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14 J. L. METCALF ET AL. <br />postdoctoral researcher who uses ancient DNA methods to <br />answer questions in ecology, evolution, conservation, forensics <br />and history (https: / /sites.google.com /site /jessicalmetcalf /). A. <br />P.M. is a Professor at CU working on a wide range of evolu- <br />tionary and conservation - focused research projects of native <br />species (http: / /stripe.colorado.edu / —am /Site /Martin_Lab). To <br />find out more about cutthroat trout conservation in Colorado, <br />please see http:/ /wildlife. state. co. us /Research /Aquatic /Cutthroat <br />Trout. <br />Data accessibility <br />Historical and modern sequence data sets are available on <br />NCBI GenBank under accession numbers JX195488 JX195497. <br />Alignments of sequence data and haplotype frequency data <br />can be found at doi: 10.5061/dryad.b4783. <br />A haplotype frequency table for 53 modern populations as <br />well as fish stocking data can be found at http://stripe.colo- <br />rado.edu/—am/Site/Trout.html. <br />Supporting information <br />Additional Supporting Information may be found in the online <br />version of this article. <br />Fig. S1 (a) Plot showing a decrease in average PCR success <br />across all samples as target amplicon size increased. Mito- <br />chondrial amplicons ranged from 91 to 135 basepairs. (B) <br />Logistic regression of PCR amplification success (1) or failure <br />(0) as a function of fragment size for 322 PCR reactions. <br />Chi square = 39.0657; df = 1; P = 0.0000. <br />Table S1 List of museum samples used in the study, including <br />information on the drainage, museum, specimen accession <br />number, collector, year collected, collection locality, the num- <br />ber of DNA extractions completed at the University of Colora- <br />do (CU) and the Australian Center for Ancient DNA (ACAD), <br />and the number of DNA samples that yielded successful <br />amplification of DNA. <br />Table S2 Mitochondrial DNA primers sequences used in the <br />study. <br />Table S3 Modern cutthroat trout populations sampled across <br />seven drainage basins in Colorado and New Mexico. <br />Table S4 The extant lineage, the diagnostic SNPs for each line- <br />age (based on 430 bps), and the number of historic samples <br />that have all of the diagnostic SNPs of each extant lineage. <br />Table S5 Number of ND2 mitochondrial haplotypes assigned <br />to extant major lineages from fish that were sampled from 53 <br />populations across major drainage systems. <br />Please note: Wiley- Blackwell are not responsible for the content <br />or functionality of any supporting materials supplied by the <br />authors. Any queries (other than missing material) should be <br />directed to the corresponding author for the article. <br />© 2012 Blackwell Publishing Ltd <br />