The Koala Who Could

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Villalba, J. J., Provenza, F. D. & Bryant, J. Consequences of the interaction between nutrients and plant secondary metabolites on herbivore selectivity: benefits or detriments for plants? Oikos 97, 282–292 (2002). Demographic history was inferred from the diploid sequence of each of the three koalas, using a pairwise sequential Markovian coalescent (PSMC) method 65. We conducted a range of preliminary analyses and found that PSMC plots were not sensitive to the values chosen for the maximum number of iterations ( N), the number of free atomic time intervals ( p), the maximum time to the most recent common ancestor ( t), and the initial value of ρ. Based on these investigations, our final PSMC analyses of the three genome sequences used values of N = 25, t = 5, ρ = 1 and p = 4 + 25 × 2 + 4 + 6. The number of atomic time intervals is similar to that recommended for analyses of modern human genomes 65, which are similar in size to the koala genomes. We determined the variance in estimates of N e using 100 bootstrap replicates. Replicate analyses in which we varied the values of p, t and ρ produced PSMC plots that were broadly similar to those using our chosen ‘optimal’ settings (Supplementary Fig. 10). Clarkson, C. et al. Human occupation of northern Australia by 65,000 years ago. Nature 547, 306–310 (2017).

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Grant, J. et al. Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation. Nature 487, 254–258 (2012). The Bilbo 61053 assembly described in this paper is version MSTS01000000 and consists of sequences MSTS01000001– MSTS01001906. For the Bilbo assembly Illumina X Ten reads are submitted under PRJEB19457 and PacBio reads under PRJEB19889. We also report genomic evidence of expansions within the taste receptor families that would enable the koala to optimize ingestion of leaves with a higher moisture and nutrient content in concert with the concentration of toxic plant secondary metabolites in their food plants. The koala’s ability to ‘taste water’ is potentially enhanced by an apparent functional duplication of the aquaporin 5 gene 45, 46, 47 (Supplementary Table 14 and Supplementary Note). Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Sydney, New South Wales, AustraliaHrdina, F. & Gordon, G. The koala and possum trade in Queensland, 1906–1936. Aust. Zool. 32, 543 (2004). Phillips, S. S. Population trends and the koala conservation debate. Conserv. Biol. 14, 650–659 (2000). How microbiomes can help inform conservation: landscape characterisation of gut microbiota helps shed light on additional population structure in a specialist folivore Taylor, A. C. et al. Conservation genetics of the koala ( Phascolarctos cinereus): low mitochondrial DNA variation amongst southern Australian populations. Genet. Res. 69, 25–33 (1997).

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Wang, J. COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Mol. Ecol. Resour. 11, 141–145 (2011). Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia Department of the Environment. Phascolarctos cinereus (combined populations of Queensland, New South Wales and the Australian Capital Territory) in Species Profile and Threats Database (Department of the Environment, Canberra, Australian Capital Territory, 2016). These magnificent mammals get their name form an Aboriginal * term meaning, ‘ no drink’. It’s believed this is because koalas get almost all their moisture from the leaves they eat, and rarely drink water.Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011). Miners, J. O. & Birkett, D. J. Cytochrome P4502C9: an enzyme of major importance in human drug metabolism. Br. J. Clin. Pharmacol. 45, 525–538 (1998). Seymour, A. M. et al. High effective inbreeding coefficients correlate with morphological abnormalities in populations of South Australian koalas ( Phascolarctos cinereus). Anim. Conserv. 4, 211–219 (2001).

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Custom scripts to identify gene families with expansion within the koala, Diprotodontia, Australidelphia and marsupial lineages; (2) custom scripts to identify refined repeat calls; and (3) code used to generate SNP genotypes from exon capture data are available at https://github.com/DrRebeccaJ/KoalaGenome. Data availability Kimble, B. et al. In vitro hepatic microsomal metabolism of meloxicam in koalas ( Phascolarctos cinereus), brushtail possums ( Trichosurus vulpecula), ringtail possums ( Pseudocheirus peregrinus), rats ( Rattus norvegicus) and dogs ( Canis lupus familiaris). Comp. Biochem. Physiol. C Toxicol. Pharmacol. 161, 7–14 (2014). Cheng, Y. et al. Characterisation of MHC class I genes in the koala. Immunogenetics 70, 125–133 (2018). Rebecca N. Johnson, Siobhan Dennison, Don Colgan, David E. Alquezar-Planas, Val Attenbrow, Mark D. B. Eldridge, Kyle M. Ewart, Greta J. Frankham, Kristofer M. Helgen, Matthew Hobbs, Andrew King, Linda E. Neaves & Belinda Wright

Xu, W. et al. An exogenous retrovirus isolated from koalas with malignant neoplasias in a US zoo. Proc. Natl. Acad. Sci. USA 110, 11547–11552 (2013).

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Department of Translational Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, CyprusThe long-read-based genome enabled the de novo assembly of complex, highly duplicated immune gene families and comprehensive annotation of immune gene clusters 53, 57, 58. These include the major histocompatibility complex ( MHC) 59, as well as T cell receptors ( TCR), immunoglobulin ( IG) (Supplementary Fig. 9, Supplementary Tables 17 and 18, and Supplementary Note), natural killer cell (NK) receptor 58 and defensin 60 gene clusters. Together these findings provide a starting point for new disease research and allow us to interrogate the immune response to the most significant pathogen of the koala, C. pecorum.