About the Project
Recent genomic research has revealed that structural variation, ranging from small insertions and deletions to major chromosomal rearrangements, can have an outsized biological impact compared to simple sequence mutations. However, our understanding of structural variants has been biased, both due to technical limitations in their detection, and because of a top-down approach that focuses on the variants with the largest impacts on traits or diseases. Technological advances in our ability to study multiple assembled genomes from a population (i.e. pangenomics) has opened the door to unbiased bottom-up investigation of structural variants with better power and resolution than ever before. This presents an opportunity to gain a comprehensive understanding of their origins, impacts and evolution.
This PhD project will focus primarily on the butterfly Danaus chrysippus, a species that the Martin lab and collaborators have been establishing as a useful model for evolutionary genomics. The student will study a new pangenome dataset for this butterfly, along with thousands of published genomes available for other lepidopterans, to address general questions, such as:
- What factors determine the rate at which structural variants evolve?
- How do different structural variants affect recombination?
- What is the fate of genes within a rearranged genomic region?
- How does pangenomics impact the accuracy of genome-wide association study (GWAS)?
This is an entirely computational project. In addition to analysis of large genomic datasets, the project will involve software development and can incorporate a simulation component, if desired.
Background reading on structural variation within Danaus chrysippus:
- Kim K-W et al. 2022. Stepwise evolution of a butterfly supergene via duplication and inversion. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856):20210207. https://doi.org/10.1098/rstb.[contact details available in the full listing]
- De-Kayne R et al. 2025. Incomplete recombination suppression fuels extensive haplotype diversity in a butterfly colour pattern supergene. PLOS Biology. 23(2):e3003043. https://doi.org/10.1371/journal.pbio.3003043
Background reading on pangenomics:
- Fang B, Edwards SV. 2026. Pangenomes: new tools for ecological and evolutionary genomics. Trends in Ecology & Evolution. 41(3):230–244. https://doi.org/10.1016/j.tree.[contact details available in the full listing]
- Wood DP et al. 2026. European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility. Nat Commun. 17(1):9693. https://doi.org/10.1038/s[contact details available in the full listing]
For more information on the project, eligibility and how to apply for the School's PhD programme, please visit the School's PhD programme page.
Please download and complete the mandatory documents from the EastBio “how to apply” website, before proceeding with your application.
Applicants should apply to the PhD in Biological Sciences with Internship programme via the University of Edinburgh’s admissions portal (Euclid) with a start date of 01 October 2027.
Important: Before applying, please send your referees the EastBio reference form to ensure reference letters are submitted using the correct format.
When completing the Euclid application, applicants should include:
- the project title
- the proposed research supervisor(s)
- anticipated funding source (i.e., EastBio/ Edinburgh Doctoral College Award)
- the completed EastBio application form, uploaded to the Research Proposal Section
- referee details or completed reference letters using the template EastBio reference form. Please note: If you submit only the referee details, they will automatically receive a link to upload their reference letter. However, the submitted letter must be using the template form, so please share this with them in advance.
The closing date for applications to be submitted to Euclid is midday on Monday 16 November 2026.
Reference letters will be accepted up to 2 weeks after the closing date.
Submitted applications will remain under consideration during the shortlisting process until 22 February 2027, when successful candidates will be invited to interview. If any information is missing from your application, we will contact you through Euclid to request this. Please check your emails and the Euclid portal regularly.
Please be aware The University reserves the right, in its sole discretion, to amend or withdraw any of the advertised scholarships, without further notice.
Funding Notes
This 4 year PhD project is fully funded. Applicants will be considered for either an EastBio BBSRC Doctoral Landscape Award or the University of Edinburgh Doctoral College Award. Successful applicants will join the EastBio cohort as an EastBio-funded or associate-funded student. Those joining will undertake a mandatory training programme which includes a 3-month placement. This is open to students worldwide has financial support with a monthly stipend at the UKRI standard rate, funding towards project costs, and tuition fee cover. For further guidance; EastBio website; no separate application is required for consideration of the University of Edinburgh Doctoral College Award.
