AI-powered insights into susceptibility of parrots to viral infection, CASE project with Ebony Forest and Durrell Wildlife Conservation Trust / Jersey Zoo

AI-powered insights into susceptibility of parrots to viral infection, CASE project with Ebony Forest and Durrell Wildlife Conservation Trust / Jersey Zoo

Project Description

Supervisors

Professor Cock van Oosterhout, School of Environmental Sciences, University of East Anglia

Professor Jim Groombridge, Durrell Institute of Conservation and Ecology, University of Kent

Professor David Richardson, School of Biological Sciences, University of East Anglia

Dr Herán Morales, Globe Institute, University of Copenhagen

 

Scientific Background

Population bottlenecks erode genetic variation, which makes threatened species susceptible to viral epidemics. So, what makes an individual Resistant, Tolerant, or Susceptible (R/T/S) to a virus? That is the key question we aim to answer in this PhD study. We have gathered data on viral outbreaks over ~20 years and sequenced hundreds of bird genomes, working on some of the best-studied avian models (Mauritius parakeet, ringneck parakeet, red-crowned parakeet, and orange-bellied parrot). The PhD candidate will study data from the Mauritius parakeet to develop an AI model that can predict the response to viral infection based on genomics data. Moreover, there is the option to conduct fieldwork in Mauritius to gather additional field data, and for comparative genomics analyses.

 

Research Methodology

During this PhD project, we will sequence genomes of 531 already-sampled full-sib pairs with known R/T/S status. (This is funded by recently awarded NERC grant). The PGR will conduct bioinformatic analyses on these data, focussing on immune genes, and perform a comparative genomic analysis across parakeets and parrots. They will construct an AI model to identify genomic predictors of R/T/S in the Mauritius parakeet, and they will conduct analysis in SLiM to examine how genomic erosion reduces immunogenetic diversity, and how that affects disease susceptibility. The PGR will test the following hypotheses:

  1. Genome erosion increases susceptibility to viral infection.
  2. Inbred individuals are more susceptible to viral infection.
  3. Individuals with Runs of Homozygosity (ROH) spanning immune genes are more susceptible to viral infection.
  4. Differences in alleles at immune genes explain variation in disease status of birds.

 

Objectives

Develop a multispectral imaging dataset of marine litter materials by extending the existing VL dataset.

Design and evaluate DL models capable of classifying marine litter types using multispectral data, with a focus on achieving robustness to varying spectral channel configurations and illumination conditions.

Implement and validate device-independent representations. Investigate and apply domain adaptation and transfer learning techniques to develop models that generalize across different imaging devices, including future sensors with unknown spectral sensitivities.

 

Training

AI modelling, SLiM modelling (i.e., an individual based model to assess population viability), genomics analysis, immune gene analysis, applied bird conservation, comparative genomics, and tropical field work (optional).

 

Person Specification

Prior experience in computer coding (e.g., Python, SLiM), AI modelling, and understanding of evolutionary or conservation genetics / genomics is desirable. Good teamwork skills are essential.

Acceptable first degree subjects: Evolutionary Biology, Genetics, Conservation Biology

Project code: VANOOSTHERHOUT_UEA_ARIES26_CASE

All ARIES CASE studentships include a three to 18-month placement with the non-academic CASE partner during their period of study. The placement offers experience designed to enhance professional development.

References

  • Speak, S.A., Birley, T., Bortoluzzi, C., Clark, M.D., Percival-Alwyn, L., Morales, H.E., van Oosterhout, C., 2024. Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations. Molecular Ecology Resources, 24(7), e13967. https://doi.org/10.1111/1755-0998.13967
  • van Oosterhout, C., Supple, M.A., Morales, H.E., Birley, T., Tatayah, V., Jones, C.G., Whitford, H.L., Tollington, S., Ruhomaun, K., Groombridge, J.J. et al., 2025. Genome engineering in biodiversity conservation and restoration. Nature Reviews Biodiversity, pp.1-13. https://doi.org/10.1038/s41586-024-08458-x
  • Femerling, G., van Oosterhout, C., Feng, S., Bristol, R.M., Zhang, G., Groombridge, J.J., Gilbert, M.T.P. & Morales, H.E., 2023. Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction. Molecular Biology and Evolution, 40(12), msad256. https://doi.org/10.1093/molbev/msad256
  • Silver, L. W., Farquharson, K. A., Peel, E., Gilbert, M. T. P., Belov, K., Morales, H. E., and Hogg, C. J. 2025. Temporal loss of genome‐wide and immunogenetic diversity in a near‐extinct parrot. Molecular Ecology, 34(9), e17746. https://doi.org/10.1111/mec.17746
  • van Oosterhout, C., 2024. AI-informed conservation genomics. Heredity, 132(1), pp.1-4. https://www.nature.com/articles/s41437-023-00666-x

Key Information

  • This studentship has been shortlisted for funding under the UKRI NERC DLA funding scheme and will commence on 1 October 2026. The closing date for applications is 23:59 on 7 January 2026.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a fully-funded studentship, which covers fees, maintenance stipend (£20,780 p.a. for 2025/26) 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