Project Description

A full project description can be found on Find a PhD. Please see below for additional information about this project:

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.

Essential skills

  • 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 skills

  • Experience in fieldwork
  • Experience in handling large high-throughput sequencing datasets
  • Experience in Linux-based bioinformatics computing

Photo by Davina Derous.

Supervisors

Marius Wenzel

Primary Supervisor:

Profile: Marius Wenzel
Email: marius.wenzel@abdn.ac.uk
Institution: University of Aberdeen
Department/School: School of Biological Sciences

Sarah Helyar

Secondary Supervisor:

Profile: Sarah Helyar
Email: s.helyar@qub.ac.uk
Institution: Queen's University, Belfast
Department/School: School of Biological Sciences

Stuart Piertney

Additional 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
Lab page

Research Methods

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 morphotypes; 2) change gene expression 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 morphotypes. 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 will examine genome-wide divergence between morphotypes, which will require extensive fieldwork (UK/Ireland) in year 1 to collect samples. The molecular work and data analyses are expected to be completed half-way through year 2, depending on logistics.

The second work package will involve lab experimentation on a subset of samples collected in year 1 that will be maintained in microcosms. The molecular work and analyses are expected to be completed by the end of year 2, though this is flexible and logistics associated with WP1 may mean that this work is likely to be completed concurrently with WP1. The 3-month internship will take place by the end of year 2, once experimentation has been completed.

The final package will use results obtained from WP1+WP2 to identify a suite of candidate genes that are then examined in a large set of field samples obtained in year 1 and supplemented by additional fieldwork in year 3 if required. This work is expected to be completed by end 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

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