Roycroft, EmilyMacDonald, AnnaMoritz, CraigMoussalli, AdnanMiguez, Roberto PortelaRowe, Kevin C.2023-01-272023-01-270027-8424http://hdl.handle.net/1885/284001Australia has the highest historically recorded rate of mammalian extinction in the world, with 34 terrestrial species declared extinct since European colonization in 1788. Among Australian mammals, rodents have been the most severely affected by these recent extinctions; however, given a sparse historical record, the scale and timing of their decline remain unresolved. Using museum specimens up to 184 y old, we generate genomic-scale data from across the entire assemblage of Australian hydromyine rodents (i.e., eight extinct species and their 42 living relatives). We reconstruct a phylogenomic tree for these species spanning ∼5.2 million years, revealing a cumulative total of 10 million years (>10%) of unique evolutionary history lost to extinction within the past ∼150 y. We find no evidence for reduced genetic diversity in extinct species just prior to or during decline, indicating that their extinction was extremely rapid. This suggests that populations of extinct Australian rodents were large prior to European colonization, and that genetic diversity does not necessarily protect species from catastrophic extinction. In addition, comparative analyses suggest that body size and biome interact to predict extinction and decline, with larger species more likely to go extinct. Finally, we taxonomically resurrect a species from extinction, Gould’s mouse (Pseudomys gouldii Waterhouse, 1839), which survives as an island population in Shark Bay, Western Australia (currently classified as Pseudomys fieldi Waite, 1896). With unprecedented sampling across a radiation of extinct and living species, we unlock a previously inaccessible historical perspective on extinction in Australia. Our results highlight the capacity of collections-based research to inform conservation and management of persisting species.The Initiative is supported by funding from Bioplatforms Australia through the Australian Government National Collaborative Research Infrastructure Strategy. This project was also supported by funding (to E.R.) from the Holsworth Wildlife Research Endowment (Equity Trustees Charitable Foundation and the Ecological Society of Australia), the Museums Victoria 1854 Student Scholarship, and the Alfred Nicholas Fellowship (University of Melbourne). E.R. was supported by an Australian Government Research Training Program Scholarship and the Dame Margaret Blackwood Soroptimist Scholarship. We thank Niccy Aitken for advice with laboratory protocols, Peter McDonald for contributing ear clips from Z. pedunculatus, and Peter Smissen for contributing DNA extractions for a number of species. We are also indebted to collections staff and to many individuals who contributed material at the Australian Biological Tissue Collection, South Australian Museum, Australian Museum, Museums Victoria, Western Australian Museum, Queensland Museum, Museum and Art Gallery of the Northern Territory, and Natural History Museum in London. We thank Pierre-Henri Fabre for assistance in sampling specimens from London. We also thank Melbourne Bioinformatics and Research Platform Services at the University of Melbourne for access to high-performance computing resourcesapplication/pdfen-AU© 2021 The authorsbiodiversityconservationexon capturephylogeny |phylogenomics202110.1073/pnas.20213901182021-11-28