Recent historical bottlenecks and restricted gene flow in one of the last remaining stronghold populations of the southern black-throated finch (Poephila cincta cincta)

Habitat fragmentation is a key driver of reduced genetic connectivity and loss of genetic variation among populations, elevating the risk of inbreeding depression and reduced adaptive potential. The endemic, nationally endangered southern black-throated finch ( Poephila cincta cincta ) has experienced severe range contractions since the rise of pastoralism. Using a panel of genome-wide single nucleotide polymorphisms, we characterised spatial genetic structure for a remaining stronghold population in the Desert Uplands Bioregion of Queensland, Australia. We mapped effective migration surfaces and tested for isolation by resistance to identify potential barriers to gene flow, estimated contemporary effective population sizes and reconstructed the demographic history of this population. We found evidence of restricted gene flow between localities only 16 km apart and strong isolation by geographic distance. Landscape resistance modelling identified areas of suitable woodland habitat that facilitated effective dispersal. More restricted gene flow in the southern range of this population is likely influenced by the fragmentation of suitable vegetation communities. Contemporary effective population sizes were near or below 1000, and we detected two historical population bottlenecks (> 50% decline) occurring around 60–100 and 700 years ago. Given recent evidence that the Desert Uplands population is genetically isolated from the only other stronghold population in Townsville, the results of this study suggest future losses of genetic diversity and adaptive potential may continue without effective management. To improve the long-term persistence of southern-black throated finch across their range, prioritising the conservation and restoration of habitat that promotes genetic connectivity is essential.