Data from: Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context

Mandeville E, Walters A, Nordberg B, Higgins K, Burckhardt J, Wagner C

Date Published: June 19, 2019

DOI: https://doi.org/10.5061/dryad.6s7d02q

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Title VCF file (gzipped)
Downloaded 1 time
Description VCF file containing data for 1286 individuals and 12666 loci. Minor allele frequency cut-off of 0.05 was used, and at least 60% of individuals have data at each retained site. Loci with >2 alternative alleles are excluded.
Download variants_0.6_maf0.05.recode.vcf.gz (47.68 Mb)
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Title entropy input file
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Description Input file for entropy including 1286 individuals and 12666 loci. Data are in genotype likelihood form - this file was made by simplifying a VCF using the script vcf2mpgl.pl
Download entropy_in_0.6_maf0.05.mpgl.gz (25.75 Mb)
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Title script for converting vcf to mpgl
Downloaded 2 times
Description This perl script converts VCF output to mpgl format, a simplified version of genotype likelihoods that forms the input for the entropy clustering analysis
Download vcf2mpgl.pl (3.268 Kb)
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Title Script for environmental correlates of hybridization outcomes
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Description This script does the model averaging described in the paper and displayed in Fig. 5.
Download model_averaging_trout_MuMIn.R (8.023 Kb)
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Title Response variable data for model averaging
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Description Response variables summarizing genomic outcomes of hybridization across 27 locations in the North Fork Shoshone River basin
Download response_var_18jan18.csv (1.048 Kb)
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Title Predictor variables for model averaging
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Description Environmental and historical data associated with locations where hybrid individuals were sampled. Input for model_averaging_trout_MuMIn.R
Download predictors_var_26july18.csv (2.852 Kb)
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Title YSC_RBT_allind_barcode_key_detailed
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Description Metadata for sequenced individuals
Download YSC_RBT_allind_barcode_key_detailed.csv (93.42 Kb)
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Title Simulation code - main file
Downloaded 2 times
Description This code runs simulations presented in the paper. Note, this script requires a function found in simulate_func.R (accessed with source() at the top of the script).
Download simulate_hyb_main.R (5.762 Kb)
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Title Simulation code - functions
Downloaded 2 times
Description This script contains functions to simulate individual-based genomic outcomes of hybridization. Migration, population size, and starting proportions of individuals in each species can be adjusted.
Download simulate_func.R (4.795 Kb)
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When using this data, please cite the original publication:

Mandeville EG, Walters AW, Nordberg BJ, Higgins KH, Burckhardt JC, Wagner CE (2019) Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context. Molecular Ecology, online in advance of print. https://doi.org/10.1111/mec.15175

Additionally, please cite the Dryad data package:

Mandeville E, Walters A, Nordberg B, Higgins K, Burckhardt J, Wagner C (2019) Data from: Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context. Dryad Digital Repository. https://doi.org/10.5061/dryad.6s7d02q
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