Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments

Abstract

The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHe=0.20, PL% = 68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene flow and adapt across divergent environments as long as the required food source is available.

Inbreeding and disease avoidance in a free‐ranging koala population

“…SNP genotyping was conducted as in Kjeldsen et al. (2018) by Diversity Arrays Technology, Canberra, using their proprietary DArTseq technology. DArTseq utilises a combination of next‐generation sequencing platforms and DArT complexity‐reduction methods (Courtois et al., 2013; Cruz, Kilian, & Dierig, 2013; Kilian et al., 2012; Raman et al., 2014), and, similar to DArT methods based on array hybridisations, the protocol is optimised for organism and application by selecting the most appropriate complexity reduction method.…”

Histological survey for oxalate nephrosis in Victorian koalas (Phascolarctos cinereus)

“…7 A disease similar to primary hyperoxaluria has recently been reported in a closely related colony of the Australian native marsupial Gilbert's potoroo (Potorous gilbertii). 8 The Mount Lofty Ranges koalas may be more at risk of genetic disease due to their reduced diversity 9 following several population bottlenecks in their history. 10 Koalas in South Australia primarily originate from Victoria.…”

“…10 A recent genetic study has shown that South Australian koalas are closely related to those in Victoria and have lower genetic diversity than undisturbed northeastern populations. 9 Therefore, if an inherited disease similar to primary hyperoxaluria was the cause of oxalate nephrosis in Mount Lofty Ranges koalas, it would be expected that Victorian koalas, from which these koalas originated, would also be affected. However, oxalate nephrosis has not previously been reported in Victorian koalas.…”

Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia (Oreochromis niloticus) in Egypt

“…DArTseq TM reduced-representation libraries were prepared as described by Sansaloni et al (2011) and Kilian et al (2012). In short, optimization of the complexity reduction process for Nile tilapia was achieved by using a combination of PstI and HpaII methylation-sensitive restriction enzymes for digestion and unique barcode sequences ligated onto the ends of each resulting fragment (Kilian et al, 2012;Lind et al, 2017;Kjeldsen et al, 2019). Bridge amplification was achieved by incorporating a PstI specific adaptor with an Illumina flow-cell attachment region, primer sequence, and unique barcode coupled with the reverse HpaII specific adaptor containing a second Illumina flowcell attachment sequence (Lind et al, 2017;Schultz et al, 2018;Kjeldsen et al, 2019).…”