FASTA, ADMIXTURE/SIMULATIONS, PCA, HAPLOTYPE BLOCK/ANCESTRY_HHM INPUT FILES

(1) Individual and concatenated fasta files for 3,037 Autosomal and 163 Z linked markers identified using ddRAD-seq protocols for 290 Mallards, American black ducks, and hybrids. Concatenated fasta files are provided by chromosome, as well as a fasta file with mitochondrial sequences. (2) Run-ready ped/map input files of 163 Z-linked and 3,037 autosomal ddRAD-seq markers for PCA and ADMIXTURE analyses for 290 Mallards, American black ducks, and hybrids. Additionally, simulation code and run-ready ped/map ADMIXTURE files are provided. (3) Run-ready input files for BAYESCAN are provided. (4) Simulation code and steps to take for haplotype block and ANCESTRY_HHM analyses.