Dataset DOI: 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

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 )

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