README for comparative_phylogenetic_141014.zip Directory contents: - japanese_stickleback_141014.genepop - complete_dmu.phy - complete_NeiD.phy - gill_raker_all_141014.csv - sia_all_141014.csv - phyogenetic_analysis_and_pmc_bootstrapping_141014.R - phylogenetic_sample_size_tests_with_parameter_ratios_141014.R - parametric_bootstrapping_functions_141014.R - japanese_stickleback_141014.genepop: This file is a genepop file containing genotype data for 10 microsatellite markers used to generate population trees. Population codes are clarified in the file. - complete_dmu.phy - complete_NeiD.phy These files are the tree files stored in the Newick format constructed using the Populations software. Both trees are used for all comparative analyses. - sia_all_141014.csv A CSV file containing mean SIA and standard deviation data for all populations of PA, JA and PF across Japan. Also includes numbers of individuals analysed (n). - gill_raker_all_141014.csv A CSV file containing data on mean gill raker size and standard deviation for populations of PA, JA and PF fish across Japan. Also includes numbers of individuals analysed (n) - phyogenetic_analysis_and_pmc_bootstrapping_141014.R An R script detailing how to perform phylogenetic analyses and plc bootstrapping included in the paper. Requires the source file, “parametric_bootstrapping_functions_141014.R” to run. Will also produce plots used in supplementary material - phylogenetic_sample_size_tests_with_parameter_ratios_141014.R An R script to perform tests of sample size on power and to draw plots of ratios of parameter estimates varying with sample size. Requites source file “parametric_bootstrapping_functions_14104.R” to run.