dr Sarah Helyar is a molecular ecologist at Queen’s University Belfast and has extensive experience in marine population genetics and conservation, with a strong focus on applying genomics to field populations. She will contribute her expertise in marine landscape-scale population genomics studies and conservation management. Prof Stuart Piertney is Chair in Molecular Ecology and Evolution at the University of Aberdeen and has long-standing experience in using molecular markers to address ecological and evolutionary questions in natural populations. He will contribute his expertise in speciation genomics, phylogeography and intertidal ecology, and will help interpret results from all genomics analyses. Dr Craig Wilding is an evolutionary geneticist at Liverpool John Moores University. He has pioneered genomics work on Actinia equina, publishing a reference genome and characterising mitogenomic divergence between colour morphs. He will contribute his experience in the reproductive biology and genomics of the study system.
Proposed Timetable
The project will be divided into three broad work packages:
The first work package (WP1) comprises extensive field work (UK/Ireland) to build a comprehensive DNA databank that later work packages will rely on. Tissue samples will be taken and preserved in situ. Live individuals will be collected from a limited number of field sites and transported back to the laboratory where they will be maintained in aquarium facilities and protocols for phenotypic measurements and DNA/RNA extraction will be optimised. This work is expected to be completed within the first half of year 2.
The second work package (WP2) involves experimental trials on live individuals maintained in microcosms, followed by DNA/RNA extraction and high-throughput sequencing. After pilot experiments to optimise experimental protocols, the main experiments are expected to be completed by the end of year 2. The 3-month internship will then take place once experimentation has been completed.
The third work package (WP3) comprises extensive analysis of the DNA/RNA sequencing data obtained in WP2 to develop a suite of candidate genes that will then be genotyped throughout the extensive DNA samples obtained in WP1, with opportunity to supplement spatial coverage by additional fieldwork if required. The genotyping and subsequent phylogeographic/population genetics analyses are expected to be completed within the second half of year 3.
Time for writing up thesis chapters and publications is allocated throughout the project, depending on when work packages are completed, and at least the final 6 months are dedicated to completing the thesis.
QUADRAT Themes
- biodiversity
Partners
Not applicable at this time.
