Dr Richard Badge
No more applications being accepted
Funded PhD Project (European/UK Students Only)
Gibbons are the smallest of the apes and comprise a group of highly endangered species, key to the ecology of Asian tropical forests. Gibbons are threatened by habitat loss and have been identified as priority species for conservation by the IUCN. International conservation efforts have focused on habitat preservation, but degradation of tropical forests through palm oil planting is inexorable. As a result, maintenance, genetic management, and expansion of zoo populations are essential to gibbon conservation. Twycross Zoo is a world leader in primate welfare, research and conservation and plays a key role in the preservation of captive gibbon populations. Also the Zoo’s Director of Life Sciences, Dr Charlotte Macdonald, is Chair of the Gibbon Taxon Advisory Group for the European Association of Zoos and Aquaria (EAZA).
In addition to their critical role in tropical ecosystems, gibbons are of intense interest to evolutionary biologists, having exceptionally fluid genome structure, highlighted in the publication of the gibbon genome in 2014. Not only are gibbon genomes evolving rapidly, but this evolution is hypothesised to be driven by mobile genetic elements, or transposons. This observation presents an excellent opportunity for fundamental research into genome evolution and dynamics (a research focus of the Genetics Department) to synergise with modern genomic analysis for the advancement of animal husbandry, welfare and conservation. In particular, transposon insertions are fundamental to understanding the pace of gibbon genome evolution, but additionally enable robust and cost-effective molecular analysis of relatedness. This analysis is essential for maintaining genetic health, the identification of species and hybrids, and potentially, genetic tagging of individuals for molecular ecology studies.
A pilot study has demonstrated that we can identify novel (i.e. absent from the reference genome) gibbon transposon insertions. Having established feasibility, this PhD project involves expansion of this marker panel to gain insights into genome evolution, and conservation genetics. The pivotal role that Twycross Zoo plays in captive gibbon population management means the project will have unprecedented access to samples. Successful development of individual specific genetic markers will directly impact on animal welfare and health, improving the long-term viability of captive populations. In addition the potential to resolve taxonomic ambiguities will be an important contribution to gibbon systematics, and fundamental research on rapid genome evolution in these species will lead to new knowledge of primate genome dynamics.
Techniques involved in the project:
The experimental aspects of the project involve primate biosample handling, nucleic acid extraction, construction of genomic libraries, PCR, nucleic acid electrophoresis, DNA sequencing (Sanger and NGS) and bioinformatic analysis of gibbon and related ape genomes. During placements at Twycross Zoo the student will be trained in the practical and legislative technicalities of collecting, managing and utilising samples from endangered animals (including CITES). The student will also be trained in interpreting the Zoo’s research activity to the visiting public
To apply you need to prepare a brief personal statement (1000 words max) saying how your education and experience fit the project, and complete the online application form, indicating the project and supervisors above. The studentship is project-based (i.e. candidates apply to carry out the research project described above, at the University of Leicester) but is hosted within the BBSRC Funded Midlands Integrative Biosciences Training Partnership (MIBTP) programme. The studentship is subject to the benefits and requirements of this programme (See Funding Notes). More information on MIBTP can be found at: http://www2.warwick.ac.uk/fac/cross_fac/mibtp/
MIBTP Benefits: Full 4-year student stipend, including registration fees and living allowance (UK nationals and EU nationals who have been UK residents for three years or more are eligible for full stipend). EU nationals who have not been UK residents for three years or more, are eligible, but will receive only fee support.
MIBTP Requirements: Candidates MUST have A-level (or equivalent) Mathematics OR evidence of attendance (and good marks) at a University Course providing advanced (NOT introductory) training in numeracy. Highlight the Courses you feel satisfy this Mathematics requirement, especially if you do not have A-level (or equivalent) Mathematics.
Badge RM, Alisch RS, Moran JV. ATLAS: a system to selectively identify human-specific L1 insertions. Am J Hum Genet. 2003 Apr;72(4):823-38. Epub 2003 Mar 11. PubMed PMID: 12632328; PubMed Central PMCID: PMC1180347
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, et al., Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679. PubMed PMID: 25209798; PubMed Central PMCID: PMC4249732.
How good is research at University of Leicester in Biological Sciences?
FTE Category A staff submitted: 37.40
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