Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance

This dataset was used to examine the phylogeographic genetic structure of Eastern three lined skink Bassiana duperreyi. It comprises  SNP data used for population genetics and phylogenetic reconstruction. The data were used to provide foundational work for the detailed taxonomic re-evaluation of this species complex and to reinforce the need for biodiversity assessment to include an examination of cryptic species and/or cryptic diversity below the level of species. Such information on lineage diversity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally., Briefly, samples of tissue were collected from across the range of the species, Bassiana duperreyi, including from Australian Museums, DNA was extracted, double digested and genotyped for SNP markers using the technology of Diversity Arrays Technology (DArT, Canberra). The data were analysed in the software package dartR available on the CRAN repository, as per the script provided. Structure across the landscape was used to inform assessment of the impact of regional scale disturbance.
Skin tissues and extracted DNA were provided to DArT for processing, sequencing and informative SNP marker identification using DArTseqTM (Kilian et al., 2012). DArT performed a genome complexity reduction technique using double digestion of genomic DNA with two restriction endonucleases PstI (5′- CTGCA|G- 3′) and SphI (5′- GCATG|C- 3′), fragment-size selection and next-generation sequencing on an Illumina HiSeq2500 (CA, USA). Sequences were processed using proprietary DArT analytical pipelines (for full ..., The script necessary to undertake the SNP analyses depends on the R software package dartR.base available on the Comprehensive R Archive Network (CRAN). dartR.base works with adegenet genlight objects such as those in the file list provided.
Software for undertaking phylogenetic analysis on the SNPs include SVDQuartets (Singular Value Decomposition Quartets, Chifman & Kubatko, 2014) available through Paup (Swofford, 2003)., # Data from: Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance

This Dryad entry contains the datafiles and associated R script to prepare the data in a form conducive to analysis, including the analyses presented in the companion article. They include SNP datasets for the Eastern three-lined skink *Bassiana duperreyi*.

## Description of the data and file structure

The SNP data comprises a matrix of entities (individuals) versus attributes (loci) taking on the states 0 for homozygous reference allele, 2 for homozygous alternate allele and 1 for the heterozygous state. As such, the data have no units of measurement but do when summed, conveniently, represent the frequency of the alternate allele.

The data are stored in compressed form as an adegenet genlight object with associated locus metadata (e.g. callrate, reproducibility) and individual metadata (e.g. latitude, longitude, population). The SNP ...