This repository contains a series of datasets and scripts used in analyses for the manuscript with which this repository is associated. They include:

1) admixturegraphs.R: A script use to setup and compare admixture graph models using Bayes Factors in the admixturegraph R package.
2) Files for running a BPP analysis to estimate divergence times under a network model: bpp.txt (sequence data), bpp_laredoensis_multiorigin_oldB.ctl (control file with commands for analysis), bpp_laredoensis.Imap.txt (mapping file for assigning individuals to species), BPP_divtimes.r (post processing R script for calibrating divergence time estimates).
3) GeneticDiversity.R: Script for calculating various genetic diversity statistics from SNP data in R.
4) IBS_analysis.R: Script for performing Identity-By-State analysis using SNP data in R.
5) laredoensis_snps.vcf: SNP variants in variant call format.
6) Files for performing demographic modelling in fastsimcoal2: jointMAF files(joint site frequency spectrum calculations for each population), .est files (prior and rules file for single and multi-origin models), .tpl files (template execution files).
7) laredoensis_STRUCTURE.ustr: input SNP file for STRUCTURE
8) mrbayes_laredoensis.nex: File for MrBayes analysis with data and execution commands
9) nQuire.slurm: slurm script for performing ploidy estimation on samples using Trimmomatic, BWA, samtools and nQuire software.
10) pnet_laredoensis.nex: Nexus file with data and commands for performing phylogenetic network analysis in PhyloNet.