Table 2 Likelihood ratio test (LRT) results for positive selection in cp genes using the branch-site model from codeml and assuming the foreground branch as subgenus Passiflora. The null model assumes no positive selection, whereas the alternative model allows for positive selection on the foreground branch. A significant LRT statistic and p-value (< 0.05) indicate evidence for positive selection
Gene | Null Model (lnL) | Alternative Model (lnL) | LRT | P value | Positive selection |
|---|---|---|---|---|---|
atpA | -5416.731061 | -5412.139146 | 9.183.830.000.000.070 | 0e0 | True |
atpB | -4653.663776 | -4632.246694 | 4.283.416.399.999.890 | 0e0 | True |
atpE | -1191.894703 | -1191.132408 | 1.524.589.999.999.850 | 0e0 | True |
atpF | -2936.756742 | -2936.616616 | 2.802.520.000.003.270 | 6.62e-63 | True |
atpH | -557.53033 | -557.53033 | 0.0 | 1.00e0 | False |
atpI | -1875.054947 | -1875.054947 | 0.0 | 1.00e0 | False |
ccsA | -3482.990348 | -3465.913442 | 3.415.381.200.000.080 | 0e0 | True |
cemA | -3022.996837 | -3022.996837 | 0.0 | 1.00e0 | False |
clpP | -1268.888758 | -1248.732428 | 4.031.265.999.999.960 | 0e0 | True |
matK | -7323.240373 | -7316.877636 | 12.725.473.999.999.400 | 0e0 | True |
ndhA | -3537.27328 | -3536.501507 | 1.543.545.999.999.150 | 0e0 | True |
ndhB | -2501.650325 | -2501.650326 | -0.0019999993965029716 | 1.00e0 | False |
ndhC | -1081.116279 | -1081.116279 | 0.0 | 1.00e0 | False |
ndhD | -5493.044036 | -5492.610016 | 8.680.400.000.009.680 | 8.70e-191 | True |
ndhE | -1006.688506 | -1006.688506 | 0.0 | 1.00e0 | False |
ndhF | -11,525.529656 | -11,525.491883 | 755.460.000.000.894 | 3.57e-18 | True |
ndhG | -1975.749812 | -1975.266312 | 967.0 | 2.68e-212 | True |
ndhH | -4165.476882 | -4165.476882 | 0.0 | 1.00e0 | False |
ndhI | -1745.53302 | -1745.009447 | 10.471.460.000.001.800 | 1.02e-229 | True |
ndhJ | -1238.696502 | -1238.696502 | 0.0 | 1.00e0 | False |
ndhK | -2009.235367 | -2009.235361 | 0.012000000104308128 | 9.13e-1 | False |
petA | -3048.800084 | -3046.458667 | 4.682.833.999.999.790 | 0e0 | True |
petB | -1793.004653 | -1793.004653 | 0.0 | 1.00e0 | False |
petD | -1297.723744 | -1295.681768 | 40.839.520.000.000.400 | 0e0 | True |
petG | -217.777657 | -217.777657 | 0.0 | 1.00e0 | False |
petL | -330.530003 | -319.888169 | 21.283.668.000.000.000 | 0e0 | True |
petN | -185.581145 | -185.581145 | 0.0 | 1.00e0 | False |
psaA | -5526.801735 | -5523.994622 | 5.614.225.999.999.790 | 0e0 | True |
psaB | -5221.967328 | -5221.967338 | -0.020000001415610313 | 1.00e0 | False |
psaC | -651.040484 | -649.461902 | 3.157.164.000.000.100 | 0e0 | True |
psaI | -426.171134 | -426.171134 | 0.0 | 1.00e0 | False |
psaJ | -405.111325 | -403.265708 | 3.691.234.000.000.050 | 0e0 | True |
psbA | -2879.213041 | -2873.140644 | 12.144.794.000.000.600 | 0e0 | True |
psbB | -3969.137739 | -3969.137739 | 0.0 | 1.00e0 | False |
psbC | -3405.428198 | -3405.428198 | 0.0 | 1.00e0 | False |
psbD | -2203.354638 | -2203.354637 | 0.0019999993965029716 | 9.64e-1 | False |
psbE | -449.236923 | -449.236923 | 0.0 | 1.00e0 | False |
psbF | -217.278231 | -214.649417 | 5.257.628.000.000.020 | 0e0 | True |
psbH | -623.084017 | -622.001225 | 21.655.840.000.000.300 | 0e0 | True |
psbI | -198.445739 | -198.094300 | 7.028.780.000.000.260 | 7.08e-155 | True |
psbJ | -249.380412 | -248.211244 | 23.383.360.000.000.100 | 0e0 | True |
psbK | -628.334431 | -6288.78510 | -1.088.158.000.000.050 | 1.00e0 | False |
psbL | -220.155601 | -220.155601 | 0.0 | 1.00e0 | False |
psbM | -209.740165 | -209.740165 | 0.0 | 1.00e0 | False |
psbN | -291.213313 | -291.213313 | 0.0 | 1.00e0 | False |
psbT | -197.355030 | -197.355.030 | 0.0 | 1.00e0 | False |
psbZ | -390.653136 | -390.653136 | 0.0 | 1.00e0 | False |
rbcL | -5756.967145 | -5725.125326 | 63.683.637.999.998.400 | 0e0 | True |
rpl14 | -1743.031898 | -1743.031898 | 0.0 | 1.00e0 | False |
rpl16 | -1444.679184 | -1444.679184 | 0.0 | 1.00e0 | False |
rpl2 | -2389.389656 | -2389.389656 | 0.0 | 1.00e0 | False |
rpl23 | -1020.163902 | -1020.163902 | 0.0 | 1.00e0 | False |
rpl33 | -762.190101 | -762.101070 | 17.806.200.000.015.000 | 1.28e-40 | True |
rpl36 | -474.175797 | -474.175797 | 0.0 | 1.00e0 | False |
rpoB | -13,348.809868 | -13,348.327628 | 964.480.000.000.447 | 9.44e-212 | True |
rpoC1 | -9121.134828 | -9109.852291 | 22.565.074.000.000.900 | 0e0 | True |
rpoC2 | -17,383.464617 | -17,349.835137 | 672.589.600.000.009 | 0e0 | True |
rps11 | -2454.706719 | -2454.706719 | 0.0 | 1.00e0 | False |
rps12 | -784.166964 | -746.559065 | 7.521.579.800.000.010 | 0e0 | True |
rps14 | -1115.535563 | -1115.535563 | 0.0 | 1.00e0 | False |
rps15 | -1533.141721 | -1530.759860 | 4.763.721.999.999.600 | 0e0 | True |
rps19 | -959.329801 | -958.189129 | 2.281.344.000.000.040 | 0e0 | True |
rps2 | -3380.312648 | -3380.312648 | 0.0 | 1.00e0 | False |
rps3 | -3196.291978 | -3193.633343 | 5.317.270.000.000.480 | 0e0 | True |
rps4 | -2550.391045 | -2550.391045 | 0.0 | 1.00e0 | False |
rps8 | -1734.476247 | -1734.476247 | 0.0 | 1.00e0 | False |
ycf3 | -1172.304022 | -1172.304022 | 0.0 | 1.00e0 | False |
ycf4 | -2492.693465 | -2492.693467 | -0.0040000006556510925 | 1.00e0 | False |