PhD Scholarship in Molecular Evolution at Uppsala University

Applications are invited for a PhD position in computer science to join Uppsala University. The funding allows successful candidate to work for four years. Applications should be sent before May 13, 2019.

Project description: One of the major objectives in evolutionary genetics is to understand the molecular basis and mechanisms of phenotypic variation and differentiation between species. Two classical candidates underlying phenotypic change are protein coding sequences and functional sequences that regulate gene expression. Here, changes of the DNA sequence itself or epigenetic modifications can influence the phenotype. However, the relative importance of these two sequence classes and the role of epigenetic modifications is still unclear. Flycatchers provide a good model system to study this question. Collared flycatcher (Ficedula albicollis) and pied flycatcher (Ficedula hypoleuca) have been a model of speciation research for decades, and a rich source of genomic, transcriptomic and epigenomic data have become available. In particular, data on naturally occurring hybrids provides the opportunity to study the molecular basis and mechanisms of reproductive isolation in an ecologically relevant setting. Moreover, genomic data of the more distantly related Taiga flycatcher (Ficedula albicilla) permits studying molecular evolution also at larger time-scales.

Duties: The project will start by the identification and characterization of gene regulatory elements in the collared flycatcher genome. In addition, you will establish associations between regulatory elements and their target genes. For this purpose, you will use bioinformatic software and machine learning approaches to analyse a rich source of genomic, transcriptomic and epigenomic data. This exploration will form the background for all subsequent analysis. You will then perform comparative analysis between flycatcher populations, in the context of speciation research as well as on larger evolutionary time-scales. The ultimate goal of the project is to gain a conceptual understanding of the role of molecular evolution and adaptation at different evolutionary time-scales and levels. This applies to genetic and epigenetic changes in protein coding sequences, regulatory elements and transposable elements. You will acquire cutting-edge skills in bioinformatics and statistical analysis, which are essential for modern biology research. In addition, the project will involve mathematical modelling.

Qualifications required: To be eligible for a PhD-student position the applicant must hold a master degree (or equivalent) in mathematics, bioinformatics or biology, at the time of appointment. The applicant with a mathematics background must have an interest in molecular evolution and population genetics, and a readiness to acquire relevant skills in bioinformatics. The applicant with a bioinformatics or biology background must have a readiness to acquire relevant skills in computer science, statistics and mathematics. Candidates must be able to express themselves fluently in spoken as well as written English. In addition, the applicant must be able to work independently, have good collaborative skills and be able to communicate (both spoken as well as written). The applicant must have integrity and personal maturity, be able take initiative and handle setbacks.

Position: The graduate program covers four years of full-time study. The position can be combined with teaching or other duties at the department (maximum 20%), which prolongs the employment with the corresponding time. The salary will be set according to local agreements. Rules governing PhD candidates are set out in the Higher Education Ordinance Chapter 5, 1-7 and in Uppsala university’s rules and guidelines More information about postgraduate studies at Uppsala University is available at


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