DOI: 10.5061/dryad.c866t1gjg
title: Data and code from: Pleistocene climatic changes drive expansion and fragmentation in a widespread arid zone specialist, <em>Petrogale lateralis</em>

description: This is a genomic dataset of exon sequences for the black-footed
 rock-wallaby (Petrogale lateralis). It consists of population-level
 sampling based on museum skins and contemporary samples from across the
 five subspecies of Petrogale lateralis. There are multiple
 datasets used for various analyses, including phylogenetic network and
 tree analyses, evaluation of individual heterozygosity levels, analyses of
 admixture, population connectivity and diversity, and demographic history.
description: # Data and code from: Pleistocene climatic changes drive expansion and
 fragmentation in a widespread arid zone specialist, *Petrogale lateralis*
 Dataset DOI: [10.5061/dryad.c866t1gjg](10.5061/dryad.c866t1gjg) ##
 Description of the data and file structure README for Dryad Data
 Submission   Principal Investigator Contact Information Name: Sally Potter
 Institution: Macquarie University Email:
 [sally.potter@mq.edu.au](mailto:sally.potter@mq.edu.au)   Title: Exon
 sequence data for *Petrogale lateralis* to examine phylogeographic and
 population history Description: This dataset contains exon sequences
 generated as part of the study " Pleistocene climatic changes drive
 expansion and fragmentation in a widespread arid zone specialist,
 *Petrogale lateralis*", published in [Molecular Ecology]. Data were
 collected to examine the evolutionary and demographic history of the
 black-footed rock-wallaby in Australia. The dataset includes 1096 exon
 sequences from 97 individuals representing widespread sampling of the five
 *Petrogale lateralis* sub-species. SNP and full exon sequence data are
 used for phylogenetic and population genetic analyses to examine the
 divergence history of the sub-species and the genetic diversity and
 demographic history of the populations across the distribution of
 *Petrogale lateralis*. Analyses reveal a history of recent divergence and
 demographic expansion, followed by contemporary lack of gene flow and
 potential bottlenecks for isolated populations. Funding: This project was
 supported by the Australian Research Council LP180100315 and FT210100715
 awarded to Sally Potter, as well as BioPlatforms Australia ‘Oz Mammals
 Genomics’ Initiative funded through the Australian Government National
 Collaborative Research Infrastructure Strategy (NCRIS).   ### Files and
 variables File 1 Name: Metadata_lateralis.csv File 1 Description: A
 Comma-Separated Values (CSV) file with metadata information about each
 sample, including sequence ID, BioPlatforms Australia facility sample ID,
 tissue number, voucher number, species ID, population ID, geographic
 location, raw sequence identifier on NCBI short read archive, sample
 collection age, experimental design for the exon capture. File 2 Name:
 lateralis_nohistorical_noIsland_PopGenome.phy File 2 Description:
 concatenated exon alignment of 1934 loci coded with ambiguity codes in
 PHYLIP format for 64 *Petrogale lateralis* individuals. This dataset
 excludes historical samples and samples from islands (mainland only) used
 for PopGenome analysis. File 3 Name: lateralis_noOG.phy File 3
 Description: concatenated exon alignment of 1934 loci coded with ambiguity
 codes in PHYLIP format for 97 *Petrogale lateralis* individuals. This
 dataset does not include any outgroup samples (used for phylogenetic
 network analysis). File 4 Name: lateralis_wOG.phy File 4 Description:
 concatenated exon alignment of 1934 loci coded with ambiguity codes in
 PHYLIP format for 97 *Petrogale lateralis* individuals and four outgroup
 samples (used for phylogenetic analysis). File 5 Name: lateralis_OTUs.phy
 File 5 Description: concatenated exon alignment of 1934 loci coded with
 ambiguity codes in PHYLIP format for 12 *Petrogale lateralis* individuals
 that represent operational taxonomic units and two outgroup samples (used
 for MCMCtree analysis). File 6 Name: lateralis_OTUs_codons.phy File 6
 Description: concatenated exon alignment of 1934 loci coded with ambiguity
 codes in PHYLIP format for 12 *Petrogale lateralis* individuals that
 represent operational taxonomic units and two outgroup samples (used for
 MCMCtree analysis).This dataset represents the third codon only sites.
 File 7 Name: lateralis_mainland_8pop_100loci.phy File 7 Description: input
 files for MIGRATE analysis that includes sequence data for 100 exon loci
 for mainland populations to assess gene flow history. File 8 Name:
 lateralis_1SNP_ALL_individuals.fasta File 8 Description: FASTA sequence
 file of a single SNP per exon concatenated into single alignment for all
 individuals of *Petrogale lateralis*. File 9 Name:
 lateralis_1SMP_mainland_individuals.fasta File 9 Description: FASTA
 sequence file of a single SNP per exon for only mainland individuals of
 *Petrogale lateralis.* File 10 Name: lateralis_wOG_ALLSNPs.fasta File 10
 Description: FASTA file of all SNPs for all individuals of *Petrogale
 lateralis* and the four outgroup individuals. File 11 Name:
 lateralis_1SNPb_treemix.input.gz File 11 Description: TreeMix input file
 with allele counts per population per SNP for 1934 (a single SNP per
 exon). File 12 Name: lateralis_ALL_SNPs_treemix.input.gz File 12
 Description: TreeMix input file with allele counts per population per SNP
 for all SNPs in the dataset. File 13 Name: parmfile_8pop_100loci File 13
 Description: input control file for Migrate-n analysis of *Petrogale
 lateralis* for 100 loci and mainland populations. File 14 Name:
 plateralis_OTUs_DD.tre File 14 Description: treefile for input into
 mcmctree analysis consisting of the operational taxonomic units and the
 outgroups. File 15 Name: mcmctree_plateralis_OTUs.ctl File 15 Description:
 input control file for mcmctree divergence dating analysis. File 16 Name:
 lateralis_pops_all_sorted.csv File 16 Description: A CSV file of metadata
 for SNP files for use in R including sample ID and population ID. File 17
 Name: lateralis_coordinates.csv File 17 Description: A CSV file of
 metadata for SNP files used for isolation-by-distance (IBD) analysis in R
 including sample ID, population ID and latitude and longitude. File 18
 Name: lateralis_nohistorical_PopGenome.phy File 18 Description:
 concatenated exon alignment of 1934 loci coded with ambiguity codes in
 PHYLIP format for 88 *Petrogale lateralis* individuals. This dataset
 excludes historical samples used for PopGenome analysis. File 19 Name:
 mcmctree_lateralis_OTUs.phy File 19 Description: A phylip sequence file of
 15 *Petrogale* individuals representing a single representative per
 population/subspecies used as input in mcmctree to estimate divergence
 times.  File 1 Name: IBD_lateralis.R File 1 Description: R script used to
 calculate isolation-by-distance. File 2 Name: PopGenome_code.R File 2
 Description: R script used to calculate within and between nucleotide
 diversities (Dxy, pi). File 3 Name: TajimaD_PopGenome.R File 3
 Description: R script used to calculate Tajima'92s D for each
 population. File 4 Name TajimaD_PopGenome_CoalescentSimulation.R File 4
 Description: R script used to run coalescent simulations to test for
 significance of Tajima'92s D. File 5 Name: tess3r_code_lateralis.R
 File 5 Description: R script used to estimate genetic clusters using tess3
 analysis Species: \- Scientific name: *Petrogale lateralis* \- Common
 name: black-footed rock-wallaby Methods: \- DNA extraction: salting-out
 method and DNeasy Blood and Tissue Kit \- Sequencing platform: Illumina
 HiSeq 2500 and Illumina NovaSeq 6000 (100bp paired-end run) \- Assembly
 tool: raw sequencing data was processed, assembled and aligned using the
 Exon Capture Pipeline for Phylogenetics (ECPP, cf5
 [https://github.com/Victaphanta/ECPPcf2](https://github.com/Victaphanta/ECPPcf2) ) Usage Notes: \- All files are in standard formats (e.g., FASTA, PHYLIP, CSV). \- Genotypes are coded as CTGA or ambiguity codes (e.g., S,K,Y). \- Individuals missing data are indicated as "N". \- Raw sequencing data are available on SRA outlined in 1.1.Metadata_lateralis.csv Preferred citation: Potter S, Moritz C, Ottewell K, Roycroft E, MacDonald A, Byrne M, Cooper S, Pearson D, Eldridge M (2026) Two Contrasting Demographic Processes Shape the Divergence and Evolution of the Widespread Arid Zone Specialist, *Petrogale lateralis. Molecular Ecology*