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Heredity (Edinb). 2018 Sep 12. doi: 10.1038/s41437-018-0144-4. [Epub ahead of print]

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

Author information

1
Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia. shannon.kjeldsen1@my.jcu.edu.au.
2
Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia.
3
Science for Wildlife, PO Box 286, Cammeray, NSW, 2062, Australia.
4
San Diego Zoo Institute for Conservation Research, Escondido, CA, 92027, USA.
5
Centre for Tropical Biodiversity and Climate Change, Division of Research and Innovation, James Cook University, Cairns, QLD, 4878, Australia.
6
School of Agriculture and Food Science, The University of Queensland, St Lucia, QLD, 4072, Australia.
7
Ecoplan Australia, PO Box 968, Torquay, VIC, 3228, Australia.
8
Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia.
9
Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia.

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; 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.

PMID:
30209291
DOI:
10.1038/s41437-018-0144-4

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