The recent sequencing of genomes of closely related species and of many individuals from the same species enables the study of speciation and the inference of the history of populations. Standard phylogenetic methods reduce entire populations to single points in genotypic space by modelling evolution as a process in which a single gene mutates along the branches of a phylogeny. In this project, we envisage developing new theory and software to tackle the problem of species tree estimation.
In our group, we have developed a new method called POlymorphisms-aware phylogenetic MOdel (PoMo). It extends any DNA substitution model and additionally accounts for polymorphisms in the present and in the ancestral population by expanding the state space to include polymorphic states in a continuous-time Markov process (DeMaio et al., 2016). PoMo performs well incomplete lineage sorting because ancestral populations can be in a polymorphic state. We have estimated species trees from neutrally evolving sites of genomes of recently diverged populations such as baboon species (Rogers et al., 2019)
While this approach substantially enhanced the tools available to study speciation, a major gap remains in that traits – which are key to many speciation events (Servedio et al., 2011) – were not implemented in these models. In this PhD project, the student will fill this gap by extending the PoMo approach to trait evolution, in order to build more realistic models of speciation.
The group is also interested in analysing data from evolutionary processes at very short time-scales such as time series of expression data for different species as they are observed in experimental evolution studies (e.g. on fruit flies).
The project is particularly well-suited for students with a keen interest in computational biology, phylogenetics, or population genetics. Prior experience in programming (python, C++ or Java) or statistics would be a plus.
Informal enquires should be send to Carolin Kosiol ([Email Address Removed] )
How To Apply
Please make a formal application to the School of Biology through our Online Application Portal.
We require the following documents; CV, personal statement, 2 references, academic qualifications, English language qualification (if applicable).
Keywords: Evolutionary Genomics, Phylogenomics, Modelling, Bioinformatics, Computational Biology
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