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Conservation genomics of the ‘Endangered’ long-nosed bandicoot (Perameles nasuta) population at North Head, Sydney, Australia

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Abstract

Wildlife species impacted by habitat loss and fragmentation often require conservation efforts to maintain populations. Long-nosed bandicoots (Perameles nasuta) still persist within the highly urbanised matrix of northern Sydney (Australia). One population at North Head, Sydney, is currently listed as an Endangered population due to its small size, apparent isolation and other threats. To support future management, we used 1,446 single nucleotide polymorphism markers (SNPs) from 167 bandicoots to: i) assess the assumption of isolation and determine if genetic structuring is present between North Head and individuals from 11 other localities in northern Sydney, and ii) investigate genetic diversity over time in the North Head population from 2002 to 2018. Analyses confirmed population structuring and genetic divergence between North Head and greater northern Sydney. Three distinct populations were identified that corresponded to geographic localities (North Head, northern Sydney and Mosman). All populations were significantly differentiated (FST = 0.171–0.345), suggesting local genetic drift between localities. North Head genetic diversity indices estimated between 2002 to 2018 showed relatively constant levels of allelic richness (1.90–2.00) and observed heterozygosity (HO = 0.231–0.310) along with minor levels of inbreeding (FIS 0.020–0.052). The identification of some individuals sampled on North Head that were assigned to other populations suggests some sporadic geneflow into the population has occurred and may have assisted with maintaining genetic diversity. These data suggest that the North Head population is distinct from other northern Sydney populations and has relatively constant levels of genetic diversity.

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Availability of data and materials

Genomic data has been uploaded to DRYAD. Accession number: https://doi.org/10.5061/dryad.f7m0cfxvk.

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Acknowledgements

Thanks to Australian Wildlife Conservancy, NSW National Parks and Wildlife Service, Taronga Conservation Society and the Mammal Collection, Australian Museum for providing samples. Thanks to the Sydney Harbour Federation Trust for funding. Thanks also to M. Hall, E. Lee, L. de Gail, and J. Dargan for long term sample collection, the Australian Centre for Wildlife Genomics (Australian Museum) staff for assistance with laboratory work, and C. Van Der Wal, K. Yi Tea, M. Lott and K. Ewart for assistance with data analysis. Funding for this work was provided by the Sydney Harbour Federation Trust and Australian Wildlife Conservancy.

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This study was funded by the Sydney Harbour Federation Trust and Australian Wildlife Conservancy.

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Correspondence to Mark de Bruyn.

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The methods were performed in accordance with the following ethics approvals and licensing. Animal Research Authority (ARA) – Secretary’s Animal Care and Ethics Committee approval for Biodiversity Conservation Restoration, North Head. Department of Primary Industry (DPI) Scientific Licence 101,333—Biodiversity conservation and restoration at North Head. Office of Environment and Heritage (OEH) Animal Research Authority (ARA) – Secretary’s Animal Care and Ethics Committee approval for Long-nosed Bandicoot Recovery Program AEC 000,214/05 (OEH).

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Nelson, H.V., Frankham, G.J., Leo, V. et al. Conservation genomics of the ‘Endangered’ long-nosed bandicoot (Perameles nasuta) population at North Head, Sydney, Australia. Conserv Genet 22, 745–756 (2021). https://doi.org/10.1007/s10592-021-01356-z

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