May 14, 2014 These files contain the PAML control files, sequence files and tree files to replicate data from Dalziel et al. 2014 (Tables 1-3) with PAML v4.6 (Yang et al. 2007). We have provided 'template files' for each type of analysis. All analyses can use the sequence file "Seq_ATP1A1.txt" which contains 2826bp of data for all 36 sequences used in this study. To obtain data for 34 and 20 sequence trees (Supplemental Tables 4-6) to test the effects of tree topology simply detete the appropriate species from this sequence file (and the corresponding tree files). ##Branch Models (Table 1; Yang 1998)## One-ratio model - Use the control-file "OneRatio.ctl" and tree-file "ATP1A1.trees". Free-ratios model - Use the control-file "FreeRatios.ctl" and tree-file "ATP1A1.trees". Selection along a particular Branch - To test for evidence of a w-ratio >1 along a particular branch (e.g. Branch D), use the control-file "BranchSite_BranchD.ctl" and the tree-file "BranchSite_BranchD.trees". Selection along a particular Branch (null)-To run the null model (w=1) to compare with your test for evidence of a w-ratio >1 along a particular branch (e.g. Branch D), use the control-file "BranchSite_BranchDnull.ctl" and the tree-file "BranchSite_BranchD.trees". ##Branch-site Models (Table 2; Yang & Nielsen, 2002; Bielawski & Yang, 2004; Zhang et al. 2005; Yang et al. 2005; Yang 2007)## Branch-Site Model A - Use the control-file "BranchSite_BranchD.ctl" and tree-file "BranchSite_BranchD.trees". The null Model A that fixes ?2 = 1 (Zhang et al. 2005) - Use the control-file "BranchSite_BranchDnull.ctl" and tree-file "BranchSite_BranchD.trees". ##Clade Models (Table 3) ## Clade Model C - Use the control-file "ModelC_a1a_a1b.ctl" and the tree-file "ModelC_a1a_a1b.trees". M2a_rel null model (Weadick & Chang, 2012) - Use the control-file "M2a_rel.ctl" and the tree-file "ModelC_a1a_a1b.trees". References: Bielawski JP, Yang ZH (2004) A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of Molecular Evolution, 59, 121-132. Weadick CJ, Chang BSW (2012) An improved likelihood ratio test for detecting site-specific functional divergence among clades of protein-coding genes. Molecular Biology and Evolution, 29, 1297-1300. Yang ZH (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution, 15, 568-573. Yang ZH (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24, 1586-1591. Yang ZH, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution, 19, 908-917. Yang ZH, Wong WSW, Nielsen R (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution, 22, 1107-1118. Zhang JZ, Nielsen R, Yang ZH (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution, 22, 2472-2479.