Quantification and characterisation of genetic diversity and population structure of wild fisheries species (HAERTY_EI_ARIES27_CASE)
Key details
- Application Deadline
- 16 December 2026 23:59 UK Time
- Location
- Earlham Institute
- Funding Type
- Competition funded project (Students worldwide)
- Start Date
- 1 October 2027
- Mode of Study
- Full-time or Part-time
- Programme Type
- PhD
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Project Description
Primary Supervisor - Dr Wilfried Haerty
The characterisation of genetic diversity and demographic structure of fish populations are essential in assessing and maintaining stocks sustainability.
Population structure and genetic diversity of stocks have mainly been assessed using limited genetic markers. While useful for broad population estimates, these methods lack power to quantify gene flow and cannot detect structural variants. Furthermore, fish population demographics are commonly estimated from otolith growth rings, a destructive method requiring specialist expertise and sacrifice of individuals. In contrast, long-read DNA sequencing generates genome fragments tens to hundred of kilobases with high accuracy capturing both single nucleotide and structural variants. These technologies also detect chromatin methylation, enabling non-lethal and accurate age prediction from small tissue samples.
With CEFAS researchers, this project aims at 1) generating pangenomes to capture genomic variation, 2) quantifying genetic diversity, 3) characterising population demographics for commercially harvested populations of two species: the Atlantic Blue Fin tuna (Thunnus thynnus) and the Atlantic herring (Clupea harengus). These species exhibit contrasting population trends in UK waters. The Atlantic Bluefin tuna has recovered from severe decline and is now classified by the IUCN as Least Concern, whereas herring stocks continue to fluctuate and face reduced catch limits. By comparing diversity, population structure, and demographic patterns in these species, the project will provide insights into their evolutionary histories and support more effective, sustainable fisheries management.
The student will gain highly transferable skills in bioinformatics, genomics, and population genetics, fisheries management and evidence-based policy making. Engagement with academic and industrial collaborators will provide exposure to advanced long-read sequencing methodologies and analytical approaches. The project is expected to generate at least two publications. Participation in journal clubs, lab-meetings, conferences, and collaborative research networks will support professional development and scientific independence. The student will be encouraged to explore new questions inspired by their aspirations, such as population modelling, and demographic forecasting. Leveraging our collaborative networks, the student could extend the geographical remits of their investigations.
We are looking for an enthusiastic student with interests in genomics, population genomics applied to the sustainable management of fish stock. Experience in population genetics and genomics would be desirable.
Entry Requirements
At least UK equivalence Bachelors (Honours) 2:1. English Language requirement (Faculty of Science equivalent: IELTS 6.5 overall, 6 in each category)
Funding
ARIES studentships are subject to UKRI terms and conditions. Successful candidates who meet UKRI’s eligibility criteria will be awarded a fully-funded studentship, which covers fees, maintenance stipend (£21,805 p.a. for 2026/27) and a research training and support grant (RTSG). A limited number of studentships are available for international applicants, with the difference between 'home' and 'international' fees being waived by the registering university. Please note, however, that ARIES funding does not cover additional costs associated with relocation to, and living in, the UK, such as visa costs or the health surcharge.
ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Projects have been developed with consideration of a safe, inclusive and appropriate research and fieldwork environment. Academic qualifications are considered alongside non-academic experience, with equal weighting given to experience and potential.
After submitting their application for the relevant ARIES project(s), applicants are expected to complete the ARIES Equality and Diversity Form Applicants - 2027 Entry – Fill in form. One form is required per application, so applicants applying to more than one project must complete a separate form for each.
Please visit www.aries-dtp.ac.uk for further information.
References
Etherington G, Ciezarek A, Mehta T, Barker T, Durrant A, Fraser F, Henderson S, Irish N, Kaithakottil G, Knitlhoffer V, Ali S, Trong T, Watkins C, Swarbreck D, Gharbi K, Benzie J, Haerty W. 2025. Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly. Sci Rep. 15(1):16057. doi: 10.1038/s41598-025-01300-y.
Ciezarek A.G., Mehta T.K., Man A., Ford A.G.P., Kavembe G.D., Kasozi N., Ngatunga B.P., Shechonge A.H., Tamatamah R., Cnaani A., Di Palma F., Turner G.F., Genner M.J., Haerty W. 2024. Ancient and ongoing hybridization in the Oreochromis cichlid fishes. Mol Biol Evol 41(7):msae116 doi: https://doi.org/10.1093/molbev/msae116.
Ciezarek A., Ford A.G.P., Etherington G.J., Kasozi N., Malinsky M., Mehta T.K., Penso-Dolfin L., Ngatunga B.P., Shechonge A., Tamatamah R., Haerty W., Di Palma F., Genner M.J., Turner G.F.. 2022. Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes. Aquaculture 548:737637.
Chevrier T., Bonhommeau S., Thompson M, Farley J, Del Vecchio G, Nieblas AE, Cowart DA, Nguyễn JI, Bernard S, Guiguen Y, Cabau C, Klopp C, Zoller JA, Horvath S, Brooke R, Lu AT, Pellegrini M, Chanut J. 2026. Searching for Shared Epigenetic Clocks: Evaluating Ultra-Conserved Markers in a de Novo Genome Assembly of the Albacore Tuna. GeroScience 48 (3): 3831–3845
Anastasiadi D., Kasmi Y., Stransky C., Casas L., Eschbach E., Piferrer F. 2026. An Epigenetic Clock for Accurate Age Prediction in Atlantic Cod Populations for Improved Fisheries Management. Molecular Ecology Resources 26 (3): e70109.