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.
Highlights
We expect that such findings will (1) help confirm the presence of two Australian subspecies of brushtailed rabbit-rats, (2) have consequences for the conservation management of the brush-tailed rabbit-rat as well as other species in the region and (3) showcase how the success or failure of conservation efforts to protect this flagship species is likely to inform future management of small- to medium-sized mammals in northern Australia
A similar trend was present for expected heterozygosity, observed heterozygosity, Wright’s inbreeding coefficient and the locus polymorphic index
We found no overlap in niche hypervolumes between the two lineages, based on either the Jaccard or Sorenson similarity metrics
Summary
We further predict that strong differences in environmental conditions of the realised niche between major lineages will be present, due to the species presence on climatically unique offshore islands as well as the large (~800 km) geographic distances between some mainland populations We expect that such findings will (1) help confirm the presence of two Australian subspecies of brushtailed rabbit-rats, (2) have consequences for the conservation management of the brush-tailed rabbit-rat as well as other species in the region and (3) showcase how the success or failure of conservation efforts to protect this flagship species is likely to inform future management of small- to medium-sized mammals in northern Australia. For each of the ancestral populations (identified by the most suitable number in the cross-entropy plot, described above), we calculated the niche hypervolume of five environmental variables that have previously been shown to be important correlates of brush-tailed rabbit-rat distribution (von Takach et al 2020) These included three climatic variables (mean annual rainfall, mean maximum temperature of the hottest month and mean minimum temperature of the coldest month) taken from the SILO database Analysis of spatial autocorrelation of genotypes identified significant values of the autocorrelation coefficient r persisting for distances exceeding 100 km (Supplementary Fig. S6), there was a substantial reduction in r between 1 and 5 km
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