# READ-ME file for data and scripts associated with the manuscript: # # Comeault et al. 2016 "Color phenotypes are under similar genetic # control in two distantly related species of Timema stick insect" Evolution. # # each data file is associated with at least 1 script that contains details # on the type of data contained within each data file and the analyses carried # out on that given data file. # # below we give a brief description of each data file and the scripts containing # associated analyses. Data and associated scripts are available in Dryad: XX Short sequence reads are available under NCBI BioProject Accessions: PRJNA284835 and XX IDs: 284835 and XX file_name: details: associated scripts tcris_color_data.txt: this file contains phenotypic color measurements for the sample of T. cristinae individuals and is required in the script: script_phenotypic_analyses.R tpod_color_data.txt: this file contains phenotypic color measurements for the sample of T. podura individuals and is required in the script: script_phenotypic_analyses.R tcris_genabel_genos.raw: this file contains discrete genotype information for all T. cristinae individuals and is required in the scripts: script_genABEL_gwam.R, script_LD_compare_between_species.R, and script_LD_decay_1.R tpod_genabel_genos.raw: this file contains discrete genotype information for all T. podura individuals and is required in the scripts: script_genABEL_gwam.R, script_LD_compare_between_species.R, and script_LD_decay_1.R tcris_genabel_phenos.txt: this file contains discrete phenotypic information for all T. cristinae individuals and is required in the scripts: script_genABEL_gwam.R, script_LD_compare_between_species.R, and script_LD_decay_1.R tpod_genabel_phenos.txt: this file contains discrete phenotypic information for all T. podura individuals and is required in the scripts: script_genABEL_gwam.R, script_LD_compare_between_species.R, and script_LD_decay_1.R tpod_gemma.geno: this file contains imputed genotype information for all T. podura individuals and is required in the script: script_PCA_on_genotypes.R tcristinae_draft_0.3.scalen.dsv: this file contains scaffold ordering information for v0.3 of the T. cristinae genome assembly and is required in the scripts: script_genABEL_gwam.R, script_LD_compare_between_species.R, and script_LD_decay_1.R gemma_data (directory): this directory contains phenotypic and genetic input files used for multi-locus gwa mapping analyses: files within this directory can be used to run the scripts contained within the "gemma" directory contained within the "scripts.zip" archive.