Population genomics of decline and local extinction in the endangered Australian Pookila

Abstract

Modern sequencing approaches, especially museum genomics, have unlocked the potential to integrate genome-scale data from across decades of collections to reconstruct population decline and extinction. Understanding species declines, both pre- and post-anthropogenic impact, is critical for data-driven approaches to conservation and genetic management of endangered species worldwide. This is especially important in Australia, where the ecological consequences of European invasion have resulted in the highest rate of mammal extinction in the world. Using historical museum specimens, cryopreserved cell cultures, and field tissue collections, we generate genomic data (1298 nuclear exons and whole mitogenomes) from extinct and surviving populations of the endangered Australian Pookila (Pseudomys novaehollandiae), a species that has suffered severe declines since European invasion in 1788. Our results reveal 23.2–35.3 % of unique genetic diversity has been lost to local extinction in Victoria in the past 50 years, with ongoing population decline and inbreeding exacerbated by natural barriers to dispersal. We show that small, isolated remnant populations are especially vulnerable to extinction, reinforced by the extinction of seven out of 12 historically recorded populations in Victoria. Future extinction of any one of three Victorian populations examined here will result in the loss of 15–46 % of remaining unique alleles. We recommend genetic rescue within Victoria as a critical management intervention, in combination with the continuation of population monitoring and adaptive habitat management, to save P. novaehollandiae from extinction. Broadly, we demonstrate how integrating historical and contemporary collections can provide crucial guidance for genetic management and conservation of threatened species.