Please contact Jessica Metcalf (jessicalmetcalf@gmail.com) with questions about genetic of historic museum samples. For questions about on-going cutthroat trout genetics projects focusing on modern populations, please contact Andrew Martin (am@colorado.edu) For specific questions regarding fish stocking histories, please contact Christopher Kennedy (Chris_Kennedy@fws.gov). For management related questions, please contact Kevin Rogers (Kevin.Rogers@state.co.us). Files 1) "Museum_sample_table.xlsx" - Sample table for the historic specimens, which includes the number of extractions performed at each laboratory. 2) "Fasta_historic" - There are three fasta files for the 30 museum samples. Two fasta files for non-continuous ND2 partial gene sections and one fasta file for COI partial gene sequences. 3) "ND2COI_unique_430bp_HapNet.nex" - unique haplotypes used to generate the parsimony haplotype newtwork shown in Figure 4. The sequence data includes a concatenation of two non-continuous portions of the ND2 gene and one section of COI gene. 4) "All_subspecies_tree_430bp.zip" - alignment of unique haplotypes present in subspecies of cutthroat trout (Oncorhynchus clarkii). The sequence data includes a concatenation of two non-continuous portions of the ND2 gene and one section of COI gene. For some subspecies, sequence data for the COI gene was not available. Sequences originally published in Loxterman & Keeley 2012 include genbank #'s JQ747557ÐJQ747623. Sequences originally published in Metcalf et al. 2007 include genbank #'s EF673223 - EF673276. All_subspecies_unique.nex All_subspecies_unique_PhyML.tre All_subspecies_unique_BEAST.tre 5) "AMOVA_subsample_scripts.zip" - custom scripts for subsampling modern data set to the size and drainage structure of the historic data set. 3 files. subsample.py test_subsample.py run_amova.R 6) "Weird_Bear_Creek_Kennedy_2010.pdf" report on the history of Bear Creek cutthroat trout population.