Future-proofing the koala: synergizing genomic and environmental data for effective species management

Climatic and evolutionary processes are inextricably linked to
conservation. Avoiding extinction in rapidly changing environments often
depends upon a species’ capacity to adapt in the face of extreme selective
pressures. Here, we employed exon capture and high-throughput
next-generation sequencing to investigate the mechanisms underlying
population structure and adaptive genetic variation in the koala
(Phascolarctos cinereus), an iconic Australian marsupial that represents a
unique conservation challenge because it is not uniformly threatened
across its range. An examination of 250 specimens representing 91 wild
source locations revealed that five major genetic clusters currently exist
on a continental scale. The initial divergence of these clusters appears
to have been concordant with the Mid-Brunhes Transition (∼ 430–300 kya), a
major climatic reorganization that increased the amplitude of Pleistocene
glacial-interglacial cycles. While signatures of polygenic selection and
environmental adaptation were detected, strong evidence for repeated,
climate-associated range contractions and demographic bottleneck events
suggests that geographically isolated refugia may have played a more
significant role in the survival of the koala through the Pleistocene
glaciation than in situ adaptation. Consequently, the conservation of
genome-wide genetic variation must be aligned with the protection of core
koala habitat to increase the resilience of threatened populations to
accelerating anthropogenic threats. Finally, we propose that the five
major genetic clusters identified in this study should be accounted for in
future koala conservation efforts (e.g. guiding translocations), as
existing management divisions in the states of Queensland and New South
Wales do not reflect historic or contemporary population structure.