Genomic analysis of extinction risk in birds


Genomic analysis of extinction risk in birds


Project Description


Professor Jim Groombridge, University of Kent – Contact me

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

Dr Hernan Morales, GLOBE Institute, University of Copenhagen

Dr Simon Tollington, School of Animal Rural and Environmental Sciences, Nottingham Trent University

Scientific Background

Understanding predictors of extinction risk is crucial to address the global biodiversity crisis. Whilst ecological predictors of extinction are well-known, the impact of genomic diversity is less-well understood. Reference genomes and resequencing data for many hundreds of species have become available to guide conservation, and the next challenge is to integrate these data with detailed ecological data and IUCN Red List of these species.

This PhD project will (i) identify and study genome features that can predict extinction risk across two well-studied groups of birds, parrots (Psittaciformes, 421 species) and falcons (Falconiformes, 66 species), and (ii) test whether immunogenomic diversity (and other genomic features) can predict species-specific differences in susceptibility to two viruses that are emerging infectious diseases.

The parrots and falcons share a recent evolutionary history and yet comprise the full range of Red List status, from non-threatened to extinct species, as well as highly invasive species. In this PhD studentship we ask the question what makes species vulnerable to extinction, and what makes others such successful invaders? Furthermore, each group of birds harbours a well-documented viral pathogen; Beak and Feather Disease Virus (BFDV) in Psittaciformes and Falcon adenovirus in Falconiformes. Closely related species differ markedly in their susceptibility to these viruses (i.e., mortality rate), and the PhD student will determine what underpins these differences.

Research methodology

The student will compile whole genome sequences for each of the ~500 species from the available databases. Genomes for missing extant species will be sequenced using modern and museum samples accessible through existing collaborations with the zoo community. Extinct species will be sampled via museum collaborations. Genome data will be analysed using bioinformatic tools (including those developed by the supervisory team). Viral pathogen prevalence across each group will be data-mined from published literature.


The student will receive comprehensive training in conservation biology and genomics of extant species DICE (Kent), theoretical evolutionary genomics (UEA), museum DNA sequencing and SLiM modelling (GLOBE Institute, University of Copenhagen).

Person Specification

We seek a highly motivated individual with expertise in bioinformatics, a strong academic background in natural sciences and a keen interest in conservation science.


  • 1 van Oosterhout, C., Speak, S. A., Birley, T., Bortoluzzi, C., Percival-Alwyn, L., Urban, L. H., Groombridge, J. J., Segelbacher, G. and Morales, H. E. (2022) ‘Genomic erosion in the assessment of species extinction risk and recovery potential’, bioRxiv. doi: 10.1101/2022.09.13.507768.
  • 2 Femerling, G., Van Oosterhout, C., Feng, S., Bristol, R. M., Zhang, G., Groombridge, J. J., Gilbert, M. T. P. and Morales, H. E. (2022) ‘Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction’, BioRxiv. doi: 10.1101/2022.12.20.521169.Femerling, G., Van Oosterhout, C., Feng, S., Bristol, R. M., Zhang, G., Groombridge, J. J., Gilbert, M. T. P. and Morales, H. E. (2022) ‘Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction’, BioRxiv. doi: 10.1101/2022.12.20.521169.
  • 3 Jackson, H. A., Percival-Alwyn, L., Ryan, C., Albeshr, M. F., Venturi, L., Morales, H. E., Mathers, T. C., Cocker, J., Speak, S. A., Accinelli, G. G., Tollington, S. and van Oosterhout. (2022) ‘Genomic erosion in a demographically recovered bird species during conservation rescue’, Conservation Biology. Wiley. doi: 10.1111/cobi.13918.
  • 4 Wilder et al. (2023). The contribution of historical processes to contemporary extinction risk in placental mammals. Science 380 (6643), eabn5856.
  • 5 Fogell, D. J., Martin, R. O. and Groombridge, J. J. (2016) ‘Beak and feather disease virus in wild and captive parrots: an analysis of geographic and taxonomic distribution and methodological trends’, Archives of Virology. Springer, pp. 2059-2074. doi: 10.1007/s00705-016-2871-2.

Key Information

  • This project has been shortlisted for funding by the ARIES NERC DTP and will start on 1st October 2024. The closing date for applications is 23:59 on 10th January 2024.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship, which covers fees, stipend (£18,622 p.a. for 2023/24) and research funding. International applicants are eligible for fully-funded ARIES studentships including fees. Please note however that ARIES funding does not cover additional costs associated with relocation to, and living in, the UK. We expect to award between 4 and 6 studentships to international candidates in 2024.
  • ARIES students benefit from bespoke graduate 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.
  • 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, visa requirements notwithstanding.
  • 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 ask to complete the form by the University to which you apply.
  • ARIES funding is 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. See for more information

Applications open

Click here to apply at University of Kent