- To investigate the significance of environmentally-induced epigenetic variations as a source of phenotypic plasticity for asexually reproducing organisms
- To determine if selection favours asexual genotypes with a high capacity for epigenetic-mediated plasticity
- To learn and use methodologies such as WGBS, RNA-seq and Chip-seq as well as to learn computational epigenetics
As natural populations face unprecedented rates of environmental change, understanding the underlying mechanism behind plasticity, adaptation and driving forces of evolution is paramount if we are to predict how and which populations and species are most likely to cope and which are most vulnerable to extinction. The key for this prediction lies partly in understanding the basis of molecular and phenotypic plasticity and epigenetic variation. The ecological importance of phenotypic plasticity, especially for asexual species, has long been recognised as a means of adaptive strategy and survival when organisms are exposed to variable environments. In asexual species epigenetic variation and plasticity is thought to drive phenotypic plasticity. Epigenetic modifications and plasticity is achieved by altering the expression of the genes in response to environmental cues without modifying the DNA sequence. Thus it is thought that selection usually favours species with high capacity for epigenetic plasticity. The environmentally-induced epigenetic variations not only can provide higher adaptive capacity throughout the lifespan of an individual but also have the potential to provide higher epigenetic plasticity in subsequent generations, providing them with a survival advantage upon encountering a similar stressor.
In this project, the epigenetics of plasticity and adaptation will be investigated in two phenotypically plastic sentinel species, Chlamydomonas reinhardtii and Daphnia magna. During this project the student will set out to: 1) generate and select Chlamydomonas reinhardtii and Daphnia magna strains tolerant to several environmentally relevant stressors, 2) To identify epi-alleles associated with phenotypic plasticity and adaptation, 3) To investigate the potential of inheritance of epigenetically-acquired plasticity in non-exposed subsequent generations. Overall, this project will result in achieving a better understanding of how species evolve in response to fluctuations in their natural habitats.
During this project the student will work in the newly established Daphnia Facility (part of the £2m investment into Environmental Omics) at University of Birmingham. During this time the student will learn about Daphnia biology and culturing as well as conducting actute and chronic exposures according to the OECD guidelines. Most importanly, this is a cross-disciplinary project utilising state-of-the-art technologies, such as RNA-seq, whole genome bisulfite sequencing (WGBS) and reduced representation sequencing (RRBS). These approaches will resut in generation of substantial amount of complex data which will require traning in computational biology and modelling.
Training and Skills
CENTA students are required to complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to the student's projects and themes.
Specialist training will be provided in environmental epigenomics and genomics, toxicology, risk assessment and computational biology by Mirbahai, Coates and Colbourne.
Year 1: Learn an array of skills in molecular and environmental toxicology, in particular epigenomics, transcriptomics, and computational biology, as well as learning how to conduct high quality toxicity testing in Daphnia. Establish and validate a robust experimental set-up to study the epigenetics of adaptation.
Year 2: Conduct multigenerational selection assays to: 1) generate tolerant strains, 2) profile the transcriptome and methylome of the tolerant and sensitive strains, 3) analyse the complex sequencing datasets and to link epiallels with phenotypic endpoints
Year 3: During this year the student will investigate the potential of inhertance of the epigenetically-mediated phenotypic plasticity and higher level of tolerence to stressors.
Partners and collaboration (including CASE)
This project will align with and build upon the ongoing NERC funded project: Cracking the Code of Adaptive Evolution (PI: John Colbourne, Co-PIs: Luisa Orsini, Mark Viant, Leda Mirbahai, Shan He, Lindsey Leach). Thus the PhD student will not only benefit from the expertise of the two post-doctoral fellows working on this project but will also benefit from the involvement of the project partners and collaborators listed on this grant application. This project and the NERC funded project, are part of a major research activity to understand the inter-relationships between phenotypic plasticity, epigenetic change and conventional evolution by natural selection.
We seek an exceptional candidate with a life sciences undergraduate degree (First class honours), or Master’s degree (can be pending) with the latter in fields such as bioinformatics or epigenetics. Knowledge of computational skills and prior experience of working with Unix/Linux command line environments, SQL, as well as either Perl, Python, Ruby or a comparable scripting language will be desirable. Previous work experience in research laboratories (e.g. internships), publications and research prizes will be advantageous. To apply, the applicant is required to complete and highlight all their relevant expertise and academic achievements in the CENTA studentship application form as well as the University of Birmingham online application form. Pre-application enquiries are encouraged. For further information and enquires contact: firstname.lastname@example.org