DOI: 10.5061/dryad.6s7d02q
title: Data from: Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context

description: Hybridization can profoundly affect the genomic composition and phenotypes
 of closely related species, and provides an opportunity to identify
 mechanisms that maintain reproductive isolation between species. Recent
 evidence suggests that hybridization outcomes within a species pair can
 vary across locations. However, we still don't know how extensive
 variation in outcomes of hybridization is across geographic replicates,
 and what mechanisms drive that variation. In this study, we described
 hybridization outcomes across 27 locations in the North Fork Shoshone
 River basin (Wyoming, USA) where native Yellowstone cutthroat trout and
 introduced rainbow trout co-occur. We used genomic data and hierarchical
 Bayesian models to precisely identify ancestry of hybrid individuals.
 Hybridization outcomes varied across locations. In some locations, only
 advanced backcrossed hybrids towards rainbow trout and pure rainbow trout
 were present, while other locations had a broader range of individuals,
 including both parental species and first-generation hybrids. Using an
 individual-based simulation, we found that outcomes of hybridization in
 the North Fork Shoshone River basin deviate substantially from what we
 would expect under assumptions of random mating and no selection against
 hybrids. Since this implies that some mechanisms of reproductive isolation
 function to maintain parental taxa and a diversity of hybrid types, we
 then modeled hybridization outcomes as a function of environmental
 variables and stocking history that are likely to affect prezygotic
 barriers to hybridization. Variables associated with history of fish
 stocking were the strongest predictors of hybridization outcomes, followed
 by environmental variables that might affect overlap in spawning time and
 location.
description: VCF file
 (gzipped)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 &gt;2 alternative alleles are excluded.variants_0.6_maf0.05.recode.vcf.gzentropy input fileInput 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.plentropy_in_0.6_maf0.05.mpgl.gzscript for converting vcf to mpglThis perl script converts VCF output to mpgl format, a simplified version of genotype likelihoods that forms the input for the entropy clustering analysisvcf2mpgl.plScript for environmental correlates of hybridization outcomesThis script does the model averaging described in the paper and displayed in Fig. 5.model_averaging_trout_MuMIn.RResponse variable data for model averagingResponse variables summarizing genomic outcomes of hybridization across 27 locations in the North Fork Shoshone River basinresponse_var_18jan18.csvPredictor variables for model averagingEnvironmental and historical data associated with locations where hybrid individuals were sampled. Input for model_averaging_trout_MuMIn.Rpredictors_var_26july18.csvYSC_RBT_allind_barcode_key_detailedMetadata for sequenced individualsSimulation code - main fileThis 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).simulate_hyb_main.RSimulation code - functionsThis 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.simulate_func.R