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Conservation genomics of endangered bird species in zoos (OOSTERHOUTUENV20ARIES)


Project Description

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 (http://www.cpsg.org/our-approach/one-plan-approach-conservation). 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.


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.


PERSON SPECIFICATION

Excellent communication skills and quantitative skills (e.g. bioinformatics), and a real passion for conservation.


More information on the supervisor for this project: https://people.uea.ac.uk/en/persons/c-van-oosterhout
Type of programme: PhD
Start date: October 2020
Mode of study: Full-time or part-time
Studentship length: 3.5 years
Partner: Chester Zoo
Eligibility requirements: First degree in Biology (e.g. Ecology, Evolution, Conservation Biology, Genomics)

Funding Notes

This project has been shortlisted for funding by the ARIES NERC Doctoral Training Partnership, and will involve attendance at mandatory training events throughout the PhD.

Shortlisted applicants will be interviewed on 18/19 February 2020.

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.

For further information, please visit View Website

References

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.

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.

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.

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