Recent divergence and microgeographic genetic structure in an endangered Australian songbird: the southern black-throated finch

Anthropogenic habitat loss and climate change threaten global biodiversity. Effective conservationmanagement requires a detailed understanding of geographic structure, genetic diversity, and thedemography of threatened species. The black-throated finch, Poephila cincta, is an Australian songbirdwith two subspecies: atropygialis and cincta. The southern subspecies, cincta, has experienced an~80% range contraction over the last century and is listed as endangered but genetic surveys of it areincomplete. Here, we use a combination of reduced representation and whole genome sequencing toexamine genetic differentiation, spatial genetic structure, and demographic history in both forms of thisspecies. We find that atropygialis and cincta are genetically distinct despite a history of divergence withgene flow and geographically isolated by a biogeographic barrier known as the Einasleigh Uplands.Since they last shared a common ancestor ~400,000 years ago, the two subspecies have experienceddistinct demographic trajectories: population expansion in atropygialis and population decline in cincta.We find that the two remnant population centers of cincta, from the Galilee Basin and the TownsvilleCoastal Plain, each represent genetically distinct lineages that last shared appreciable levels of geneflow ~4,000 years ago. Moreover, we report striking microgeographic genetic structure from theTownsville Coastal Plain between populations <20 km apart associated with barriers to dispersalcaused by anthropogenic habitat modification over the last 50 years: namely the construction of theRoss River Dam. Our findings highlight the urgent need for a conservation approach that prioritizeshabitat restoration to re-establish population connectivity in the endangered southern black-throatedfinch.