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No abstract

Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world’s most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (FST = 0.21–0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.

Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250–400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained a SNP dataset from 64 museum specimens (date 1879–1960), 102 ‘recent’ (1989–2012) and 52 ‘current’ (2015–2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. Museum sampling showed population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range. Population decline has led to minimal loss of genetic diversity since the 1980’s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. A rapid population decline, coupled with the regent honeyeater’s high mobility, means a detectable genomic impact of this decline has not yet manifested. Extinction may occur in this nomadic species before a detectable genomic impact of small population size is realised. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.