Data from: Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus); a dietary-specialist species distributed across heterogeneous environments
Kjeldsen, Shannon R., James Cook University
Raadsma, Herman W., University of Sydney
Leigh, Kellie A., University of Sydney
Tobey, Jennifer R., San Diego Zoo Institute for Conservation Research
Phalen, David, University of Sydney
Krockenberger, Andrew, James Cook University
Ellis, William A., Agriculture and Food
Hynes, Emily, Ecoplan Australia, Torquay, Australia
Higgins, Damien P., University of Sydney
Zenger, Kyall R., James Cook University
Published Aug 07, 2018 on Dryad.
Cite this dataset
Kjeldsen, Shannon R. et al. (2018). Data from: Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus); a dietary-specialist species distributed across heterogeneous environments [Dataset]. Dryad. https://doi.org/10.5061/dryad.1683r1s
The Australian koala is an iconic marsupial with 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 taxonomic classification of three koala sub-species, 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 (ie. Blue Mountains region; AvHecorr=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.
P. cinereus SNP sequences
A fasta file containing 5,264 short sequences tags from P. cinereus samples collected opportunistically across Australia from 2009-2016. Each tag contains an allele identifier, along with SNP position and mutation (with the dominant/reference SNP being listed first). Eg. 15907811|F|0--48:G>A. Produced using the commercial provider, Diversity Arrays Technology (DArTseq).For further information, please contact the corresponding author.