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*EASTBIO* Bayesian approach to model evolutionary trajectories in experimental evolution

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  • Full or part time
    Dr C Kosiol
    Prof M Ritchie
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

BBSRC Thematic Group: Frontier Bioscience
When populations adapt to new environments (e.g., new temperatures or new diets) this often leaves signatures in the genome. With Evolve and Resequencing (ER) studies we try to repeat these processes under controlled settings to gain insight into the process of adaptation.
1) The PhD student will develop a novel Gaussian process model-based analyses of allelic frequency changes under selection, which incorporate prior information about shifts in the environment and allow tracking of the course of gene frequency changes during adaptation. The Kosiol group has devised a preliminary Gaussian process model for the trajectories of experimental evolution studies (Topa et al.,2015). The student will extend the Gaussian process models by inferring (i) the timing of the genetic response, and (ii) the influence of genomic structure varying spatially along the chromosomes.
2) The PhD student will analyse real data from experimental evolution studies by the groups of Lesley Lancaster (University of Aberdeen) on the seed beetle Callosobruchus maculatus and on Drosophila species by Mike Ritchie (Universtity of St Andrews). We will resequence frozen samples to monitor allele frequencies over the generations in multiple populations resulting in time-series data. This is only possible because of recent advances in fast and cheap whole-genome sequencing.
3) We further aim to understand specific loci, gene networks, and genetic pathways associated with different timings of the genetic response.
The project is a collaboration between Dr Carolin Kosiol (CK, University of St Andrews), Prof Mike Ritchie (MR, University of St Andrews) and Dr Lesley Lancaster (LL, University of Aberdeen). CK is a recently appointed Lecturer in Bioinformatics, she has developed models for experimental evolution data and has experience with handling large scale Next Generation Sequencing data sets. MR is a world-renowned evolutionary biologist who has published >150 papers including influential research on the interplay between sexual selection, genetics and the process of speciation. MR’s recent research projects include a series of papers on measuring genomic responses to experimental evolution under altered sexual selection in Drosophila (e.g., Veltsos et al., 2017). LL has gained international recognition for her conceptual advances in eco-evolutionary dynamics of thermal tolerances, food resource use, and life history (e.g., Lancaster, 2016).

Funding Notes

This project is eligible for the EASTBIO Doctoral Training Partnership: http://www.eastscotbiodtp.ac.uk/

This opportunity is only open to UK nationals (or EU students who have been resident in the UK for 3+ years immediately prior to the programme start date) due to restrictions imposed by the funding body.

Apply by 5.00 pm on 5 January 2020 following the instructions on how to apply at: http://www.eastscotbiodtp.ac.uk/how-apply-0

Please also upload the EASTBO Application Form as an additional document to the University of St Andrews online Application.

Informal inquiries to the primary supervisor are very strongly encouraged.

References

Topa et al. (2015) Bioinformatics 31:1762. Veltsos et al. (2017) Nat Commun 8:2072. Lancaster (2016) Nat Climate Change 6:618.

Related Subjects

How good is research at University of St Andrews in Biological Sciences?

FTE Category A staff submitted: 50.45

Research output data provided by the Research Excellence Framework (REF)

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