ARIES Project - Prof Jim Groombridge

Bird in flight

ARIES Project

Genomic analysis of extinction risk in birds - Professor Jim Groombridge

Ecology and Biodiversity

Genomic analysis of extinction risk in birds  

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. 

Training

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). 

Supervisory Team 

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.  

References

  • 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. 
  • 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. 
  • 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. 
  • Wilder et al. (2023). The contribution of historical processes to contemporary extinction risk in placental mammals. Science 380 (6643), eabn5856. 
  •  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. 

How to apply

Candidates should apply using the online application form, indicating the project they wish to be considered. Deadline to submit a form is 10th January 2024, 23:59 GMT. 

You will need to upload:

  • CV  - no more than 2 pages
  • One page Cover Letter - you may wish to give details about your academic/professional background, your future career plans, your interests etc. You could also detail here why you are a good candidate for this project, and how your skills, experiences, and qualifications mean you are well suited to the PhD. Don’t worry if you don’t have experience outside of your degree – we recognise that different people have different opportunities to gain experience and you won’t be disadvantaged. You might discuss what training you think you need to become a successful researcher, or what your aspirations are for the future. We are really interested in your potential as well as what you’ve already achieved.
  • Scanned copies of your official degree transcript(s) - if the originals are not in English, you will need to provide official translations. If you have not yet graduated, you should be able to obtain an interim transcript showing the results from your degree to date (if you are only one semester into your course – for example an MSc – then this is not needed).