This archive contains code and extra files necessary to perform the analyses detailed in the manuscript

'Annotation': 'Ssal_chromosome_annotation.bed', which provides positions of protein coding loci (adapted from Ssa.RefSeq.db and excluding putative pseudogenes and non-coding RNA).

'Code': text files containing commented code used for file conversions and running analyses.

'Extra files for LFMM & BayEnv2': input files with environmental data, and population variance-convariance matrix, needed for performing LFMM & BayEnv2 analyses.

'Extra files for XPEHH': individual chromosome maps and lists of individuals in each population, needed for performing XPEHH analysis.

'Utility files': 'Midway_positions.txt' provides positions midway between adjacent SNPs, used to define haploblock boundaries for annotation; 'Pruned_SNPs.txt' lists the 33,133 SNPs retained after LD pruning, *.spid files are required for file conversions by PGDSpider.