DOI: 10.5061/dryad.b4783
title: Data from: Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout

description: Many species are threatened with extinction and efforts are underway
 worldwide to restore imperiled species to their native ranges. Restoration
 requires knowledge of species’ historic diversity and distribution, which
 may not be available. For some species, many populations were extirpated
 and humans moved individuals beyond their native range before native
 diversity and distribution were documented. Moreover, traditional
 taxonomic assessments often failed to accurately capture phylogenetic
 diversity. We illustrate a general approach for estimating regional native
 diversity and distribution by assembling a large archive of historical
 records documenting human-mediated change in the distribution of cutthroat
 trout (Oncorhynchus clarkii) coupled with a phylogenetic analysis of 19th
 century (before intensive fish stocking) and contemporary DNA samples. Our
 study of the trout in the southern Rocky Mountains uncovered six divergent
 lineages, two of which went extinct, probably in the early 20th century. A
 third lineage, previously declared extinct, was discovered surviving in a
 single stream outside of its native range. Comparison of the historic and
 modern distributions with stocking records revealed that the current
 distribution of trout largely reflects intensive stocking early in the
 late 19th and early 20th century from two phylogenetically and
 geographically distinct sources. Our documentation of recent extinctions,
 undescribed lineages, errors in taxonomy, and dramatic range changes
 induced by human movement of fish underscores the importance of the
 historical record when developing and implementing conservation plans for
 threatened and endangered species.
description: Museum_sample_TableSample Table includes metadata associated with the historic specimens.Fasta files containing museum dataThere 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.Fasta_historic.zipND2COI_unique_430bp_HapNetNexus 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.AMOVA_subsample_scripts"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.Weird_Bear_Creek_Kennedy_2010USFWS report on the history of Bear Creek cutthroat trout population.All_subspecies_tree_430bpalignment 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.treND2 haplotype table for 53 modern populationsWe 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.ND2_haplotype_table_April11_2012.xls