Data from: Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout

 

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Title Museum_sample_Table
Downloaded 66 times
Description Sample Table includes metadata associated with the historic specimens.
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Title Fasta files containing museum data
Downloaded 34 times
Description 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.
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Title ND2COI_unique_430bp_HapNet
Downloaded 39 times
Description Nexus formatted sequence file containing 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.
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Title AMOVA_subsample_scripts
Downloaded 22 times
Description "AMOVA_subsample_scripts.zip" - custom scripts for subsampling modern data set to match the number of samples in each drainage in the historic data set. 3 files.
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Title Weird_Bear_Creek_Kennedy_2010
Downloaded 142 times
Description USFWS report on the history of Bear Creek cutthroat trout population.
Download Weird_Bear_Creek_Kennedy_2010.pdf (474.2 Kb)
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Title All_subspecies_tree_430bp
Downloaded 40 times
Description 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 JQ747557–JQ747623. 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
Download All_subspecies_tree_430bp.zip (20.29 Kb)
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Title ND2 haplotype table for 53 modern populations
Downloaded 43 times
Description We sequenced a 648 or 889 base pair region of the ND2 gene for at least 10 individuals from 53 contemporary populations. This table shows ND2 haplotypes present in each population sampled, number of fish sampled per population, and the number of fish belonging to each haplotype. Haplotypes are either defined by a genbank number and an abbreviated short name that is used by Parks and Wildlife (KBRkey). Major mtDNA lineage designations include (GCR = Gunnison/Colorado, YMP = Yampa, SP = South Platte, RG = Rio Grande, YS= Yellowstone cutthroat trout and RB = Rainbow trout.
Download ND2_haplotype_table_April11_2012.xls (2.195 Mb)
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When using this data, please cite the original publication:

Metcalf JL, Love Stowell SL, Kennedy CM, Rogers KB, McDonald D, Keepers K, Epp J, Cooper A, Austin JJ, Martin AP (2012) Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout. Molecular Ecology 21(21): 5194–5207. http://dx.doi.org/10.1111/mec.12028

Additionally, please cite the Dryad data package:

Metcalf JL, Love Stowell SL, Kennedy CM, Rogers KB, McDonald D, Keepers K, Epp J, Cooper A, Austin JJ, Martin AP (2012) Data from: Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.b4783
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