Non-invasive sampling reveals landscape genetic structure in the threatened ghost bat (Macroderma gigas) in an ore-rich region of Western Australia.

Bat species are expected to exhibit low genetic structuring due to their high mobility. Thus, habitat connectivity is important to maintain gene flow and genetic diversity to retain evolutionary potential. The ghost bat (Macroderma gigas) is a large carnivorous bat endemic to Australia. Listed as Vulnerable, the species has a disjunct distribution across northern Australia and is patchily distributed at local scales due to limited roost habitat availability and anthropogenic impacts. Here, we survey the genetic diversity and structure of M. gigas in the isolated, arid Pilbara bioregion in Western Australia, primarily using non-invasively collected faecal DNA samples obtained from roosts. Faecal and tissue samples, representing 399 individuals, were genotyped using an optimised autosomal marker panel, with a subset also being sequenced at the mitochondrial D-Loop region to investigate historical gene flow. Spatially-explicit Bayesian clustering analyses of autosomal markers revealed low genetic structure and high levels of gene flow amongst the two Pilbara subregions, with some further structuring evident within the Hamersley Ranges. Mitochondrial DNA sequencing showed strong geographic structuring of haplotypes between the subpopulations, with only a small number of shared haplotypes indicating low levels of maternal gene flow. Such patterns across the two marker types are consistent with maternal philopatry and male-mediated gene flow that has previously been described for this species. Conservation actions for the ghost bat in the Pilbara should therefore recognise maintenance of connectivity between roosts and subregions is important to maintain gene flow for this threatened species in the face of anthropogenic threats.