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Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species‐wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220‐km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long‐term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad‐free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision‐making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.

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Context. The introduction of the cat (Felis catus) to Australia has been a key driver of the decline and extinction of the continent's endemic mammals. Currently, there is no clear long-term solution to controlling feral populations of cats at a landscape scale. As such, understanding how environmental conditions and habitat attributes can mediate the coexistence between introduced predators and native mammals can improve management outcomes for threatened species. Aim. We sought to compare the differences in habitat use by feral cats and a remnant population of the endangered northern quoll (Dasyurus hallucatus) to understand what environmental variables allow these two mesopredators to coexist in tropical savanna of Cape York Peninsula, Queensland. Methods. We deployed grids of motion-activated cameras three times per year over a 3-year period, across Eucalyptus tetrodonta-dominated plateaux known to be inhabited by feral cats and northern quolls. We modelled the spatial variation in the frequencies of detection of feral cats and northern quolls (referred to as 'habitat use'), as a function of biotic and abiotic environmental variables by using a generalised linear model for consistent variables and a generalised linear mixed-effect model for fluctuating variables. Key results. Habitat use by feral cats was most frequent in areas with high fire frequencies and low tree basal area, whereas habitat use by northern quolls was most frequent in areas of high basal area of E. tetrodonta (a commonly used den tree species), topographic ruggedness, and long-unburnt savanna. Conclusions. Frequent fires in tropical savanna promote habitat use by feral cats and can result in a reduction of critical habitat for northern quolls. Implications. We postulate that remnant populations of northern quolls on Cape York Peninsula occur in less frequently burnt refugia, primarily on top of plateaux that support high-biomass tropical savanna dominated by E. tetrodonta. Our findings highlighted that threatened mammals can persist alongside introduced predators in tropical savanna but are dependent on the maintenance of structurally complex habitat.