For STRUCTURE, unless otherwise noted in the results, each analysis was performed without any prior population assignment and was performed at least 3 times with similar results using > 10,000 replicates and 5000 burn-in cycles under the admixture model. For analyses using smaller marker sets (24 and 48 markers) longer runs were necessary to achieve similar results on multiple run comparisons. For 24 and 48 marker sets, 50,000 replicates and 10,000 burn-in cycles were used with the exception of 24 markers selected using In4 (four population informativeness). For these analyses, 100,000 replicates and 20,000 burn-in cycles were necessary. For all analyses reported we used the “infer α” option with a separate α estimated for each population (where α is the Dirichlet parameter for degree of admixture). Runs were performed under the λ = 1 option where λ parameterizes the allele frequency prior and is based on the Dirichlet distribution of allele frequencies.
