Low genetic diversity and high inbreeding in one of the last chlamydia-free strongholds for New South Wales koalas

Abstract The genetic consequences of population isolation include inbreeding, genetic diversity loss and loss of adaptive potential. Koalas across south-western Sydney (New South Wales, Australia) may be vulnerable to isolation due to major roads and cleared forest. A few sites within south-western Sydney are some of the last chlamydia-free sites for koalas. Low genetic diversity and potentially low adaptive potential could lead to local extinction of these chlamydia-free sites. Using reduced representation sequencing, we assessed population differentiation, genetic diversity, relatedness, inbreeding, and gene flow across seven sites in south-western Sydney and the Southern Highlands. We found south-western Sydney koalas had significantly lower diversity, higher relatedness and inbreeding than Southern Highlands koalas. There was no evidence of contemporary gene flow from the more genetically diverse Southern Highlands sites into south-western Sydney. The separation between south-western Sydney and the Southern Highlands likely explains the lower genetic diversity among south-western Sydney sites. It may also explain why chlamydia is yet to reach these sites. However, there is evidence of a disease-front movement of chlamydia from Wingecarribee up into Wollondilly which has high gene flow with Campbelltown, a chlamydia-free site. While gene flow from south to north is low, the risk of chlamydia entering the chlamydia-free sites from a few migrants is notable. With possible low adaptive potential of south-western Sydney sites, a new threat of chlamydia entering the system may lead to population declines in these stronghold areas.