Population genomics of Uperoleia daviesae (Anura: Myobatrachidae) highlights the vulnerability of naturally fragmented short-range endemics to urban development

Shengyao Lin , Peter James Mcdonald, Alistair Stewart, Carolyn J. Hogg, Luke W. Silver, Sam C. Banks, Graeme R. Gillespie, Raphael K. Didham, Renee A. Catullo

Urbanisation and land use change threaten short-range endemic amphibians. Uperoleia daviesae, the Howard River toadlet, is a threatened frog species endemic to sandsheet heath, a unique, naturally patchy mosaic of habitats near Darwin in Australia’s Northern Territory. We generated a chromosome-level genome assembly and performed genome-wide SNP analyses using data from 115 individuals across 15 sites to assess dispersal patterns, genetic diversity, anthropogenic impacts, and conservation targets. Our findings reveal a history of past connectivity, followed by recent genetic subdivision, partly due to urban expansion. Regions 2 (north of Girraween and Humpty Doo) and 3 (south of Bees Creek and Lloyd Creek) contain most of the genetic diversity within the species. The two isolated populations, Region 1 (north of Howard Springs) and Region 4 (near Wickham and Weddell), each harbour unique alleles. We recommend treating local populations as a metapopulation and developing targeted conservation actions in each region. In-situ conservation actions, such as establishing protected areas or translocation, should be considered to maintain gene flow and genetic diversity. These findings provide a foundation for evidence-based management of U. daviesae and contribute to broader discussions on the conservation of short-range endemic species in increasingly urbanised landscapes.