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EASTBIO How repeatable is speciation?


School of Biological Sciences

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Dr K Lohse , Dr Simon Martin No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Speciation involves the build up of barriers to genetic exchange. A number of population genomic studies on closely related taxa of study systems. However, despite this wealth of speciation genomic case studies and the rapid development of methods that allow to infer speciation history from sequence variation, it remains unclear how repeatable (or idiosyncratic) speciation processes are, that is, to what extent the same genes, genes families and genomic regions are involved in the build up reproductive isolation. And integral part of this project is the systematic comparison of speciation histories of different butterfly sister species pairs – inferred from population genomic data – in light of phylogenetically shared and derived features along their genomes. The student will analyse population genomic data 18 sister pair species of European butterflies using a novel statistical framework for decomposing patterns of sequence variation into genomic maps of past population processes (e.g. gene flow and background selection) developed in the Lohse Lab.

This project will examine how repeatable speciation processes are by conducting systematic comparisons between recently diverged species pairs of European butterflies as a test case.
• Are candidate gene families underlying prezygotic barrier traits (e.g. gene families involved in the production of detection of mating cues) repeatedly involved in triggering the shut-down of gene flow?
• Do particular genomic regions (sex chromosomes, areas of low recombination) act as nuclei for barrier formation between diverging species?
• How often are inversions involved in the build up of reproductive barriers?
• Do sister species pairs that form secondary contact zones show more clustering of barrier regions compared to sympatric pairs?
• How should/can one best compare genomic maps of population parameters between taxa that are based on different coordinate systems, i.e. reference genomes?
The PhD student will be part of an ERC funded research group working on the speciation biology of European butterflies and will obtain state of the art training in genomics, bioinformatics and advanced evolutionary genetics and statistics. The lead supervisor, Konrad Lohse, brings extensive experience in population genetics and insect speciation genomics. The group has developed statistical methods to model divergence and gene flow between species. Co-supervisors Simon Martin and Dominik Laetsch bring ample experience in butterfly speciation genomics and bioinformatics respectively. Additional training will be provided through tailored bioinformatics and coding workshops. The project also provides opportunities to interact with a number of national (Darwin Tree of Life project, Sanger; Alex Hayward, Exeter) and international collaborators (Roger Vila, Barcelona; Nick Barton, IST Austria).

Applicants should have at least an upper 2.1 degree in a relevant subject (evolutionary or computational biology or a related quantitative field) and a strong enthusiasm for speciation research. Relevant training will be provided, but any previous experience in population genetics, applied maths and/or bioinformatic/computational skills would be a great advantage. This project is entirely computational with scope for testing and developing new inference approaches.

The School of Biological Sciences is committed to Equality & Diversity: https://www.ed.ac.uk/biology/equality-and-diversity

How to Apply:
The “Institution Website” button will take you to our Online Application checklist. Complete each step and download the checklist which will provide a list of funding options and guide you through the application process.

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership http://www.eastscotbiodtp.ac.uk/how-apply-0. This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition fees. The fee difference will be covered by the University of Edinburgh for successful international applicants. Please refer to UKRI website (https://www.ukri.org/our-work/developing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/) and Annex B of the UKRI Training Grant Terms and Conditions (https://www.ukri.org/wp-content/uploads/2020/10/UKRI-291020-guidance-to-training-grant-terms-and-conditions.pdf) for full eligibility criteria.

References

• Ravinet et al. 2017. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J. Evol. Biol., 30: 1450-1477.
• Ebdon et al. 2020. The Pleistocene species pump past its prime: evidence from European butterfly sister species. bioRxiv 2020.09.04.282962
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