Genomics identifies koala populations at risk across eastern Australia.

Koalas are an iconic, endangered, Australian marsupial. Disease, habitat destruction, and catastrophic mega-fires have reduced koalas to remnant patches of their former range. With increased likelihood of extreme weather events and ongoing habitat clearing across Australia, koala populations are vulnerable to further declines and isolation. Small, isolated populations are considered at risk when there is increased inbreeding, erosion of genomic diversity, and loss of adaptive potential, all of which reduce their ability to respond to prevailing threats. Here, we characterized the current genomic landscape of koalas using data from The Koala Genome Survey, a joint initiative between the Australian Federal and New South Wales Governments that aimed to provide a future-proofed baseline genomic dataset across the koala's range in eastern Australia. We identified several regions of the continent where koalas have low genomic diversity and high inbreeding, as measured by runs of homozygosity. These populations included coastal sites along southeast Queensland and northern and mid-coast New South Wales, as well as southern New South Wales and Victoria. Analysis of genomic vulnerability to future climates revealed that northern koala populations were more at risk due to the extreme expected changes in this region, but that the adaptation required was minimal compared with other species. Our genomic analyses indicate that continued development, particularly linear infrastructure along coastal sites, and resultant habitat destruction are causing isolation and subsequent genomic erosion across many koala populations. Habitat protection and the formation of corridors must be employed for all koala populations to maintain current levels of diversity. For highly isolated koala populations, active management may be the only way to improve genomic diversity in the short term. If koalas are to be conserved for future generations, reversing their genomic isolation must be a priority in conservation planning.