Below is the data for Figure 5B, Figur 5D, Figure 5F, Figure 6C, and Figure 6E The Average and standard deviation(STDEV) for every subgroup was computed, Pair T tests were also carried out. The primary distance and Ka/ka data for each subgroup were also listed. Data for Figure 5B Distances E2F4/5 E2F1/2/3 Bf:Ci 0.4186 0.7082 Bf:Sp 0.4925 0.5207 Bf:Nv 0.465 0.8799 Bf:Ta 0.4735 0.5596 Ci:Sp 0.3925 0.891 Ci:Nv 0.4959 1.2252 Ci:Ta 0.5213 1.1874 Sp:Nv 0.5928 1.1037 Sp:Ta 0.5719 0.928 Nv:Ta 0.38 1.1257 Average 0.4804 0.9129 STDEV 0.0707 0.2533 Pair T test P=0.0005 Data for Figure 5D Distances E2F1 E2F3 E2F4 Cf:Bt 0.0615 0.2656 0.0508 Cf:Hs 0.0787 0.2756 0.058 Cf:Mm 0.1369 0.2696 0.0766 Cf:Rn 0.1442 0.596 0.0709 Cf:Gg 0.4256 0.4044 0.2784 Cf:Xt 0.6021 0.4695 0.3445 Cf:Tn 0.7123 0.7291 0.4881 Bt:Hs 0.086 0.0218 0.0588 Bt:Mm 0.1422 0.0539 0.0803 Bt:Rn 0.1522 0.1076 0.0745 Bt:Gg 0.4435 0.3687 0.2784 Bt:Xt 0.6098 0.3938 0.3258 Bt:Tn 0.7147 0.6629 0.4881 Hs:Mm 0.153 0.0425 0.0709 Hs:Rn 0.1468 0.0852 0.068 Hs:Gg 0.4474 0.3783 0.2793 Hs:Xt 0.6249 0.3938 0.3343 Hs:Tn 0.7391 0.6629 0.4897 Mm:Rn 0.0453 0.0461 0.0272 Mm:Gg 0.4635 0.3727 0.2801 Mm:Xt 0.6116 0.402 0.3316 MM:Tn 0.7448 0.6559 0.4731 Rn:Gg 0.4675 0.652 0.2818 Rn:Xt 0.6121 0.4908 0.337 Rn:Tn 0.7422 0.7219 0.4756 Gg:Xt 0.5938 0.4738 0.3483 Gg:Tn 0.6707 0.7027 0.4833 Xt:Tn 0.7125 0.6955 0.4219 Average 0.4316 0.4069 0.2634 STDEV 0.2579 0.2331 0.1667 Pair T test E2F1:E2F4 P=1.13433E-09 E2F3:E2F4 P=1.58919E-06 Data for Figure 5F kaks E2F1 E2F2 E2F3 E2F4 Hs:Mm 0.1585 0.1844 0.1126 0.0824 Hs:Cf 0.1238 0.229 0.5071 0.0708 Hs:Bt 0.1277 0.1695 0.0774 0.0674 Mm:Cf 0.1601 0.2309 0.4511 0.0838 Mm:Bt 0.1507 0.1467 0.1662 0.0854 Cf:Bt 0.103 0.1914 0.5355 0.0638 Average 0.1373 0.1920 0.3083 0.0756 STDEV 0.0228 0.0332 0.2113 0.0094 Pair T test E2F1:E2F4 P=0.00013 E2F2:E2F4 P=0.00048 E2F3:E2F4 P=0.04512 Data for Figure 6C Distance RB1 RBL1 RBL2 Hs:Bt 0.068 0.0558 0.0394 Hs:Cf 0.0693 0.0509 0.0276 Hs:Mm 0.0909 0.0957 0.0914 Hs:Rn 0.1017 0.1092 0.1002 Hs:Gg 0.2958 0.2329 0.2417 Hs:Dr 0.5992 0.4685 0.489 Bt:Cf 0.0598 0.0362 0.0321 Bt:Mm 0.0968 0.0905 0.0972 Bt:Rn 0.1102 0.1061 0.1079 Bt:Gg 0.2914 0.2269 0.2288 Bt:Dr 0.5951 0.4654 0.4949 Cf:Mm 0.1072 0.0895 0.0953 Cf:Rn 0.1135 0.0998 0.1041 Cf:Gg 0.2888 0.2246 0.2407 Cf:Dr 0.5869 0.4669 0.4939 Mm:Rn 0.0467 0.0433 0.0469 Mm:Gg 0.3156 0.2351 0.2839 Mm:Dr 0.6063 0.4698 0.5122 Rn:Gg 0.3201 0.2448 0.3004 Rn:Dr 0.6042 0.4745 0.5172 Gg:Dr 0.5487 0.4669 0.5045 Average 0.2817 0.2263 0.2404 STDEV 0.2140 0.1704 0.1875 Pair T test RB1:RBL1 P=7.3584E-05 RB1:RBL2 P=5.48814E-05 Data for Figure 6E Ka/ks RB1 RBL1 RBL2 Hs:Mm 0.086 0.0785 0.0753 Hs:Cf 0.137 0.0835 0.0484 Hs:Bt 0.1167 0.0909 0.0561 Hs:Rn 0.0943 0.0991 0.081 Mm:Cf 0.1106 0.07 0.0775 Mm:Bt 0.0959 0.0748 0.0683 Mm:Rn 0.12 0.0678 0.0803 Cf:Bt 0.1251 0.0653 0.0472 CF:Rn 0.112 0.0832 0.0834 Bt:Rn 0.0952 0.0901 0.0744 Average 0.1092 0.0803 0.0692 STDEV 0.0161 0.0111 0.0137 Pair T test RB1:RBL1 P=0.0026 RB1:RBL2 P=0.0011 Title: 123 Description No. of Taxa : 5 Data File : C:\Documents and Settings\lihuan cao\×ÀÃæ\90.meg Data Title : 123 Data Type : Amino acid Analysis : Pairwise distance calculation Compute : Distances only Include Sites : ============================== Gaps/Missing Data : Pairwise Deletion Substitution Model : ============================== Model : Amino: Poisson correction Substitutions to Include : All Pattern among Lineages : Same (Homogeneous) Rates among sites : Uniform rates No. of Sites : 386 d : Estimate [1] #E2F45-Bf [2] #E2F45-Ci [3] #E2F45-Sp [4] #E2F45-Nv [5] #E2F45-TA [ 1 2 3 4 5 ] [1] [2] 0.4186 [3] 0.4925 0.3925 [4] 0.4650 0.4959 0.5928 [5] 0.4735 0.5213 0.5719 0.3800 Title: 123 Description No. of Taxa : 5 Data File : C:\Documents and Settings\lihuan cao\×ÀÃæ\91.meg Data Title : 123 Data Type : Amino acid Analysis : Pairwise distance calculation Compute : Distances only Include Sites : ============================== Gaps/Missing Data : Pairwise Deletion Substitution Model : ============================== Model : Amino: Poisson correction Substitutions to Include : All Pattern among Lineages : Same (Homogeneous) Rates among sites : Uniform rates No. of Sites : 540 d : Estimate [1] #E2F123-Bf [2] #E2F123-Ci [3] #E2F123-Sp [4] #E2F123-Ta [5] #E2F123-Nv [ 1 2 3 4 5 ] [1] [2] 0.7082 [3] 0.5207 0.8910 [4] 0.8799 1.2252 1.1037 [5] 0.5596 1.1874 0.9280 1.1257 Data Type : Amino acid Analysis : Pairwise distance calculation Compute : Distances only Include Sites : ============================== Gaps/Missing Data : Pairwise Deletion Substitution Model : ============================== Model : Amino: Poisson correction Substitutions to Include : All Pattern among Lineages : Same (Homogeneous) Rates among sites : Uniform rates No. of Sites : 600 d : Estimate [1] #E2F1-Cf [2] #E2F1-Bt [3] #E2F1-Hs [4] #E2F1-Mm [5] #E2F1-Rn [6] #E2F1-Gg [7] #E2F1-Xt [8] #E2F1-Tn [ 1 2 3 4 5 6 7 8 ] [1] [2] 0.0615 [3] 0.0787 0.0860 [4] 0.1369 0.1422 0.1530 [5] 0.1442 0.1522 0.1468 0.0453 [6] 0.4256 0.4435 0.4474 0.4635 0.4675 [7] 0.6021 0.6098 0.6249 0.6116 0.6121 0.5938 [8] 0.7123 0.7147 0.7391 0.7448 0.7422 0.6707 0.7125 Title: 123 Description No. of Taxa : 8 Data File : C:\Documents and Settings\lihuan cao\×ÀÃæ\976.meg Data Title : 123 Data Type : Amino acid Analysis : Pairwise distance calculation Compute : Distances only Include Sites : ============================== Gaps/Missing Data : Pairwise Deletion Substitution Model : ============================== Model : Amino: Poisson correction Substitutions to Include : All Pattern among Lineages : Same (Homogeneous) Rates among sites : Uniform rates No. of Sites : 523 d : Estimate [1] #E2F3Cf [2] #E2F3Bt [3] #E2F3Hs [4] #E2F3Mm [5] #E2F3Rn [6] #E2F3Gg [7] #E2F3Xt [8] #E2F3Tn [ 1 2 3 4 5 6 7 8 ] [1] [2] 0.2656 [3] 0.2756 0.0218 [4] 0.2696 0.0539 0.0425 [5] 0.5960 0.1076 0.0852 0.0461 [6] 0.4044 0.3687 0.3783 0.3727 0.6520 [7] 0.4695 0.3938 0.3938 0.4020 0.4908 0.4738 [8] 0.7291 0.6629 0.6629 0.6559 0.7219 0.7027 0.6955 Title: 123 Description No. of Taxa : 9 Data File : E:\e2f-last\distance\E2F4.meg Data Title : 123 Data Type : Amino acid Analysis : Pairwise distance calculation Compute : Distances only Include Sites : ============================== Gaps/Missing Data : Pairwise Deletion Substitution Model : ============================== Model : Amino: Poisson correction Substitutions to Include : All Pattern among Lineages : Same (Homogeneous) Rates among sites : Uniform rates No. of Sites : 441 d : Estimate [1] #E2F4-Cf [2] #E2F4-Bt [3] #E2F4-Hs [4] #E2F4-Mm [5] #E2F4-Rn [6] #E2F4-Gg [7] #E2F4-Xt [8] #E2F4-1-Tn [ 1 2 3 4 5 6 7 8 9 ] [1] [2] 0.0508 [3] 0.0580 0.0588 [4] 0.0766 0.0803 0.0709 [5] 0.0709 0.0745 0.0680 0.0272 [6] 0.2784 0.2784 0.2793 0.2801 0.2818 [7] 0.3445 0.3258 0.3343 0.3316 0.3370 0.3483 [8] 0.4881 0.4881 0.4897 0.4731 0.4756 0.4833 0.4219 Title: 123 Description No. of Taxa : 7 Data File : E:\e2f-last\distance\rb-sub.meg Data Title : 123 Data Type : Amino acid Analysis : Pairwise distance calculation Compute : Distances only Include Sites : ============================== Gaps/Missing Data : Pairwise Deletion Substitution Model : ============================== Model : Amino: Poisson correction Substitutions to Include : All Pattern among Lineages : Same (Homogeneous) Rates among sites : Uniform rates No. of Sites : 1318 d : Estimate [1] #Rb-Hs [2] #Rb-Bt [3] #Rb-Cf [4] #Rb-Mm [5] #Rb-Rn [6] #Rb-Gg [7] #Rb-Dr [ 1 2 3 4 5 6 7 ] [1] [2] 0.0680 [3] 0.0693 0.0598 [4] 0.0909 0.0968 0.1072 [5] 0.1017 0.1102 0.1135 0.0467 [6] 0.2958 0.2914 0.2888 0.3156 0.3201 [7] 0.5992 0.5951 0.5869 0.6063 0.6042 0.5487 Title: 123 Description No. of Taxa : 7 Data File : E:\e2f-last\distance\rbl1-sub.meg Data Title : 123 Data Type : Amino acid Analysis : Pairwise distance calculation Compute : Distances only Include Sites : ============================== Gaps/Missing Data : Pairwise Deletion Substitution Model : ============================== Model : Amino: Poisson correction Substitutions to Include : All Pattern among Lineages : Same (Homogeneous) Rates among sites : Uniform rates No. of Sites : 1094 d : Estimate [1] #Rbl1-Hs [2] #Rbl1-Bt [3] #Rbl1-Cf [4] #Rbl1-Mm [5] #Rbl1-Rn [6] #Rbl1-Gg [7] #Rbl1-Dr [ 1 2 3 4 5 6 7 ] [1] [2] 0.0558 [3] 0.0509 0.0362 [4] 0.0957 0.0905 0.0895 [5] 0.1092 0.1061 0.0998 0.0433 [6] 0.2329 0.2269 0.2246 0.2351 0.2448 [7] 0.4685 0.4654 0.4669 0.4698 0.4745 0.4669 Title: 123 Description No. of Taxa : 7 Data File : E:\e2f-last\distance\rbl2-sub.meg Data Title : 123 Data Type : Amino acid Analysis : Pairwise distance calculation Compute : Distances only Include Sites : ============================== Gaps/Missing Data : Pairwise Deletion Substitution Model : ============================== Model : Amino: Poisson correction Substitutions to Include : All Pattern among Lineages : Same (Homogeneous) Rates among sites : Uniform rates No. of Sites : 1150 d : Estimate [1] #Rbl2-Hs [2] #Rbl2-Bt [3] #Rbl2-Cf [4] #Rbl2-Mm [5] #Rbl2-Rn [6] #Rbl2-Gg [7] #Rbl2-Dr [ 1 2 3 4 5 6 7 ] [1] [2] 0.0394 [3] 0.0276 0.0321 [4] 0.0914 0.0972 0.0953 [5] 0.1002 0.1079 0.1041 0.0469 [6] 0.2417 0.2288 0.2407 0.2839 0.3004 [7] 0.4890 0.4949 0.4939 0.5122 0.5172 0.5045 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) E2F1-hs E2F1-Mm 0.1585 (0.0809 0.5101) E2F1-Cf 0.1238 (0.0374 0.3024) 0.1601 (0.0719 0.4488) E2F1-Bt 0.1277 (0.0422 0.3304) 0.1507 (0.0791 0.5249) 0.1030 (0.0291 0.2829) Nei & Gojobori 1986. dN/dS (dN, dS) (Pairwise deletion) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) E2F2-Hs E2F2-Mm 0.1844 (0.0903 0.4895) E2F2-Cf 0.2290 (0.0879 0.3837) 0.2309 (0.1190 0.5155) E2F2-Bt 0.1695 (0.0771 0.4547) 0.1467 (0.1064 0.7256) 0.1914 (0.0778 0.4066) Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) E2F3-Hs E2F3-Mm 0.1126 (0.0266 0.2366) E2F3-Cf 0.5071 (0.4524 0.8921) 0.4511 (0.4500 0.9976) E2F3-Bt 0.0774 (0.0113 0.1458) 0.1662 (0.0383 0.2305) 0.5355 (0.4498 0.8398) Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) E2F4-Hs E2F4-Mm 0.0824 (0.0272 0.3301) E2F4-Cf 0.0708 (0.0271 0.3823) 0.0838 (0.0225 0.2690) E2F4-Bt 0.0674 (0.0340 0.5050) 0.0854 (0.0376 0.4404) 0.0638 (0.0357 0.5598) Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) Rb-Hs Rb-Mm 0.0860 (0.0412 0.4789) Rb-Cf 0.1370 (0.0343 0.2505) 0.1106 (0.0542 0.4901) Rb-Bt 0.1167 (0.0293 0.2508) 0.0959 (0.0455 0.4748) 0.1251 (0.0306 0.2446) Rb-Rn 0.0943 (0.0458 0.4861) 0.1200 (0.0208 0.1732) 0.1120 (0.0560 0.4996) 0.0952 (0.0496 0.5210) Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) Rbl1-Hs Rbl1-Mm 0.0785 (0.0439 0.5590) Rbl1-Cf 0.0835 (0.0236 0.2824) 0.0700 (0.0417 0.5960) Rbl1-Bt 0.0909 (0.0253 0.2778) 0.0748 (0.0423 0.5653) 0.0653 (0.0160 0.2455) Rbl1-Rn 0.0991 (0.0532 0.5374) 0.0678 (0.0209 0.3081) 0.0832 (0.0492 0.5915) 0.0901 (0.0527 0.5853) Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later m.l. analysis. Use runmode = -2 for ML pairwise comparison.) Rbl2-Hs Rbl2-Mm 0.0753 (0.0446 0.5918) Rbl2-Cf 0.0484 (0.0127 0.2628) 0.0775 (0.0466 0.6019) Rbl2-Bt 0.0561 (0.0178 0.3177) 0.0683 (0.0467 0.6837) 0.0472 (0.0141 0.2990) Rbl2-Rn 0.0810 (0.0491 0.6055) 0.0803 (0.0209 0.2598) 0.0834 (0.0511 0.6130) 0.0744 (0.0525 0.7056)