README file for supplemental data and analysis associated with Bromham L, Hua X, Cowman PF, Lanfear R (2014) Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants American Naturalist This file outlines the file structure of the proceeding data and the associated unix script to allow the rate estimation analyses in the PAML packages ****************************************************************************************** /SisterPairs.tre : Tree of all sister pairs used in the analyses from Lanfear et al (2013) ****************************************************************************************** /PAML: contains all files associated with rates estimation analyses for sister pairs with data for: Mitochondrial coding genes (atp1, matR , nad5, and rps3) Nuclear coding gene (Xdh) For each data set rates were estimated for the total branchlength, dN and dS; and cade specific dN/dS. ------------------------------------------------------------------------------------------ Mitochondrial coding: total branchlength; dN and dS; clade specific dN/dS Numbered folders correspond to sister pairs in supplementary online material Table S2 ------------------------------------------------------------------------------------------ PAML/mitochondrial/Comparisons/1...48/alignment.phy # mitochondrial input alignment for PAML, aligned in Geneious v6 with MUSCLE aligner plugin PAML/mitochondrial/Comparisons/1...48/balanced_tree.tre # input tree for PAML, trimmed from SisterPairs.tre of Lanfear et al (2013) PAML/mitochondrial/Comparisons/1...48/PAML_dNdS_cladespecific/balanced_tree.tre # input tree for PAML clade specific dN/dS calculation PAML/mitochondrial/Comparisons/1...48/PAML_dNdS_cladespecific/alignment.phy # alignment for CODEML clade specific dN/dS calculation PAML/mitochondrial/Comparisons/1...48/PAML_dNdS_cladespecific/codeml.ctl # CODEML command file for clade specific dN/dS calculation PAML/mitochondrial/Comparisons/1...48/PAML_dNdS_cladespecific/codeml # CODEML executable file PAML/mitochondrial/Comparisons/1...48/PAML_dNdS_coding/balanced_tree.tre # input tree for CODEML dN, dS calculation PAML/mitochondrial/Comparisons/1...48/PAML_dNdS_coding/alignment.phy # alignment for CODEML dN, dS calculation PAML/mitochondrial/Comparisons/1...48/PAML_dNdS_coding/codeml.ctl # CODEML command file for CODEML dN, dS calculation PAML/mitochondrial/Comparisons/1...48/PAML_dNdS_coding/codeml # CODEML executable file PAML/mitochondrial/Comparisons/1...48/PAML_Total/balanced_tree.tre # input tree for BASEML total branch length calculation PAML/mitochondrial/Comparisons/1...48/PAML_Total/alignment.phy # alignment for BASEML total branch length calculation PAML/mitochondrial/Comparisons/1...48/PAML_Total/baseml.ctl # BASEML command file for BASEML total branch length calculation PAML/mitochondrial/Comparisons/1...48/PAML_Total/baseml # CODEML executable file ------------------------------------------------------------------------------------------ Nuclear coding: total branchlength; dN and dS; clade specific dN/dS Numbered folders correspond to sister pairs in supplementary online material Table S3 ------------------------------------------------------------------------------------------ PAML/nuclear/Comparisons/1...23/alignment.phy # nuclear input alignment for PAML, aligned in Geneious v6 with MUSCLE aligner plugin PAML/nuclear/Comparisons/1...23/balanced_tree.tre # input tree for PAML, trimmed from SisterPairs.tre of Lanfear et al (2013) PAML/nuclear/Comparisons/1...23/PAML_dNdS_cladespecific/balanced_tree.tre # input tree for PAML clade specific dN/dS calculation PAML/nuclear/Comparisons/1...23/PAML_dNdS_cladespecific/alignment.phy # alignment for CODEML clade specific dN/dS calculation PAML/nuclear/Comparisons/1...23/PAML_dNdS_cladespecific/codeml.ctl # CODEML command file for clade specific dN/dS calculation PAML/nuclear/Comparisons/1...23/PAML_dNdS_cladespecific/codeml # CODEML executable file PAML/nuclear/Comparisons/1...23/PAML_dNdS_coding/balanced_tree.tre # input tree for CODEML dN, dS calculation PAML/nuclear/Comparisons/1...23/PAML_dNdS_coding/alignment.phy # alignment for CODEML dN, dS calculation PAML/nuclear/Comparisons/1...23/PAML_dNdS_coding/codeml.ctl # CODEML command file for CODEML dN, dS calculation PAML/nuclear/Comparisons/1...23/PAML_dNdS_coding/codeml # CODEML executable file PAML/nuclear/Comparisons/1...23/PAML_Total/balanced_tree.tre # input tree for BASEML total branch length calculation PAML/nuclear/Comparisons/1...23/PAML_Total/alignment.phy # alignment for BASEML total branch length calculation PAML/nuclear/Comparisons/1...23/PAML_Total/baseml.ctl # BASEML command file for BASEML total branch length calculation PAML/nuclear/Comparisons/1...23/PAML_Total/baseml # CODEML executable file ------------------------------------------------------------------------------------------ ****************************************************************************************** ****************************************************************************************** /PAML_script.txt: script to automatically change to each subfolder and run PAML for associated rate estimates This script assumes you are using a mac. If this is not the case, you may need to edit the file paths and other details of the script (such as compiling your own versions of codeml and baseml for your machine, and replacing the executables in each folder). This script assumes that the codeml and baseml executables provided will work on your mac. To grant each executable file correct permissions to run, the commands: chmod 755 codeml chmod 755 baseml have been added in the script for each instance of each codeml and baseml files in each subfolder If they don't, you will need to download and compile your own versions from here: http://abacus.gene.ucl.ac.uk/software/paml.html To use this script in terminal change directory (cd) to folder containing folders and scripts To allow script to be run change permissions using chmod 755 PAML_script.txt Run script with command ./PAML_script.txt Script will run for all mitochondrial and nuclear datasets and automatically rename output files to corresponding to pair number ****************************************************************************************** ****************************************************************************************** Result Files: For each rates estimation analysis a result file will be made with the prefix "DIV" containing details of that analysis output and the tree in newick format with estimated rates as branch length. This tree string provided the values of rate estimates for each clade in the sister pair analysis found in supplemental Table S1 In the comparisons where there are multiple lineages for each clade an averaging approach was used to obtain an estimate for each clade (see main text) ****************************************************************************************** ******************************************************************************************