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 conservation management is greatly benefited by a detailed understanding of geographic structure, genetic diversity, and demography of threatened species. The black-throated finch, <i>Poephila cincta</i>, is an Australian songbird with two subspecies: <i>atropygialis</i> and <i>cincta</i>. The southern subspecies, <i>cincta</i>, has experienced an ~80% range contraction over the last century and is listed as endangered, but genetic surveys of it are incomplete. Here, we use a combination of reduced representation and whole genome sequencing to examine genetic differentiation, spatial genetic structure, and demographic history in both subspecies of this species. We find that <i>atropygialis</i> and <i>cincta</i> are geographically isolated by a biogeographic barrier known as the Einasleigh Uplands and genetically distinct despite a history of divergence with gene flow. Since they last shared a common ancestor ~360,000 years ago, the two subspecies have experienced distinct demographic trajectories over the last ~100,000 years, characterized by population expansion in <i>atropygialis</i> and population decline in <i>cincta</i>. We find that the two remnant population centers of <i>cincta</i>, from the Galilee Basin and the Townsville Coastal Plain, each represent genetically distinct lineages that last shared appreciable levels of gene flow ~3000 years ago. Moreover, we report striking microgeographic genetic structure from the Townsville Coastal Plain between populations < 20 km apart associated with barriers to dispersal caused by anthropogenic habitat modification over the last 50 years: namely, the construction of the Ross River Dam. Our findings highlight the urgent need for a conservation approach that prioritizes habitat restoration to re-establish population connectivity in the endangered southern black-throated finch.