Sally Potter, Craig Moritz , Kym Ottewell, Emily Roycroft, Anna J MacDonald, Margaret Byrne, Steven J.B. Cooper, David J Pearson, Roberto Portela Miguez, Mark D.B. Eldridge

Organisms living in arid biomes are predicted to be at threat of extinction associated with ongoing climatic and anthropogenic change. Our understanding of species responses to Pleistocene climatic changes within these environments is still limited, particularly in Australia. Here we evaluate the demographic and evolutionary history of a widespread Australian marsupial, the black-footed rock-wallaby (Petrogale lateralis) whose contemporary distribution is highly fragmented across the arid biome and offshore islands. Combining genomic data from historical and modern samples we evaluate the divergence history of the five P. lateralis sub-species. The species has experienced a Pleistocene demographic expansion across the vast Australian arid biome, with subsequent fragmentation of populations and sub-species. Populations of the widespread sub-species P. lateralis lateralis are as divergent as sub-species within P. lateralis and there is negligible recent gene flow between most populations/sub-species. Individuals on islands have extremely low genetic diversity and high inbreeding coefficients, in contrast to the naturally fragmented mainland populations. Our results indicate historical connectivity of populations ~160-640 kya, and indications of bottlenecks for both island and some isolated mainland populations, providing important context for conservation management and potential genetic rescue. However, given the large ecological gradient and chromosomal variation within this widespread species, assessment of ecological differences will be important before decisions to mix across geographically distant populations and/or sub-species.