"alignments" folder contains concatenated ddRAD phylip alignments produced by iPyrad. `mXXp` naming scheme consistent with iPyrad parameter files. "bridledCOB.nex" contains the DNA sequence alignment for the mtDNA gene cytochrome b used in the Bayesian phylogenetic analysis. "bridledCOB.nex.con.tre" summarized posterior tree from Bayesian analysis of the mtDNA cytochrome b data. "bridledNUC.nex" contains the DNA sequence alignment for the 11 nuclear genes used in the Bayesian phylogenetic analysis. "bridledNUC.nex.con.tre" summarized posterior tree from Bayesian analysis of the 11 nuclear genes. "iPyrad_paramFiles" folder contains assembly parameters for iPyrad. `mXXp` indicates the minimum proportion of samples per locus (`min_samples_locus` iPyrad parameter). For example, `m70p` indicates that each locus is represented by at least 70% of the samples. "P_freemanorum_meristic_data.csv" the merstic data of Percina freemanorum. "P_freemanorum_meristic_specimen_info.csv" information associated with specimens of Percina freemanorum. "P_kusha_meristic_data.csv" the merstic data of Percina kusha. "P_kusha_meristic_specimen_info.csv" information associated with specimens of Percina kusha. "IQTree" folder contains bash script to run IQTree analyses and resulting treefiles. `mXXp` naming scheme consistent with iPyrad parameter files. "VCFs" folder contains bash script to run VCFTools filtering, outgroup file listing outgroup taxa to prune, input VCF file from iPyrad, and filtered VCF files. `Unlinked` indicates that SNPs have been pruned to include only one SNP per ddRAD locus. `mXXp` naming scheme consistent with iPyrad parameter files.