E selection was allowed on branches Autophagy leading to C4 clades and branches within C4 clades. The A1-A LRT compares the null model A1 with the nested model A. Both the A1 and A models allow dN/dS ratios to vary among sites and among lineages. The A1 model allows 0, dN/dS ,1 and dN/dS = 1 for all branches, and also two additional classes of codons with fixed dN/dS = 1 along prespecified foreground branches while restricted as 0, dN/dS ,1 and dN/dS = 1 on background branches. The alternative A model allows 0, dN/dS ,1 and 
dN/dS = 1 for all branches, and also two additional classes of codons under positive selection with dN/dS .1 along prespecified foreground branches while restricted as 0, dN/ dS ,1 and dN/dS = 1 on background branches. C4 lineages were marked as foreground branches. For all LRTs, the first model is a simplified version of the second, with fewer parameters, and is thus expected to provide a poorer fit to the data (lower maximum likelihood). The M1a, M8a and A1 models are null models which do not allow codons with dN/dS .1, whereas the M2a, M8 and A models are alternative models which do allow codons with dN/dS .1. The significance of the LRTs was calculated assuming that twice the difference in the log of maximum likelihood between the two models was distributed as a chi-square distribution with the degrees of freedom (df) given by the difference in the numbers of parameters in the two nested models [34,36]. For the M1a-M2a comparison df = 2, and for M8a-M8, A1-A and M0 vs 2-rates model comparisons df = 1. Each LRT was run two times using different initial dN/dS values (0.1 and 0.4) to test for suboptimal local peaks. To identify amino acid sites potentially under positive selection, the parameter estimates from M2a, M8 and A models were used to calculate the posterior probabilities that an amino acid belongs to a class with dN/dS .1 using the Bayes Empirical Bayes (BEB) approaches implemented in PAML [37]. Independently from codeml we used the SLR program which implements “sitewise likelihood-ratio” (SLR) method for detecting Epigenetic Reader Domain non-neutral evolution, a statistical testTable 1. Analysis of the Amaranthaceae rbcL genes for positively selected sites.a b c a b dModel with positive selection log-likelihoodNull model Positively selected sitesLRT Parameters 2lParameterslog-likelihoodP-valueAnalysis for positively selected sites common for C3 and C4 clades M2a 210711.44 k = 3.00, p0 = 0.93, v0 = 0.02, ps = 0.01, vs = 2.62 k = 2.94, p0 = 0.96, p = 0.15, q = 3.04, vs = 1.56 k = 2.75, v = 0.10 32, 145, 279, 439 32, 43, 145, 225, 262, 279, 439, 443 32, 145, 225, 279, 439 M1a 210729.19 k = 2.94, p0 = 0.93, v0 = 0.02 k = 2.90, p0 = 0.94, p = 0.20, q = 5.42 NA 35.5 ,0.M210705.M8a210717.24.,0.SLRNANANANANAAnalysis for positively selected sites specific for branches leading to C4 clades A 210729.13 k = 2.94, p0 = 0.93, v0 = 0.02, ps = 0.00, vs = NA no A1 210729.13 k = 2.94, p0 = 0.93, v0 = 0.02 0.0 1.Analysis for positively selected sites specific for C4 clades A 210723.60 k = 2.94, p0 = 0.92, v0 = 0.02, ps = 0.01, vs = 3.15 281, 309 A1 210726.15 k = 2.94, p0 = 0.92, v0 = 0.02 5.1 0.a M1a (nearly neutral), M2a (positive selection), M8a (beta v = 1) and M8 (beta v) are PAML site models; A1 and A are PAML branch site models; SLR is “sitewise likelihood-ratio” method. b k is transition/transversion rate ratio; v is dN/dS ratio; vs is dN/dS ratio in a class under putative positive selection; p0 and ps are proportion of codons with v,1 and v.E selection was allowed on branches leading to C4 clades and branches within C4 clades. The A1-A LRT compares the null model A1 with the nested model A. Both the A1 and A models allow dN/dS ratios to vary among sites and among lineages. The A1 model allows 0, dN/dS ,1 and dN/dS = 1 for all branches, and also two additional classes of codons with fixed dN/dS = 1 along prespecified foreground branches while restricted as 0, dN/dS ,1 and dN/dS = 1 on background branches. The alternative A model allows 0, dN/dS ,1 and dN/dS = 1 for all branches, and also two additional classes of codons under positive selection with dN/dS .1 along prespecified foreground branches while restricted as 0, dN/ dS ,1 and dN/dS = 1 on background branches. C4 lineages were marked as foreground branches. For all LRTs, the first model is a simplified version of the second, with fewer parameters, and is thus expected to provide a poorer fit to the data (lower maximum likelihood). The M1a, M8a and A1 models are null models which do not allow codons with dN/dS .1, whereas the M2a, M8 and A models are alternative models which do allow codons with dN/dS .1. The significance of the LRTs was calculated assuming that twice the difference in the log of maximum likelihood between the two models was distributed as a chi-square distribution with the degrees of freedom (df) given by the difference in the numbers of parameters in the two nested models [34,36]. For the M1a-M2a comparison df = 2, and for M8a-M8, A1-A and M0 vs 2-rates model comparisons df = 1. Each LRT was run two times using different initial dN/dS values (0.1 and 0.4) to test for suboptimal local peaks. To identify amino acid sites potentially under positive selection, the parameter estimates from M2a, M8 and A models were used to calculate the posterior probabilities that an amino acid belongs to a class with dN/dS .1 using the Bayes Empirical Bayes (BEB) approaches implemented in PAML [37]. Independently from codeml we used the SLR program which implements “sitewise likelihood-ratio” (SLR) method for detecting non-neutral evolution, a statistical testTable 1. Analysis of the Amaranthaceae rbcL genes for positively selected sites.a b c a b dModel with positive selection log-likelihoodNull model Positively selected sitesLRT Parameters 2lParameterslog-likelihoodP-valueAnalysis for positively selected sites common for C3 and C4 clades M2a 210711.44 k = 3.00, p0 = 0.93, v0 = 0.02, ps = 0.01, vs = 2.62 k = 2.94, p0 = 0.96, p = 0.15, q = 3.04, vs = 1.56 k = 2.75, v = 0.10 32, 145, 279, 439 32, 43, 145, 225, 262, 279, 439, 443 32, 145, 225, 279, 439 M1a 210729.19 k = 2.94, p0 = 0.93, v0 = 0.02 k = 2.90, p0 = 0.94, p = 0.20, q = 5.42 NA 35.5 ,0.M210705.M8a210717.24.,0.SLRNANANANANAAnalysis for positively selected sites specific for branches leading to C4 clades A 210729.13 k = 2.94, p0 = 0.93, v0 = 0.02, ps = 0.00, vs = NA no A1 210729.13 k = 2.94, p0 = 0.93, v0 = 0.02 0.0 1.Analysis for positively selected sites specific for C4 clades A 210723.60 k = 2.94, p0 = 0.92, v0 = 0.02, ps = 0.01, vs = 3.15 281, 309 A1 210726.15 k = 2.94, p0 = 0.92, v0 = 0.02 5.1 0.a M1a (nearly neutral), M2a (positive selection), M8a (beta v = 1) and M8 (beta v) are PAML site models; A1 and A are PAML branch site models; SLR is “sitewise likelihood-ratio” method. b k is transition/transversion rate ratio; v is dN/dS ratio; vs is dN/dS ratio in a class under putative positive selection; p0 and ps are proportion of codons with v,1 and v.
