DOI: 10.5061/dryad.ffbg79cx0
title: Future-proofing the koala: synergizing genomic and environmental data for effective species management

description: 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.
description: Genomic DNA was extracted from koala tissue samples (n=226) using
 either the Bioline Isolate II Genomic DNA Kit (Bioline, Eveleigh,
 Australia) or according to a high salt method (Sunnucks & Hales,
 1996). Dry specimens (skins or residual tissue on skeletal elements) from
 natural history collections (n=33) were processed using the QIAGEN DNeasy
 Blood & Tissue Kit (Qiagen, Hildon, Germany) according to the
 protocol developed by Fulton, Wagner and Shapiro, (2012). A custom
 in-solution exon capture procedure was designed according to Bragg et al.,
 (2017). Genomic libraries (700-1400 ng total) were prepared for each koala
 sample following the methods devised by Meyer and Kircher, (2010), with
 modifications from Bi et al., (2013). Individually indexed libraries were
 pooled in equimolar ratios and hybridized against the SeqCap EZ probes
 (Roche NimbleGen, Pleasanton, USA) to enrich for target exons, as
 described by Potter et al., (2018). Sequencing was performed as 100-bp paired-end
 reads on the HiSeq 2500, NextSeq 500 or NovaSeq 6000 platforms (Illumina,
 San Diego, CA). The resulting short-read sequence data were deposited in
 the NCBI SRA database (SRA accession: PRJNA816339) and processed using a
 variety of software packages and scripts (included with the Dryad
 package).