Data from: Natural selection and the predictability of evolution in Timema stick insects

Nosil P, Villoutreix R, de Carvalho CF, Farkas TE, Soria-Carrasco V, Feder JL, Crespi BJ, Gompert Z

Date Published: February 21, 2018

DOI: https://doi.org/10.5061/dryad.v1q13

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Title Desiccation experiment
Downloaded 6 times
Description This compressed directory contains two files. 'dessication_trials_2017.csv' provides the data for the desiccation experiment. This includes the morph type (green vs. grey or red = melanic), weights, and time to death. The second file 'commands_melExp.R' provides the R code used to analyse the data. This presents some initial exploratory analyses and the final analysis used for the paper.
Download timemaMelExp.tar.gz (2.273 Kb)
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Title Stripe freq. dependence experiment
Downloaded 4 times
Description This compressed directory contains three files related to the experimental test for frequency-dependent selection of stripe (versus no stripe). 'recapture_data.txt' provides the raw data, which includes the number of striped vs. green (unstriped) insects re-captured and the treatment ID (2 = 20% stripe, 8 = 80% stripe). The directory also includes the R code ('commands_freqDep.R') used to fit the Bayesian model (the model itself is in another text file, 'binmod', which is also included).
Download stripe_freq_experiment.tar.gz (1.383 Kb)
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Title VCF filtering scripts
Downloaded 3 times
Description This compressed directory contains two perl scripts that we used to filter the VCF files with the genetic variant data for the FHA population (2011 vs. 2013) and for the between-generation experiment.
Download popGenFilterScripts.tar.gz (1.84 Kb)
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Title Genomic change in FHA (2011-2013)
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Description This compressed directory contains the allele frequency data ('pEM_fha2011.txt' and 'pEM_fha2013.txt') and associated scripts for the analyses of genomic change (allele frequency change across the genome) for the FHA population between 2011 and 2013. The R script used for the analysis is 'FHA_genomicChangeMelStripy.R'.
Download genomicChangeFHA.tar.gz (1.383 Mb)
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Title Between-generation experiment genomic change
Downloaded 3 times
Description This compressed directory contains the allele frequency data ('p*') and associated scripts for the analyses of genomic change (allele frequency change across the genome) for the between-generation experiment (the source population for this was OGA). The R script used for the analysis is 'OGAgenomicChangeMelStripy.R'.
Download genomicChangeOGA.tar.gz (6.167 Mb)
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Title Within-generation experiment genomic change
Downloaded 3 times
Description This compressed directory contains the allele frequency data ('in_p_ecol*', column three gives the maximum likelihood allele frequency estimates) and associated scripts for the analyses of genomic change (allele frequency change across the genome) for the within-generation experiment (the source population for this was FHA). The R script used for the analysis is 'exp_genomicChangeMelStripy.R'.
Download genomicChangeEcol.tar.gz (100.3 Mb)
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Title Scripts for mel-stripe selection analysis
Downloaded 6 times
Description This compressed directory contains two R scripts used to estimate selection coefficients for FHA (between 2011 and 2013 = 'fhaAbcMel.R') and during a within-generation release-recapture experiment (also at FHA = 'fhaEcolSmel.R'). Additional data (text) files required by these scripts are included ('ecolGbsHost.txt', 'snpids_fha', 'SurvivalGbs.txt', and 'fha2013pheno.txt'). Larger R data workspaces and genetic data files referenced in the scripts have been uploaded individually ('pntest_fha2011.txt', 'pntest_fha2013.txt', 'fhaAbcMel.rdat', 'fhaAbcEcolSMel.rdat').
Download melstripeSelectionFHA.tar.gz (626 Kb)
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Title Genotype estimates for FHA 2011
Downloaded 4 times
Description Matrix of genotype estimates (mean of the posterior with genetoypes coded as 0, 1 or 2, but the mean being non-integer valued) for FHA in 2011. Rows denote SNPs and columns denote individuals. See scripts in melstripeSelectionFHA.tar.gz for details.
Download pntest_fha2011.txt.gz (115.5 Mb)
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Title Genotype estiamtes for FHA in 2013
Downloaded 3 times
Description Matrix of genotype estimates (mean of the posterior with genetoypes coded as 0, 1 or 2, but the mean being non-integer valued) for FHA in 2013. Rows denote SNPs and columns denote individuals. See scripts in melstripeSelectionFHA.tar.gz for details.
Download pntest_fha2013.txt.gz (133.5 Mb)
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Title R workspace for mel-stripe selection inference in FHA
Downloaded 4 times
Description This R workspace contains the results from fhaAbcMel.R, which runs the selection inference for the FHA between 2011 and 2013. It is required by fhaEcolSmel.R.
Download fhaAbcMel.rdat (697.7 Mb)
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Title Genetic variant data for mapping color
Downloaded 3 times
Description This BCF file (binary version of VCF) contains the genetic variant data used for mapping color in Timema cristinae.
Download Tcristinae_FHA.color.bin.bial.noindel.qs2...01.bcf (905.5 Mb)
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Title Genetic variant data for mapping stipre (pattern)
Downloaded 3 times
Description This BCF file (binary version of VCF) contains the genetic variant data used for mapping stripe (pattern) in Timema cristinae.
Download Tcristinae_FHA.stripe.bin.bial.noindel.qs...01.bcf (826.0 Mb)
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Title Traiting mapping
Downloaded 3 times
Description This compressed directory contains the input files (see input) and scripts (see scripts) used for genome-wide association mapping of stripe and color. README files are included in the input and scripts sub-directories.
Download tcr_gwas.tar.gz (507.9 Mb)
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Title Time series data and melanistic morph analysis
Downloaded 5 times
Description This compressed directory contains four files relevant for the color (green vs. melanistic) morph time series analysis. The raw data is in 'Tcris_master_27.csv'. The associated R script 'bigMelanisticAnalysis.R' contains the code used to fit the Bayesian models for this data set and includes descriptions of relevant variables in the main data file. The JAGS models referenced in the R script are 'hiermod-refugio' and 'mod-hv'.
Download melTimeSeriesAnalysis.tar.gz (17.88 Kb)
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Title Time series data and ARMA analyses
Downloaded 3 times
Description This compressed directory contains the data, models and scripts used for the ARMA model fits of the time series data for Timema cristiane (raw data = Tcris_master_26.csv, note the 2017 data are added to this in the R script), Geospiza fortis (fortis.csv), Geospiza scandens (scandens.csv), Panaxia dominula (data_medionigra.csv), and Biston betuleria (mothdat.csv). Except for the Timema data, these data were obtained from published studies (as described and documented in the paper), but are also included here for completeness. The main R script for fitting the ARMA models is 'predictingEvoAnalyses.R'. It relies on functions defined in 'predictingEvoFuncs.R', which are sourced at the beginning of the 'predictingEvoAnalyses.R' script. The individual JAGS models for the different ARMA models are defined in the 'dp-arma*model' text files, where * denotes the AR and MA lags.
Download ARMAanalyses.tar.gz (25.51 Kb)
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Title R workspace for mel-stripe selection experiment
Downloaded 3 times
Description This R workspace contains the results from fhaEcolSmel.R.
Download fhaAbcEcolSMel.rdat (698.4 Mb)
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Title Scripts and data for the linkage map
Downloaded 5 times
Description This compressed directory contains a series of perl sciprts and data files that we used to generate the linakge map for Timema cristinae. The specific steps we took, including some annotation/documentation of the scripts we used are in the README file. the offspringGenotype*txt data are included in a separate file.
Download lm2map.tar.gz (2.217 Mb)
Download README (12.45 Kb)
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Title Genotype data for mapping families
Downloaded 4 times
Description This compressed directory contains the genotype data for the three mapping families (A, B, and C). These are required for the mapping scripts we also uploaded.
Download offspringGenDat.tar.gz (1.862 Mb)
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When using this data, please cite the original publication:

Nosil P, Villoutreix R, de Carvalho CF, Farkas TE, Soria-Carrasco V, Feder JL, Crespi BJ, Gompert Z (2018) Natural selection and the predictability of evolution in Timema stick insects. Science 359(6377): 765-770. https://doi.org/10.1126/science.aap9125

Additionally, please cite the Dryad data package:

Nosil P, Villoutreix R, de Carvalho CF, Farkas TE, Soria-Carrasco V, Feder JL, Crespi BJ, Gompert Z (2018) Data from: Natural selection and the predictability of evolution in Timema stick insects. Dryad Digital Repository. https://doi.org/10.5061/dryad.v1q13
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