Genomic approaches to conserving the endangered Tasmanian devil

Abstract

The Tasmanian devil is threatened with extinction in the wild due to the transmissible cancer, devil facial tumour disease (DFTD). This thesis aims to utilise conservation genomic techniques and apply them in novel ways to advance devil research and improve our understanding of both the disease and captive populations of devils. In the north west of Tasmania a few rare cases of devils have been recorded where DFTD has spontaneously regressed. The genomes of these regressed cases were sequenced along with control devils who succumbed to DFTD. I conducted a genome-wide association study to identify genomic variants that may underlie this rare ability for tumours to regress. Two key regions of the genome differed between cases and controls and may be involved in slowing of tumour growth, allowing time for an immune response to be mounted. The re-sequenced genomes also provided a resource for detection of variable regions for use in genotyping. Tasmanian devils suffer from low genetic diversity so identification of polymorphic markers is vital. I developed a custom genotyping assay for the Tasmanian devil targeting both neutral and functional regions of the genome. The assay has been used to assess genetic diversity in the captive devil insurance population. Relatedness and inbreeding appeared to be high amongst founders with just over 90% of allelic diversity that was brought in from the wild being passed on to the next generation. Diversity at a number of genes involved with behaviour was also investigated. Aggression and social interactions may be important factors in transmission of DFTD as tumours are spread by devils when they bite each other. Again diversity is found to be low and is presented as a baseline for future work investigating DFTD-mediated selection or genetic adaptation to captivity that may impact success of reintroduction to the wild. The research presented here makes a significant advancement in the field of conservation of the Tasmanian devil.