DOI: 10.5061/dryad.f7m0cfxvk
title: SNP genotyping of North Head and northern Sydney Long-nosed bandicoots (Perameles nasuta)

description: 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.
description: 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 &lt;100%, loci with a call rate &lt;70%
 and individuals with a call rate &lt;75% were removed from the
 analysis to ensure quality of the resulting datasets. Markers with minor
 allele frequencies of &lt;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.
description: 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.