Genotype data from: Extent of stream habitat and hybridization influence levels of genetic diversity in Redband Trout (Oncorhynchus mykiss gairdneri) populations
Data files
Oct 23, 2025 version files 1.38 MB
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README.md
2.29 KB
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Zambie_et_al._Redband_Genotypes.txt
1.38 MB
Abstract
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.
Dataset DOI: 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:
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Data was derived from the following sources:
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