Dataset from: Evolution history and the importance of genomic diversity facing climate change. The case of Agave marmorata Roezl., a microendemic agave used for mezcal production.

Vcf output from VCFtools v.0.1.15, excluding sites with over 80% of missing data. We left only sites with a maximum and minimum of two alleles, a minimum mean depth of 12, and a maximum mean depth of less or equal of 200. Sites that significantly deviated from the Hardy-Weinberg equilibrium (1e-02), a minor allele frequency (MAF) of <0.05, InDels, and individuals with more than 90% missing data were removed.