Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range

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Abstract

The koala (Phascolarctos cinereus) is an iconic Australian species that is currently undergoing a number of threatening processes, including disease and habitat loss. A thorough understanding of population genetic structuring and genomic variability of this species is essential to effectively manage populations across the species range. Using a reduced representation genome sequencing method known as double digest restriction-associated sequencing, this study has provided the first genome-wide SNP marker panel in the koala. In this study, 33,019 loci were identified in the koala and a filtered panel of 3060 high-utility SNP markers, including 95 sex-linked markers, were used to provide key insights into population variability and genomic variation in 171 koalas from eight populations across their geographic range. Broad-scale genetic differentiation between geographically separated populations (including sub-species) was assessed and revealed significant differentiation between all populations (FST range = 0.01–0.28), with the largest divergence observed between the three geographically distant subgroups (QLD, NSW and VIC) along the east coast of Australia (average FST range = 0.17–0.23). Sub-group divergence appears to be a reflection of an isolation by distance effect and sampling strategy rather than true evidence of sub-speciation. This is further supported by low proportions of AMOVA variation between sub-species groups (11.19 %). Fine-scale analysis using genome-wide SNP loci and the NETVIEW pipeline revealed cryptic genetic sub-structuring within localised geographic regions, which corresponded to the hierarchical mating system of the species. High levels of genome-wide SNP heterozygosity were observed amongst all populations (He = 0.25–0.35), and when evaluating across the species to other vertebrate taxa were amongst the highest values observed. This illustrates that the species as a whole still retains high levels of diversity which is comparable to other outbred vertebrate taxa for genome-wide SNPs. Insights into the potential for adaptive variation in the koala were also gained using outlier analysis of genome-wide SNPs. A total of 10 putative outlier SNPs were identified indicating the high likelihood of local adaptations within populations and regions. This is the first use of genome-wide markers to assess population differentiation at a broad-scale in the koala and the first time that sex-linked SNPs have been identified in this species. The application of this novel genomic resource to populations across the species range will provide in-depth information allowing informed conservation priorities and management plans for in situ koalas across Australia and ex situ around the world.

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Acknowledgments

We would like to express our gratitude to Eike Joachim Steinig for his help and support with regard to NETVIEW and various other analyses, Damien Higgins for supplying our Port Macquarie samples, Diedre de Villiers for supplying Koala Coast and Ipswich samples and David Phalen for providing samples from NSW and VIC. Monal Lal for his comments and advice on draft manuscripts and Maria Nayfa for her helpful advice regarding outlier analyses. Funding was provided via an Australian Research Council (ARC) Linkage Project grant (LP120200630), with industry funding and in-kind support from partners San Diego Zoo Koala Education & Conservation Program and James Cook University, Sydney University, and Science for Wildlife.

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Correspondence to Shannon R. Kjeldsen.

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Shannon R. Kjeldsen and Kyall R. Zenger have contributed equally to this work.

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Below is the link to the electronic supplementary material.

Supplementary Material 1

Genotype file in the STRUCTURE format containing 3060 SNP markers across all individuals. A value of ‘−9’ indicates missing data. Supplementary material 1 (XLSX 3331 kb)

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Kjeldsen, S.R., Zenger, K.R., Leigh, K. et al. Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range. Conserv Genet 17, 337–353 (2016). https://doi.org/10.1007/s10592-015-0784-3

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Keywords

  • Koala
  • Phascolarctos cinereus
  • Genetic diversity
  • ddRAD
  • Selection
  • SNP