Quantification and Characterisation of Genetic Diversity and Population Structure of Wild Fisheries Species

Project Code: HAERTY_EI_ARIES27_CASE

Quantification and Characterisation of Genetic Diversity and Population Structure of Wild Fisheries Species

Project Code: HAERTY_EI_ARIES27_CASE

Project Description

Supervisors

Dr Wilfried Haerty, Earlham Institute – contact me

Dr Jose de Vega, Earlham Institute

Dr Sam Speak, Earlham Institute

 

Scientific Background:

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

 

Project Objectives:

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.

 

Research Methodology and Training

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.

 

Person Specification:

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.

Acceptable first degree subject(s): Biology, Population Genetics, Bioinformatics, Zoology, Ecology

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.

Key Information

  • This studentship has been shortlisted for funding under the UKRI NERC DLA funding scheme and will commence on 1 October 2027. The closing date for applications is 23:59 on 16 December 2026.
  • 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 postgraduate researchers (PGRs) benefit from bespoke training and ARIES provides £2,500 to every student for access to external training, travel and conferences, on top of all Research Costs associated with the project. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside non-academic experience, and our recruitment process considers potential with the same weighting as past experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis. International applicants should check whether there are any conditions of visa or immigration permission that preclude part-time study. All advertised project proposals have been developed with consideration of a safe, inclusive and appropriate research and fieldwork environment with respect to protected characteristics. If you have any concerns, please contact us.
  • For further information, please contact the supervisor. To apply for this Studentship, follow the instructions at the bottom of the page or click the 'apply now' link.
  • ARIES is required by our funders to collect Equality and Diversity Information from all of our applicants. The information you provide will be used solely for monitoring and statistical purposes; it will remain confidential and will be stored on the UEA SharePoint server. Data will not be shared with those involved in making decisions on the award of Studentships and will have no influence on the success of your application. It will only be shared outside of this group in an anonymised and aggregated form. You will be asked to complete the form by the University to which you apply.
  • ARIES studentships are subject to UKRI terms and conditions. Postgraduate Researchers are expected to live within reasonable distance of their host organisation for the duration of their studentship. Please see https://www.ukri.org/publications/terms-and-conditions-for-training-funding/ for more information.

Apply Now

Apply now via the University of East Anglia Application Portal