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SNP genotyping of North Head and northern Sydney Long-nosed bandicoots (Perameles nasuta)

Citation

Nelson, Holly et al. (2021), SNP genotyping of North Head and northern Sydney Long-nosed bandicoots (Perameles nasuta) , Dryad, Dataset, https://doi.org/10.5061/dryad.f7m0cfxvk

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). These data are from a conservation genetics project investigating population structure and genetic diversity of the North Head Long-nosed bandicoot (Perameles nasuta) population and individuals from surrounding suburbs throughout northern Sydney.

The 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 were used to suggest that the North Head population is distinct from other northern Sydney populations and has relatively constant levels of genetic diversity.

Methods

DNA was extracted from tissue taken from 167 Long-nosed bandicoots between 2001-2019. DNA was supplied to Diversity Arrays Technology (DArT) for analysis using DArTseq™. Genomic DNA SNP data were quality-filtered in R STUDIO v.1.2.1335 using the DARTR package v1.1.11. SNPs with a repeat average <100%, loci with a call rate <70% and individuals with a call rate <75% were removed from the analysis to ensure quality of the resulting datasets. Markers with minor allele frequencies of <0.05 were removed to prevent interference of population structure. SNPs in linkage disequilibrium (LD) and monomorphic loci were also removed across all individuals during the filtering process.

Usage Notes

The dataset comprises three self-explanatory files consisting of (1) species identifiers, (2) metadata for SNP genotyping file, (3) main SNP genotyping file.

1) individual_LNB_identifiers_for_ReportSNP_singlerow_1

This file lists the individual identifiers referenced in the other two files and includes sampling locations.

2) Metadata_for_Report_LNBsinglerow_1.csv

This file provides the metadata for the main SNP genotyping file.

3) Report_DTel18-3515_SNP_singlerow_.csv

This file is the main data file comprised of the SNP genotyping.

The submitted dataset includes all SNPs prior to the filtering steps outlined in the methodology. 

Funding

Sydney Harbour Federation Trust

Australian Wildlife Conservancy

Sydney Harbour Federation Trust