Conservation genomics of endangered bird species in zoos

Javan green magpie (Cissa thalassina) sitting on a branch

The Javan green magpie (Cissa thalassina) is a critically endangered species that is endemic to the Indonesian island of Java. It is one of the bird species that is conserved at Chester Zoo.

This project will assess the long-term extinction risk of endangered bird species held in zoos.

The studentship is part of the ARIES doctoral training partnership, funded by NERC and starts October 2020.

Apply for this course

Read the eligibility criteria and application guidance below, then apply though the University of East Anglia's online application system.

Application deadline: 7 January 2020

Background

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 project will embrace this ‘One Plan’ approach, thereby significantly advancing both the study and practise of conservation.

Research methodology

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 NHM 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.

Training

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.

The team

The student will join the van Oosterhout group at the UEA, and its wider network, including close collaborators at Chester Zoo, the NHM London, EAZA, and the IUCN. At the UEA, the student will be taught computer modelling, population genomic and quantitative genetic analyses. At the NHM, they will be taught bioinformatics and sequencing. At Chester Zoo, they will gain experience with husbandry, captive breeding and data management of endangered birds in ex-situ environments.

Person specification 

We are looking for a student 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.

Eligibility

ARIES studentships are available to UK and EU applicants only.

Residency rules apply. In general, UK and EU nationals who will have been resident in the UK for three years or more at the time when their PhD begins will be eligible for a full ARIES studentship. UK and EU nationals who have been resident outside the UK but within the EU during the qualifying period will usually be eligible for a ‘fees only’ studentship, which pays research costs and tuition fees but gives no help with living expenses.

In case of uncertainty, the planned university of registration should be contacted for eligibility advice; or the ARIES administrators.

All applicants need to comply with the registered university's English-language requirements.

Applicants should have obtained or be about to obtain a First or Upper Second Class UK Honours degree, or equivalent qualifications gained outside the UK. Applicants with a Lower Second Class degree will be considered if they also have a master's degree. 

How to apply

Applications for the PhD are processed through the University's of East Anglia's online application service.

Applications will need to be supported by:

  • A full CV
  • A statement that gives (for example) details of the candidate’s interest in the studentship project, and any skills etc they can bring to it
  • Electronic copies of certificate(s) and transcript(s) for all relevant qualifications (degrees etc)
  • Two references, of which at least one must be an academic reference.

The application deadline is 12:00 on 7 January 2020.

Any questions?

If you have any questions about the project please contact

Main supervisor: Prof Cock van Oosterhout

References

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.

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.

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.

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.

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.

ARIES Doctoral Training Partnership

The ARIES (Advanced Research and Innovation in the Environmental Sciences) doctoral training partnership draws together expertise from five universities and nine research centres, as well as over forty other research-users.

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