DOI: 10.5061/dryad.3n5tb2rsd
title: Supplementary data from: A genetic assessment of natural barriers for isolating a proposed Greenback cutthroat trout reintroduction area

description: We used genetic techniques to evaluate a series of natural waterfalls for
 their potential to serve as barriers to prevent nonnative salmonids from
 entering a proposed reintroduction area for federally threatened Greenback
 cutthroat trout Oncorhynchus clarkii stomias. Genetic samples
 were collected from nonnative Brook Trout Salvelinus fontinalis at 11
 sampling reaches above and below natural waterfalls (height: ~1-3 m under
 baseflow conditions) along a 33-km segment of Colorado’s upper Cache la
 Poudre River near the outflow of the proposed reintroduction area. To
 evaluate whether upstream movement of Brook Trout is restricted by any of
 these waterfalls, we characterized longitudinal trends in genetic
 diversity along the river corridor and examined patterns of genetic
 differentiation and population structure in relation to waterfall
 locations using a panel of microsatellites. We found no evidence that the
 waterfalls served as complete movement barriers for nonnative Brook Trout
 based on genetic clustering analyses, estimates of population
 differentiation, and longitudinal genetic patterns. Our multi-locus
 assessment did not identify alleles restricted to downstream reaches, and
 the river segment was genetically homogenized. This evaluation suggests
 that the existing waterfalls do not fully prevent upstream movement by
 nonnative Brook Trout, and thus barrier modification would be needed to
 establish an isolated Greenback cutthroat trout population in the proposed
 wilderness area.
description: Brook Trout tissue samples (fin clips) were collected from 11
 sampling sites separated by waterfalls along a 33km segment of
 Colorado's Cache la Poudre River. 269 individual Brook Trout were
 genotyped at 12 previously described microsatellite
 loci: <em>SfoC113, SfoC115, SfoC129, SfoC38, SfoC88, SfoD91, SfoB52,
 SfoC24, SfoC28, SfoC79, SfoC86</em>, and <em>SfoD75
 </em>(King et al. 2012). Genomic DNA was extracted using Qiagen
 Dneasy Blood and Tissue Kits following the manufacturer’s protocol.
 Microsatellite markers were amplified using polymerase chain reaction
 (PCR) in two 10 µl multiplexes, each containing 2 µl genomic DNA, 5 µl
 Qiagen Multiplex PCR Mastermix, 0.04- 0.1 µl of each forward and reverse
 PCR primer (Table S4), and 2.18-2.2 µl nuclease free water. The thermal
 profile for PCR amplification consisted of denaturing at 95°C for 15
 minutes, 35 cycles of denaturation at 95°C for 45 seconds, annealing at
 56°C for 45 seconds, and extension at 72°C for 2 minutes, followed by a
 final extension of 60°C for 30 minutes. PCR products were treated with a
 solution of formamide and GeneScan 600 LIZ size standard and visualized
 using an Applied Biosystems 3500 genetic analyzer. Alleles were scored
 using GeneMapper version 6. King, T. L., B. A.
 Lubinski, M. K. Burnham-Curtis, W. Stott, and R. P. Morgan. 2012. Tools
 for the management and conservation of genetic diversity in Brook Trout
 (<em>Salvelinus fontinalis</em>): tri- and tetranucleotide
 microsatellite markers for the assessment of genetic diversity,
 phylogeography, and historical demographics. Conservation Genetics
 Resources, 4:539–543.
description: # Supplementary data from: A genetic assessment of natural barriers for
 isolating a proposed Greenback cutthroat trout reintroduction area
 [https://doi.org/10.5061/dryad.3n5tb2rsd](https://doi.org/10.5061/dryad.3n5tb2rsd) These data consist of microsatellite genotypes at 12 loci for 269 individual Brook Trout *Salvelinus fontinalis* collected from 11 sampling locations positioned longitudinally along a 33km segment of Colorado's Cache la Poudre River. All sampling locations are separated by waterfalls (height ranging ~1-3 meters). ## Description of the data and file structure Details for: "Stack_et_al_microsat_dataset.csv" Format: .csv Size: 29.62 KB Dimensions: 270 rows x 26 columns Variables: * Sample (column 1): unique identifiers for individual genotyped Brook Trout. - Reach (column 2): numeric identifiers for the sampling locations from which each individual was collected, ordered from downstream (1) to upstream (11). * Remaining columns: paired columns containing diploid genotypes (allele size) for 12 microsatellite loci. Column headers are locus names as described by King et al. 2012 followed by "_1" or "_2" indicating diploid copies. Numeric values for allele sizes represent total fragment length. Missing data are entered as "NA". References: King, T. L., B. A. Lubinski, M. K. Burnham-Curtis, W. Stott, and R. P. Morgan. 2012. Tools for the management and conservation of genetic diversity in Brook Trout (Salvelinus fontinalis): tri- and tetranucleotide microsatellite markers for the assessment of genetic diversity, phylogeography, and historical demographics. Conservation Genetics Resources 4(3):539–543.