DOI: 10.5061/dryad.6hdr7srd0
title: Genotype data from: Extent of stream habitat and hybridization influence levels of genetic diversity in Redband Trout (<em>Oncorhynchus mykiss gairdneri</em>) populations

description: Habitat loss and fragmentation have isolated many species into small
 geographic areas. This is especially true of stream fishes, where
 alteration of waterways has restricted many species to headwater
 tributaries, leading to low abundances and threatening loss of genetic
 diversity. In addition, hybridization and introgression with introduced
 game fishes can impact the distribution of genetic variation among native
 populations. To assess the effects of habitat extent and hybridization on
 genetic diversity in a stream-dwelling fish, we conducted a study of
 Redband Trout (Oncorhynchus mykiss gairdneri) populations within the
 southernmost drainages of the Snake River basin using a panel of 236
 neutral biallelic single-nucleotide polymorphism (SNP) markers.
 Introgression between Redband Trout and hatchery strains of coastal
 Rainbow Trout (Oncorhynchus mykiss irideus) was found in nearly half of
 the populations assessed, where high levels of admixture corresponded to
 increased heterozygosity. Independent of hybridization, the level of
 genetic diversity was found to be positively influenced by the extent of
 stream habitat available to populations. While high levels of genetic
 diversity in nonhybridized populations may correspond to elevated adaptive
 potential, increased genetic diversity due to introgression represents a
 potential concern to fitness due to the effects of outbreeding depression.
description: # Genotype data from: Extent of stream habitat and hybridization influence
 levels of genetic diversity in Redband Trout (*Oncorhynchus mykiss
 gairdneri*) populations Dataset DOI:
 [10.5061/dryad.6hdr7srd0](10.5061/dryad.6hdr7srd0) ## Description of the
 data and file structure Genotype data for fish samples used in the
 publication: "Extent of stream habitat and hybridization influence
 levels of genetic diversity in Redband Trout (*Oncorhynchus mykiss
 gairdneri*) populations". Samples were genotyped at 236 biallelic
 single nucleotide polymorphisms (SNPs). These SNPs have all been
 identified as neutral markers. Tissue was collected from the pelvic or
 caudal fin of fish sampled, and extracted DNA was sequenced utilizing the
 Genotyping-In-Thousands by Sequencing (GT-seq) method.   ### Files and
 variables #### File: Zambie_et_al._Redband_Genotypes.txt
 **Description:** All genotype information is present in the text file
 Zambie*_*et_al._Redband_Genotypes.txt in genepop file format #####
 Variables * The first line of the text file is a title stating data is in
 genepop format * The next 236 lines of the text file give the marker names
 for the SNPs samples were sequenced at * Following lines containing marker
 names, genotype data of individual samples is given by population. At the
 start of samples from a new population, a line of text with the letters
 POP is included. Each sample is given on a seperate line with the first
 characters in the line naming the stream the individual was collected
 from. Following the characters stating the population of origin for each
 sample, genotype data for the 236 markers is given by 4 digit codes.
 Genotype data is given in the same order the markers are listed at in the
 initial lines of the file. Four digit genotype codes are either 0101,
 0102, 0202, or 0000. 01 and 02 represent the two allele states possible at
 a marker and the 4 digit code informs of both alleles a sample is
 genotyped with. A code of 0000 represents no data. ## Code/software Data
 is given as a .txt file in genepop format that can be opened and viewed in
 any text editor without requiring additional code/software ## Access
 information Other publicly accessible locations of the data: * N/A Data
 was derived from the following sources: * N/A