The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.

Devil facial tumour disease (DFTD) has decimated wild populations of Tasmanian devils (Sarcophilus harrisii) due to its ability to avoid immune detection and pass from host to host by biting. A small number of devils have been observed to spontaneously recover from the disease which is otherwise fatal. We have sequenced the genomes of these rare cases and compared them to the genomes of devils who succumbed to the disease. Genome-wide association, based on this limited sampling, highlighted two key genomic regions potentially associated with ability to survive DFTD. Following targeted genotyping in additional samples, both of these loci remain significantly different between cases and controls, with the PAX3 locus retaining significance at the 0.001 level, though genome-wide significance was not achieved. We propose that PAX3 may be involved in a regulatory pathway that influences the slowing of tumour growth and may allow more time for an immune response to be mounted in animals with regressed tumours. This provides an intriguing hypothesis for further research and could provide a novel route of treatment for this devastating disease.

A heated debate has recently emerged between tiger farmers and conservationists about the potential consequences of lifting the ban on trade in farmed tiger products in China. This debate has caused unfounded speculation about the extent of the potential market for tiger products. To fill this knowledge gap, we surveyed 1880 residents from a total of six Chinese cities to understand Urban Chinese tiger consumption behavior, knowledge of trade issues and attitudes towards tiger conservation. We found that 43% of respondents had consumed some product alleged to contain tiger parts. Within this user-group, 71% said that they preferred wild products over farmed ones. The two predominant products used were tiger bone plasters (38%) and tiger bone wine (6.4%). 88% of respondents knew that it was illegal to buy or sell tiger products, and 93% agreed that a ban in trade of tiger parts was necessary to conserve wild tigers. These results indicate that while Urban Chinese people are generally supportive of tiger conservation, there is a huge residual demand for tiger products that could resurge if the ban on trade in tiger parts is lifted in China. We suspect that the current supply of the market is predominantly met by fakes or substitutes branded as tiger medicines, but not listing tiger as an ingredient. We suggest that the Traditional Chinese Medicine community should consider re-branding these products as bone-healing medicines in order to reduce the residual demand for real tiger parts over the long-term. The lifting of the current ban on trade in farmed tiger parts may cause a surge in demand for wild tiger parts that consumers say are better. Because of the low input costs associated with poaching, wild-sourced parts would consistently undercut the prices of farmed tigers that could easily be laundered on a legal market. We therefore recommend that the Chinese authorities maintain the ban on trade in tiger parts, and work to improve the enforcement of the existing ban.

Conservation breeding programmes have become widespread as natural habitats shrink, and have been historically managed using pedigree data and an assumption that population founders are unrelated. Molecular genotyping is able to determine founder relatedness, but is rarely used. To empirically test the impact of assuming founders to be unrelated, we utilized data from 203 founding individuals and 11 subsequent years of breeding records for the Tasmanian devil (Sarcophilus harrisii) insurance population. We integrated molecular data (N = 119 founders) and detailed trapping information (N = 203 founders) to test how founder relationship assumptions impacted the genetic characteristics of the population over time (N = 942 unique individuals). We developed a method to combine molecular kinship (using the TrioML estimator), year of birth and trapping location, and integrated the resulting empirical kinship estimates into population management software. We tested the effect of using pedigree data only, versus our integrated approach, on population outcomes. Inbreeding coefficients evaluated using the integrated approach were significantly higher than pedigree-only inbreeding coefficients in the first few years following population establishment. A geographic distanceonly approach showed an association between kinship and probability of successful breeding. Our results show the value in using field and/or molecular data combined with pedigree data in conservation breeding programmes to provide new information for managing crucial populations and improving their success. We caution population managers against commencing expensive conservation breeding programmes in the absence of understanding founder relatedness, especially when wild augmentation is a goal. Long-term costs of assuming founders are unrelated include financial costs, reduced productivity and release of potentially highly inbred individuals.