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Developing mobile element based genetic markers for individual identification, captive breeding, and conservation genetics of gibbons

Project Supervisor: Dr Richard Badge

Co-supervisor: Dr Ed Hollox

Non-academic partner: Dr Charlotte Macdonald, Twycross zoo

PhD project title: Developing mobile element based genetic markers for individual identification, captive breeding, and conservation genetics of gibbons

Project outline:

Context: 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 focussed 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).

Background: 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.

Specific research: Pilot data from a previous MSc project, using Twycross Zoo gibbon samples, demonstrated that extant assays can identify novel (i.e. absent from the reference genome) transposon insertions, and that these insertions are simple to analyse. Having established feasibility, this PhD project involves expansion of this marker panel to gain greater insight into genome evolution and conservation genetics. The pivotal role that Twycross Zoo plays in captive gibbon population management means the project would 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 that will be undertaken during the project:

The experimental aspects of the project will involve primate biosample handling, nucleic acid extraction and characterisation, 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), and the integration of sample and genetic data within the European gibbon studbook. The student will also be trained in interpreting the Zoo’s research activity to the visiting public

Interview date: TBA