CODONML (in paml version 4.10.0, September 2020) bglobin.phy Model: One dN/dS ratio, Codon frequency model: F3x4 Site-class models: beta&w>1 (11 categories) ns = 17 ls = 144 Codon usage in sequences -------------------------------------------------------------------------------------------------------------------------------------- Phe TTT 5 5 5 2 3 7 | Ser TCT 1 0 2 3 3 0 | Tyr TAT 2 1 1 1 1 1 | Cys TGT 2 2 2 1 1 1 TTC 3 3 3 6 5 3 | TCC 2 2 2 3 3 3 | TAC 1 2 2 2 2 1 | TGC 0 0 0 0 0 0 Leu TTA 0 0 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 0 3 0 0 0 1 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 2 2 2 2 2 2 -------------------------------------------------------------------------------------------------------------------------------------- Leu CTT 0 0 0 0 0 0 | Pro CCT 5 2 4 3 3 2 | His CAT 2 2 1 3 3 4 | Arg CGT 0 0 0 0 0 0 CTC 3 2 2 2 2 3 | CCC 0 0 0 0 0 1 | CAC 6 6 7 5 5 2 | CGC 0 0 0 0 0 1 CTA 0 0 0 0 0 2 | CCA 2 1 2 1 1 0 | Gln CAA 0 0 0 0 0 0 | CGA 0 0 0 0 0 0 CTG 15 12 16 16 16 11 | CCG 0 1 0 0 0 1 | CAG 3 4 4 4 4 3 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------------------------------- Ile ATT 0 0 0 1 1 0 | Thr ACT 3 4 2 3 2 3 | Asn AAT 1 3 3 2 4 3 | Ser AGT 2 2 2 3 4 2 ATC 0 0 0 0 0 0 | ACC 3 3 3 3 2 3 | AAC 5 2 4 4 4 4 | AGC 0 1 1 0 0 0 ATA 0 0 0 0 0 0 | ACA 1 0 0 0 0 0 | Lys AAA 3 3 2 3 3 1 | Arg AGA 0 0 0 0 0 1 Met ATG 1 2 1 1 1 2 | ACG 0 0 0 0 0 0 | AAG 8 9 10 9 9 12 | AGG 3 3 3 3 3 2 -------------------------------------------------------------------------------------------------------------------------------------- Val GTT 3 3 5 4 4 4 | Ala GCT 6 9 7 8 7 8 | Asp GAT 5 2 2 1 1 6 | Gly GGT 4 3 3 5 4 3 GTC 2 4 2 2 2 2 | GCC 9 10 7 5 6 7 | GAC 2 6 5 3 3 3 | GGC 8 7 8 7 6 7 GTA 0 1 0 0 0 0 | GCA 0 0 0 0 1 0 | Glu GAA 2 3 2 4 4 2 | GGA 0 0 0 0 0 0 GTG 12 9 11 11 11 12 | GCG 0 0 0 1 1 1 | GAG 6 4 5 6 6 6 | GGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------- Phe TTT 5 3 6 3 4 4 | Ser TCT 0 1 2 2 4 2 | Tyr TAT 1 0 1 0 0 0 | Cys TGT 1 1 2 2 1 1 TTC 4 5 3 4 3 4 | TCC 2 3 4 1 1 2 | TAC 1 2 1 3 3 2 | TGC 0 0 0 0 1 0 Leu TTA 0 0 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 1 0 1 2 0 1 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 2 2 2 2 2 2 -------------------------------------------------------------------------------------------------------------------------------------- Leu CTT 0 1 0 0 0 1 | Pro CCT 2 1 1 4 3 2 | His CAT 3 2 2 3 2 2 | Arg CGT 0 0 0 0 0 0 CTC 3 5 4 3 4 2 | CCC 1 2 3 1 2 2 | CAC 6 5 4 6 5 8 | CGC 1 2 1 0 0 0 CTA 1 0 0 1 2 0 | CCA 0 0 1 0 0 1 | Gln CAA 0 0 0 0 0 0 | CGA 0 0 0 0 0 0 CTG 12 13 13 11 11 15 | CCG 1 1 0 0 0 0 | CAG 4 5 5 3 3 3 | CGG 0 0 0 0 1 0 -------------------------------------------------------------------------------------------------------------------------------------- Ile ATT 0 0 1 2 1 1 | Thr ACT 2 1 1 1 3 3 | Asn AAT 3 5 5 3 2 3 | Ser AGT 2 1 2 2 1 2 ATC 0 0 0 1 2 4 | ACC 3 1 3 3 3 1 | AAC 5 4 3 5 5 4 | AGC 0 1 1 1 2 1 ATA 0 1 0 1 1 0 | ACA 0 0 0 0 0 0 | Lys AAA 2 2 2 1 2 1 | Arg AGA 0 0 0 0 0 0 Met ATG 2 1 2 2 1 2 | ACG 0 0 1 0 0 0 | AAG 10 9 12 11 10 11 | AGG 3 3 2 3 2 2 -------------------------------------------------------------------------------------------------------------------------------------- Val GTT 5 5 2 3 2 3 | Ala GCT 9 7 3 8 7 6 | Asp GAT 5 2 3 6 5 4 | Gly GGT 2 3 4 2 3 1 GTC 2 3 3 1 2 3 | GCC 6 7 8 8 8 8 | GAC 4 6 4 3 3 5 | GGC 8 9 7 8 7 8 GTA 0 0 1 0 0 0 | GCA 0 0 0 1 2 2 | Glu GAA 2 1 3 2 1 1 | GGA 0 0 0 2 2 2 GTG 11 10 9 9 9 8 | GCG 0 0 1 0 1 0 | GAG 6 7 4 3 5 4 | GGG 1 1 1 1 0 0 -------------------------------------------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------------------------- Phe TTT 5 0 3 4 1 | Ser TCT 4 0 0 2 3 | Tyr TAT 1 0 0 1 1 | Cys TGT 2 1 2 0 0 TTC 2 8 5 3 4 | TCC 2 4 5 2 3 | TAC 2 2 2 2 2 | TGC 2 2 1 0 0 Leu TTA 0 0 0 0 1 | TCA 1 0 0 2 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 4 0 0 2 0 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 3 4 4 4 4 ---------------------------------------------------------------------------------------------------------------------- Leu CTT 1 1 1 2 6 | Pro CCT 3 2 1 2 0 | His CAT 4 1 3 5 6 | Arg CGT 0 1 0 1 0 CTC 3 5 6 3 2 | CCC 1 3 4 1 3 | CAC 4 5 3 0 1 | CGC 0 2 3 0 1 CTA 0 0 0 0 0 | CCA 0 0 0 0 0 | Gln CAA 1 0 1 3 2 | CGA 0 0 0 0 0 CTG 6 12 11 6 7 | CCG 0 0 0 0 0 | CAG 4 5 4 4 3 | CGG 0 0 0 0 0 ---------------------------------------------------------------------------------------------------------------------- Ile ATT 1 0 1 5 2 | Thr ACT 5 2 3 4 3 | Asn AAT 2 1 1 4 4 | Ser AGT 1 0 0 3 2 ATC 4 7 6 2 2 | ACC 4 5 4 1 1 | AAC 3 6 6 4 2 | AGC 1 1 2 2 5 ATA 0 0 0 0 0 | ACA 0 1 0 1 1 | Lys AAA 0 1 1 3 6 | Arg AGA 0 0 0 1 0 Met ATG 3 1 1 0 0 | ACG 0 0 0 0 0 | AAG 12 9 9 8 5 | AGG 2 3 3 1 2 ---------------------------------------------------------------------------------------------------------------------- Val GTT 5 0 0 8 6 | Ala GCT 5 3 4 7 9 | Asp GAT 2 2 1 3 7 | Gly GGT 6 1 1 3 1 GTC 3 5 5 3 7 | GCC 6 14 11 9 3 | GAC 4 6 5 2 1 | GGC 3 4 4 5 3 GTA 0 0 0 2 0 | GCA 1 0 0 1 4 | Glu GAA 2 0 4 3 4 | GGA 1 2 0 4 4 GTG 5 6 6 3 5 | GCG 0 0 1 0 1 | GAG 6 5 3 3 2 | GGG 2 1 3 0 1 ---------------------------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: human position 1: T:0.12500 C:0.25000 A:0.20833 G:0.41667 position 2: T:0.30556 C:0.22222 A:0.31944 G:0.15278 position 3: T:0.28472 C:0.30556 A:0.05556 G:0.35417 Average T:0.23843 C:0.25926 A:0.19444 G:0.30787 #2: tarsier position 1: T:0.13889 C:0.20833 A:0.22222 G:0.43056 position 2: T:0.30556 C:0.22222 A:0.32639 G:0.14583 position 3: T:0.26389 C:0.33333 A:0.05556 G:0.34722 Average T:0.23611 C:0.25463 A:0.20139 G:0.30787 #3: bushbaby position 1: T:0.13194 C:0.25000 A:0.21528 G:0.40278 position 2: T:0.31250 C:0.20139 A:0.33333 G:0.15278 position 3: T:0.27083 C:0.31944 A:0.04167 G:0.36806 Average T:0.23843 C:0.25694 A:0.19676 G:0.30787 #4: hare position 1: T:0.13889 C:0.23611 A:0.22222 G:0.40278 position 2: T:0.31250 C:0.20833 A:0.32639 G:0.15278 position 3: T:0.27778 C:0.29167 A:0.05556 G:0.37500 Average T:0.24306 C:0.24537 A:0.20139 G:0.31019 #5: rabbit position 1: T:0.13889 C:0.23611 A:0.22917 G:0.39583 position 2: T:0.31250 C:0.20139 A:0.34028 G:0.14583 position 3: T:0.28472 C:0.27778 A:0.06250 G:0.37500 Average T:0.24537 C:0.23843 A:0.21065 G:0.30556 #6: cow position 1: T:0.13194 C:0.20833 A:0.22917 G:0.43056 position 2: T:0.32639 C:0.20139 A:0.33333 G:0.13889 position 3: T:0.30556 C:0.27778 A:0.04167 G:0.37500 Average T:0.25463 C:0.22917 A:0.20139 G:0.31481 #7: sheep position 1: T:0.11806 C:0.23611 A:0.22222 G:0.42361 position 2: T:0.31944 C:0.18056 A:0.36111 G:0.13889 position 3: T:0.27778 C:0.31944 A:0.03472 G:0.36806 Average T:0.23843 C:0.24537 A:0.20602 G:0.31019 #8: pig position 1: T:0.11806 C:0.25694 A:0.20139 G:0.42361 position 2: T:0.32639 C:0.16667 A:0.34722 G:0.15972 position 3: T:0.22917 C:0.38194 A:0.02778 G:0.36111 Average T:0.22454 C:0.26852 A:0.19213 G:0.31481 #9: elephseal position 1: T:0.15278 C:0.23611 A:0.24306 G:0.36806 position 2: T:0.31250 C:0.19444 A:0.34028 G:0.15278 position 3: T:0.24306 C:0.34028 A:0.04861 G:0.36806 Average T:0.23611 C:0.25694 A:0.21065 G:0.29630 #10: rat position 1: T:0.13194 C:0.22222 A:0.25000 G:0.39583 position 2: T:0.29861 C:0.20139 A:0.34028 G:0.15972 position 3: T:0.28472 C:0.33333 A:0.05556 G:0.32639 Average T:0.23843 C:0.25231 A:0.21528 G:0.29398 #11: mouse position 1: T:0.13194 C:0.22917 A:0.24306 G:0.39583 position 2: T:0.29167 C:0.23611 A:0.31944 G:0.15278 position 3: T:0.26389 C:0.35417 A:0.06944 G:0.31250 Average T:0.22917 C:0.27315 A:0.21065 G:0.28704 #12: hamster position 1: T:0.12500 C:0.25000 A:0.24306 G:0.38194 position 2: T:0.33333 C:0.20139 A:0.33333 G:0.13194 position 3: T:0.24306 C:0.37500 A:0.04861 G:0.33333 Average T:0.23380 C:0.27546 A:0.20833 G:0.28241 #13: marsupial position 1: T:0.19444 C:0.18750 A:0.26389 G:0.35417 position 2: T:0.29167 C:0.22222 A:0.32639 G:0.15972 position 3: T:0.32639 C:0.30556 A:0.04167 G:0.32639 Average T:0.27083 C:0.23843 A:0.21065 G:0.28009 #14: duck position 1: T:0.14583 C:0.25694 A:0.25694 G:0.34028 position 2: T:0.31250 C:0.23611 A:0.29861 G:0.15278 position 3: T:0.10417 C:0.54861 A:0.02778 G:0.31944 Average T:0.18750 C:0.34722 A:0.19444 G:0.27083 #15: chicken position 1: T:0.15278 C:0.25694 A:0.25694 G:0.33333 position 2: T:0.31250 C:0.22917 A:0.29861 G:0.15972 position 3: T:0.14583 C:0.50000 A:0.04167 G:0.31250 Average T:0.20370 C:0.32870 A:0.19907 G:0.26852 #16: xenlaev position 1: T:0.15278 C:0.18750 A:0.27083 G:0.38889 position 2: T:0.29861 C:0.22222 A:0.31250 G:0.16667 position 3: T:0.37500 C:0.27083 A:0.13889 G:0.21528 Average T:0.27546 C:0.22685 A:0.24074 G:0.25694 #17: xentrop position 1: T:0.13889 C:0.21528 A:0.24306 G:0.40278 position 2: T:0.29861 C:0.22222 A:0.31944 G:0.15972 position 3: T:0.35417 C:0.27778 A:0.15972 G:0.20833 Average T:0.26389 C:0.23843 A:0.24074 G:0.25694 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 65 | Ser S TCT 29 | Tyr Y TAT 12 | Cys C TGT 22 TTC 68 | TCC 44 | TAC 32 | TGC 6 Leu L TTA 1 | TCA 4 | *** * TAA 0 | *** * TGA 0 TTG 15 | TCG 0 | TAG 0 | Trp W TGG 43 ------------------------------------------------------------------------------ Leu L CTT 13 | Pro P CCT 40 | His H CAT 48 | Arg R CGT 2 CTC 54 | CCC 24 | CAC 78 | CGC 11 CTA 6 | CCA 9 | Gln Q CAA 7 | CGA 0 CTG 203 | CCG 4 | CAG 65 | CGG 1 ------------------------------------------------------------------------------ Ile I ATT 16 | Thr T ACT 45 | Asn N AAT 49 | Ser S AGT 31 ATC 28 | ACC 46 | AAC 70 | AGC 19 ATA 3 | ACA 4 | Lys K AAA 36 | Arg R AGA 2 Met M ATG 23 | ACG 1 | AAG 163 | AGG 43 ------------------------------------------------------------------------------ Val V GTT 62 | Ala A GCT 113 | Asp D GAT 57 | Gly G GGT 49 GTC 51 | GCC 132 | GAC 65 | GGC 109 GTA 4 | GCA 12 | Glu E GAA 40 | GGA 17 GTG 147 | GCG 7 | GAG 81 | GGG 17 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.13930 C:0.23080 A:0.23652 G:0.39338 position 2: T:0.31005 C:0.20997 A:0.32802 G:0.15196 position 3: T:0.26675 C:0.34191 A:0.05923 G:0.33211 Average T:0.23870 C:0.26089 A:0.20792 G:0.29248 TREE # 1: (16, 17, ((14, 15), (13, ((12, (10, 11)), ((9, (8, (6, 7))), ((3, (4, 5)), (1, 2))))))); MP score: 613 lnL(ntime: 31 np: 36): -3686.133656 +0.000000 18..16 18..17 18..19 19..20 20..14 20..15 19..21 21..13 21..22 22..23 23..12 23..24 24..10 24..11 22..25 25..26 26..9 26..27 27..8 27..28 28..6 28..7 25..29 29..30 30..3 30..31 31..4 31..5 29..32 32..1 32..2 0.543890 0.773963 1.924029 0.599538 0.176193 0.055186 0.190663 0.912936 0.338765 0.289394 0.370420 0.102022 0.140254 0.193623 0.050656 0.060162 0.216763 0.064373 0.323714 0.138090 0.061478 0.095637 0.071533 0.012954 0.152086 0.160986 0.029078 0.060191 0.067818 0.173709 0.224442 2.129649 0.943145 0.571797 2.171902 2.081273 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 8.574544 (16: 0.543890, 17: 0.773963, ((14: 0.176193, 15: 0.055186): 0.599538, (13: 0.912936, ((12: 0.370420, (10: 0.140254, 11: 0.193623): 0.102022): 0.289394, ((9: 0.216763, (8: 0.323714, (6: 0.061478, 7: 0.095637): 0.138090): 0.064373): 0.060162, ((3: 0.152086, (4: 0.029078, 5: 0.060191): 0.160986): 0.012954, (1: 0.173709, 2: 0.224442): 0.067818): 0.071533): 0.050656): 0.338765): 0.190663): 1.924029); (xenlaev: 0.543890, xentrop: 0.773963, ((duck: 0.176193, chicken: 0.055186): 0.599538, (marsupial: 0.912936, ((hamster: 0.370420, (rat: 0.140254, mouse: 0.193623): 0.102022): 0.289394, ((elephseal: 0.216763, (pig: 0.323714, (cow: 0.061478, sheep: 0.095637): 0.138090): 0.064373): 0.060162, ((bushbaby: 0.152086, (hare: 0.029078, rabbit: 0.060191): 0.160986): 0.012954, (human: 0.173709, tarsier: 0.224442): 0.067818): 0.071533): 0.050656): 0.338765): 0.190663): 1.924029); Detailed output identifying parameters kappa (ts/tv) = 2.12965 Parameters in M8 (beta&w>1): p0 = 0.94315 p = 0.57180 q = 2.17190 (p1 = 0.05685) w = 2.08127 MLEs of dN/dS (w) for site classes (K=11) p: 0.09431 0.09431 0.09431 0.09431 0.09431 0.09431 0.09431 0.09431 0.09431 0.09431 0.05685 w: 0.00220 0.01518 0.03772 0.06960 0.11156 0.16524 0.23369 0.32283 0.44601 0.65084 2.08127 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 18..16 0.544 329.0 103.0 0.3121 0.1188 0.3807 39.1 39.2 18..17 0.774 329.0 103.0 0.3121 0.1691 0.5418 55.6 55.8 18..19 1.924 329.0 103.0 0.3121 0.4204 1.3468 138.3 138.8 19..20 0.600 329.0 103.0 0.3121 0.1310 0.4197 43.1 43.2 20..14 0.176 329.0 103.0 0.3121 0.0385 0.1233 12.7 12.7 20..15 0.055 329.0 103.0 0.3121 0.0121 0.0386 4.0 4.0 19..21 0.191 329.0 103.0 0.3121 0.0417 0.1335 13.7 13.8 21..13 0.913 329.0 103.0 0.3121 0.1995 0.6390 65.6 65.8 21..22 0.339 329.0 103.0 0.3121 0.0740 0.2371 24.3 24.4 22..23 0.289 329.0 103.0 0.3121 0.0632 0.2026 20.8 20.9 23..12 0.370 329.0 103.0 0.3121 0.0809 0.2593 26.6 26.7 23..24 0.102 329.0 103.0 0.3121 0.0223 0.0714 7.3 7.4 24..10 0.140 329.0 103.0 0.3121 0.0306 0.0982 10.1 10.1 24..11 0.194 329.0 103.0 0.3121 0.0423 0.1355 13.9 14.0 22..25 0.051 329.0 103.0 0.3121 0.0111 0.0355 3.6 3.7 25..26 0.060 329.0 103.0 0.3121 0.0131 0.0421 4.3 4.3 26..9 0.217 329.0 103.0 0.3121 0.0474 0.1517 15.6 15.6 26..27 0.064 329.0 103.0 0.3121 0.0141 0.0451 4.6 4.6 27..8 0.324 329.0 103.0 0.3121 0.0707 0.2266 23.3 23.3 27..28 0.138 329.0 103.0 0.3121 0.0302 0.0967 9.9 10.0 28..6 0.061 329.0 103.0 0.3121 0.0134 0.0430 4.4 4.4 28..7 0.096 329.0 103.0 0.3121 0.0209 0.0669 6.9 6.9 25..29 0.072 329.0 103.0 0.3121 0.0156 0.0501 5.1 5.2 29..30 0.013 329.0 103.0 0.3121 0.0028 0.0091 0.9 0.9 30..3 0.152 329.0 103.0 0.3121 0.0332 0.1065 10.9 11.0 30..31 0.161 329.0 103.0 0.3121 0.0352 0.1127 11.6 11.6 31..4 0.029 329.0 103.0 0.3121 0.0064 0.0204 2.1 2.1 31..5 0.060 329.0 103.0 0.3121 0.0132 0.0421 4.3 4.3 29..32 0.068 329.0 103.0 0.3121 0.0148 0.0475 4.9 4.9 32..1 0.174 329.0 103.0 0.3121 0.0380 0.1216 12.5 12.5 32..2 0.224 329.0 103.0 0.3121 0.0490 0.1571 16.1 16.2 Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: human) Pr(w>1) post mean +- SE for w 7 S 0.995** 2.074 42 S 0.845 1.856 48 T 0.942 1.997 50 D 0.990** 2.067 54 G 0.781 1.762 67 G 0.988* 2.064 85 T 0.866 1.887 123 P 0.995** 2.075 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: human) Pr(w>1) post mean +- SE for w 7 S 0.979* 2.442 +- 0.534 42 S 0.539 1.625 +- 0.846 48 T 0.833 2.176 +- 0.753 50 D 0.970* 2.430 +- 0.554 54 G 0.520 1.594 +- 0.870 67 G 0.961* 2.413 +- 0.573 85 T 0.616 1.774 +- 0.860 123 P 0.976* 2.435 +- 0.540 The grid p0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 p : 0.100 0.300 0.500 0.700 0.900 1.100 1.300 1.500 1.700 1.900 q : 0.100 0.300 0.500 0.700 0.900 1.100 1.300 1.500 1.700 1.900 ws: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500 Posterior on the grid p0: 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.997 p : 0.000 0.181 0.806 0.013 0.000 0.000 0.000 0.000 0.000 0.000 q : 0.000 0.000 0.000 0.001 0.028 0.072 0.073 0.137 0.297 0.391 ws: 0.125 0.785 0.083 0.006 0.001 0.000 0.000 0.000 0.000 0.000