When populations adapt to new environments (e.g., new temperatures or diets) this often leaves signatures in the genome. With Evolve and Resequencing (ER) studies we try to repeat these processes under controlled settings. Such new genetic approaches are transforming our ability to measure and understand genetic adaptation, but statistical analyses of such new data are not keeping pace with the ability to generate data.
A common experimental design of ER studies is to monitor allele frequencies while a population adapts to a novel treatment and compare it to a control population that does not undergo this treatment. In such systems it is very important to estimate the point when the two populations begin to diverge, the genetic response time. We bring the well-studied adaptation of Drosophila sechellia to the fruit Morinda citrifolia (“noni”) in the wild to the laboratory. Octanoic acid is a main toxic compound of the fruit of Morinda citrifolia, but D. sechellia has evolved tolerance. We will propagate populations exposed to octanoic acid food as well as control populations. The PhD student will work with researchers at the University of St Andrews and University of Aberdeen to address three goals:
1) The PhD student will generate data by carrying out an experimental evolution study on the closely related Drosophila yakuba species for adaptation to novel food resources. We will use an 'evolve and resequence' class of experimental protocols 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.
2) 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.. 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.
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. 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).
1. Topa H, Jónás Á, Kofler R, Kosiol C, Honkela A (2015). Gaussian process test for high-throughput sequencing time series: application to experimental evolution. Bioinformatics 31:1762.
2. Veltsos, P, Fang, Y, Cossins, AR, Snook, RR & Ritchie, MG (2017). Mating system manipulation and the evolution of sex-biased gene expression in Drosophila. Nature Communications 8:2072.
3. Lancaster (2016) Widespread, ongoing range expansions shape latitudinal variation in insect thermal limits. Nature Climate Change 6:618.
To apply for this project, please go to this link.