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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. [ABSTRACT FROM AUTHOR]

In our present age of extinction, conservation managers must use limited resources efficiently to conserve species and the genetic diversity within them. To conserve intraspecific variation, we must understand the geographic distribution of the variation and plan management actions that will cost-effectively maximise its retention. Here, we use a genome-wide single-nucleotide polymorphism (SNP) dataset consisting of 12,962 loci and 384 individuals to inform conservation management of the Endangered northern quoll (Dasyurus hallucatus), a carnivorous marsupial distributed patchily across northern Australia. Many northern quoll populations have declined or are currently declining, driven by the range-expanding cane toad (Rhinella marina). We (1) confirm population genomic structure, (2) investigate the contribution of each population to overall diversity, (3) conduct genomic prioritisation analyses at several spatial and hierarchical scales using popular conservation planning algorithms, and (4) investigate patterns of inbreeding. We find that the conservation of a single population, or even several populations, will not prevent the loss of substantial amounts of genomic variation and adaptive capacity. Rather, the conservation of at least eight populations from across the species distribution is necessary to retain 90 % of SNP alleles. We also show that more geographically isolated populations, such as those on islands, have very small contributions to overall diversity and show relatively high levels of inbreeding compared to mainland populations. Our study highlights the importance of conserving multiple genetically distinct populations to effectively conserve genetic diversity in species undergoing widespread declines, and demonstrates the importance of using multiple criteria to inform and prioritise conservation management. • Conserving intraspecific genomic diversity is vital for threatened species management. • Declining populations of northern quolls will lose diversity through time. • Conservation of at least eight populations will conserve >90 % of SNP alleles. • The simplest solution for conservation management may not always be the best. [ABSTRACT FROM AUTHOR]

Many of Australias smaller marsupial species have been taxonomically described in just the past 50 years, and the Dasyuridae, a speciose family of carnivores, is known to harbour many cryptic taxa. Evidence from molecular studies is being increasingly utilised to help revise species boundaries and focus taxonomic efforts, and research over the past two decades has identified several undescribed genetic lineages within the dasyurid genus Planigale. Here, we describe two new species, Planigale kendricki sp. nov. (formerly known as Planigale 1) and P. tealei sp. nov. (formerly known as Planigale sp. Mt Tom Price). The two new species have broadly overlapping distributions in the Pilbara region of Western Australia. The new species are genetically distinct from each other and from all other members of the genus, at both mitochondrial and nuclear loci, and morphologically, in both external and craniodental characters. The new species are found in regional sympatry within the Pilbara but occupy different habitat types at local scales. This work makes a start at resolving the cryptic diversity within Planigale at a time when small mammals are continuing to decline throughout Australia.

Historical population contraction and expansion events associated with Pleistocene climate change are important drivers of intraspecific population structure in Australian arid-zone species. We compared phylogeographic patterns among arid-adapted Dasyuridae ( Sminthopsis and Planigale ) with close phylogenetic relationships and similar ecological roles to investigate the drivers of phylogeographic structuring and the importance of historical refugia. We generated haplotype networks for two mitochondrial (control region and cytochrome b) and one nuclear (omega-globin) gene from samples distributed across each species range. We used Φ ST to test for a genetic population structure associated with the four Pilbara subregions, and we used expansion statistics and Bayesian coalescent skyline analysis to test for signals of historical population expansion and the timing of such events. Significant population structure associated with the Pilbara and subregions was detected in the mitochondrial data for most species, but not with the nuclear data. Evidence of population expansion was detected for all species, and it likely began during the mid-late Pleistocene. The timing of population expansion suggests that these species responded favorably to the increased availability of arid habitats during the mid-late Pleistocene, which is when previously patchy habitats became more widespread. We interpret our results to indicate that the Pilbara region could have acted as a refugium for small dasyurids.