Conservation genomics of endangered bird species in zoos

CASE award with Chester Zoo (OOSTERHOUT_UENV20ARIES)

Conservation genomics of endangered bird species in zoos

CASE award with Chester Zoo (OOSTERHOUT_UENV20ARIES)

Project Description


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

Prof Diana Bell, School of Biological Sciences, University of East Anglia

Dr Simon Tollington, Chester Zoo

Dr Matt Clarke, Natural History Museum, London


The International Union for Conservation of Nature (IUCN) produces the Red List that classifies species’ extinction risks. Nearly 100,000 of the total of 1.9 million describes species have been classified on the Red List. However, fitness data recorded in husbandry records of zoos, as well as their studbook data are currently not used in the Red List assessment. This can lead to an underestimation of the long-term extinction risk, resulting in suboptimal conservation actions. The IUCN is committed to a ‘One Plan’ approach of conservation, i.e. all available data from zoos and in situ conservation projects should be used both in Red List assessment and population management ( This ARIES DTP PhD studentship project will embrace this ‘One Plan’ approach, thereby significantly advancing both the study and practise of conservation.

Research methodology:

In this PhD project, the student will collaborate with Chester Zoo and other UK and EU zoos to gain access to studbook data of ~50 endangered bird species. In addition, the genome of some of these bird species will be sequenced (at the Natural History Museum in London) to assess the past and current rate of inbreeding. The student will use these data in a Vortex model to assess the long-term extinction risk of these bird species, and advise zoos on the optimal management strategies for the conservation of these bird species.


The student will communicate extensively with conservation practitioners at the European Association of Zoos and Aquaria (EAZA), Chester Zoos and other zoos. You will learn how to operate and download data from the Species360 database. In addition, you will gain skills in bioinformatics for the processing and analysis of whole genome sequence data at the Natural History Museum (NHM London) and the UEA. You will learn population genomic analysis and quantitative genetics, as well as population viability analysis (PVA) using the model Vortex.

Person specification:

We are looking for an individual with a degree in biology (e.g. ecology, evolution, conservation biology, genomics), with excellent communication skills and quantitative skills (e.g. bioinformatics), and a real passion for conservation.


  • [1] Gilroy, D.L., Phillips, K.P., Richardson, D.S. and Van Oosterhout, C., 2017. Toll‐like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the ‘ghost of selection past’ and quantify the ‘drift debt’. Journal of Evolutionary Biology, 30(7), pp.1276-1287.
  • [2] Tollington, S., Greenwood, A., Jones, C.G., Hoeck, P., Chowrimootoo, A., Smith, D., Richards, H., Tatayah, V. and Groombridge, J.J., 2015. Detailed monitoring of a small but recovering population reveals sublethal effects of disease and unexpected interactions with supplemental feeding. Journal of Animal Ecology, 84(4), pp.969-977.
  • [3] Tollington, S., Jones, C.G., Greenwood, A., Tatayah, V., Raisin, C., Burke, T., Dawson, D.A. and Groombridge, J.J., 2013. Long-term, fine-scale temporal patterns of genetic diversity in the restored Mauritius parakeet reveal genetic impacts of management and associated demographic effects on reintroduction programmes. Biological Conservation, 161, pp.28-38.
  • [4] Eimes, J.A., Bollmer, J.L., Whittingham, L.A., Johnson, J.A., Van Oosterhout, C. and Dunn, P.O., 2011. Rapid loss of MHC class II variation in a bottlenecked population is explained by drift and loss of copy number variation. Journal of Evolutionary Biology, 24(9), pp.1847-1856.
  • [5] Howe, K., Clark, M.D., Torroja, C.F., Torrance, J., Berthelot, C., Muffato, M., Collins, J.E., Humphray, S., McLaren, K., Matthews, L. and McLaren, S., 2013. The zebrafish reference genome sequence and its relationship to the human genome. Nature, 496(7446), p.498.

Key Information

  • This project has been shortlisted for funding by the ARIES NERC Doctoral Training Partnership, and will involve attendance at mandatory training events throughout the course of the PhD.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship - UK and EU nationals who have been resident in the UK for 3 years are eligible for a full award.
  • 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 in the subject area (see
  • This studentship will start on 1st October 2020, and the closing date for applications is 23:59 on 15th January 2020.
  • Shortlisted applicants will be interviewed on 18/19 February 2020.
  • For further information, please contact the supervisor.
  • Please note that the joint NERC-ESRC ARIES-SeNSS studentship projects have different deadlines and funding arrangements. For full details please visit, or contact

Studentship Open for Applications

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