Development and Validation of a Standardised Genomic Tool for Conservation Management of the Koala (Phascolarctos cinereus)

Abstract

Koalas (Phascolarctos cinereus) are threatened by habitat loss, fragmentation, and population isolation, increasing the risk of inbreeding and extinction. Genomic tools are valuable for guiding management decisions, and a standardised tool genomic is the most effective approach. In this study, an integrated genomic SNP assay was developed and validated as a comprehensive monitoring tool for koala conservation. The panel unifies SNP markers from previous approaches (DArTseq, exon-capture, whole-genome sequencing) into a standardised platform and incorporates novel fitness-related loci linked to immunity, thermoregulation, diet, and reproduction, alongside pathogen targets such as koala retrovirus (KoRV) and koala papillomavirus (KoAA). The assay was validated across key conservation applications, including population diversity and differentiation, parentage assignment, sex determination, provenance testing, and pathogen screening, using a variety of sample types (blood, tissue, swabs, scat), from previously tested populations across the distribution. A total of 3358 informative SNPs were identified, including 210 high-confidence outliers associated with immune and stress-response functions, indicating strong potential to capture adaptive variation. By integrating existing genomic resources with new adaptive and predominant pathogen loci, this cost-effective, standardised assay provides a unifying genomic framework for koala management, supporting applications from veterinary diagnostics to long-term monitoring under the National Koala Recovery Plan.

Keywords: Single Nucleotide Polymorphism (SNP); conservation genomics; host-pathogen interactions; population structure and diversity; standardised assay.

Figure 1

Map of eastern Australia showing state boundaries (black outline) for Queensland (QLD), New South Wales (NSW), Victoria (VIC), and South Australia (SA); Interim Biogeographic Regionalisation for Australia (IBRA v7) bioregions (dark grey outline); and the expected extant koala distribution (non-shaded area). Sampling locations are labelled as follows: 1. Magnetic Island, 2. St Lawrence, 3. Clermont, 4. Brisbane, 5. Lismore, 6. Gunnedah, 7. Port Macquarie, 8. Port Stephens, 9. Blue Mountains, 10. French Island, 11. South Gippsland, 12. Mount Lofty, and 13. Kangaroo Island.

Figure 2

Sample Quality and Performance (n400). TOP: overall sample quality scatterplot (a) read depth, (b) call rate. BOTTOM: sample type performance boxplots (c) read depth, (d) call rate. Threshold line (orange) at read depth 5 and call rate 50%.

Figure 3

Admixture plots for Koala-fixed dataset validation. (a) K = 2, (b) K = 5, (c) K = 9. Colours are aligned with published sources [13,52,54]. Populations (labelled below) (Q_MAI = Magnetic Island, Q_CMC = St Lawrence, Q_BBN = Clermont, Q_SEQ = Brisbane, N_FNC = Lismore, N_BBS = Gunnedah, N_NNC = Port Macquarie, N_SBPS = Port Stephens, N_SBBM = Blue Mountains, V_SCPE = South Gippsland, V_FRI = French Island, S_FLB = Mount Lofty, and S_KAI = Kangaroo Island) and are ordered (left to right) relative to geographical location (north to south). States outlined (QLD, NSW, VIC, SA).

Figure 4

Admixture plot for immune gene MHC II DB-β at K = 2 for seven populations (North: Q_SEQ = Brisbane, N_FNC = Lismore, N_BBS = Gunnedah, N_NNC = Port Macquarie, N_SBPS = Port Stephens, N_SBBM = Blue Mountains. South: V_SCPE = South Gippsland, V_FRI = French Island).

Figure 5

Provenance assignment (n = 311) with Koala (Fixed & Discovery) MAF > 0.01 (2661 SNPs) visualised with [NetView] at kNN = 10 and 20. Dots are individuals, coloured by pre-defined populations, labelled (see legend) and states outlined.