Prof Cock Van Oosterhout, Prof Thomas Mock, Prof Anna Godhe, Dr T Wu
No more applications being accepted
Competition Funded PhD Project (European/UK Students Only)
About the Project
Background
Recent research by our group (Mock et al. (2017) Nature 541, 536-540) discovered a previously unknown evolutionary mechanism in the diatom (Fragilariopsis cylindrus) that enables it to thrive in the extreme polar environment. This species can survive polar winters while frozen in the sea ice, and it can form blooms when the conditions turn favourable again in the spring. We discovered F. cylindrus can rapidly adapt to these dramatically changing environmental conditions by the up- and down-regulation of alleles at many genes (~3,500). The alleles appear to have diverged from each other under Darwinian selection, so that each allelic copy is adapted to a particular environmental condition. Importantly, a current large algal genome project on Skeletonema marinoi also shows high levels of divergence of alleles, suggesting that this previously unknown evolutionary process is much more widespread.
The principal objective of this PhD project is to understand how diatoms can respond to global environmental change.
Methodology
This PhD studentship will investigate the signature of natural selection in multiple genomes of S. marinoi that have been (and are currently being) sequenced. These samples are from a sediment core from the Loviisa nuclear power-plant in Finland (and a nearby control site). The sediment core samples (1980–2000) enable us to “look back into time” over a time period during which the local seawater temperature rapidly increased (from the cooling water of the power-plant). The student will conduct population genomic analyses using bioinformatics to understand how diatoms adapt to environmental change.
Training
The student will part of a large research group and will employ and develop population genomic software to enable the processing and interpretation of these “big data”. The samples are provided by our Swedish collaborators (Prof Anna Godhe) and enable us to analyse adaptive evolution caused by environmental warming. The student will visit the lab in Sweden three times during this project.
Secondary supervisors: Professor Thomas Mock (UEA), Professor Anna Godhe (University of Gothenburg), Dr Taoyang Wu (UEA).
Person specification
We are looking for a highly-motivated student with good understanding of evolution and population genetics, who has some experience with bioinformatics.
This project has been shortlisted for funding by the EnvEast NERC Doctoral Training Partnership, comprising the Universities of East Anglia, Essex and Kent, with over twenty other research partners. Undertaking a PhD with the EnvEast DTP will involve attendance at mandatory training events throughout the course of the PhD.
Shortlisted applicants will be interviewed on 12/13 February 2018.
For further information, please visit www.enveast.ac.uk/apply
For more information on the supervisor for this project, please go here: https://www.uea.ac.uk/environmental-sciences/people/profile/c-van-oosterhout
Type of programme: PhD
Start date of project: October 2018
Mode of study: Full time or part time
Length of studentship: 3.5 years
Acceptable first degree: Biology, Computational Biology, Evolutionary Biology, Genetics, and related subjects.
EnvEast welcomes applicants from quantitative disciplines who may have limited background in environmental sciences. Excellent candidates will be considered for an award of an additional 3-month stipend to take appropriate advanced-level courses in the subject area.
Minimum entry requirement: 2:1 or equivalent.
Funding Notes
Successful candidates who meet RCUK’s eligibility criteria will be awarded a NERC studentship - in 2017/18, the stipend is £14,553. In most cases, UK and EU nationals who have been resident in the UK for 3 years are eligible for a stipend. For non-UK EU-resident applicants NERC funding can be used to cover fees, RTSG and training costs, but not any part of the stipend. Individual institutes may, however, elect to provide a stipend from their own resources.
References
(i) Mock, T., Otillar, R. P., Strauss, J., McMullan, M., Paajanen, P., Schmutz, J., ... van Oosterhout, C. & Allen, A. E. (2017). Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature, 541(7638), 536-540.
(ii) Bentkowski, P., van Oosterhout, C., Ashby, B., & Mock, T. (2017). The effect of extrinsic mortality on genome size evolution in prokaryotes. The ISME journal, 11(4), 1011.
(iii) Schmidt, K., van Oosterhout, C., Collins, S., & Mock, T. (2016) The role of phenotypic plasticity and epigenetics in experimental evolution with phytoplankton. Perspectives in Phycology, 3, 29-36.
(iv) Bentkowski, P., van Oosterhout, C., & Mock, T. (2015). A model of genome size evolution for prokaryotes in stable and fluctuating environments. Genome Biology and Evolution, 7(8), 2344-2351.
(v) Ward BJ, van Oosterhout C (2016). Hybridcheck: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data. Molecular Ecology Resources 16 (2), 534-539.
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