Skip to main content

Advertisement

Table 2 Shimodaira-Hasegawa test for incongruence

From: Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses

E1 as reference tree
 Tree deltaL bp-RELL p-KH p-SH p-WKH p-WSH c-ELW p-AU
 E1 0 1 1 1 1 1 1 0.999
 E2 182.16 0 0 0.008 0 0 7.3e-33 0.000747
 E4 639.14 0 0 0 0 0 3.8e-203 0.000845
 E7 1048.70 0 0 0 0 0 0 1.8e-58
 L1 381.21 0 0 0 0 0 3.8e-104 4.2e-05
 L2 219.47 0 0 0.002 0 0 1.2e-40 2.4e-09
E2 as reference tree
 Tree deltaL bp-RELL p-KH p-SH p-WKH p-WSH c-ELW p-AU
 E1 137.43 0 0 0.023 0 0 1.3e-27 8.3e-05
 E2 0 1 1 1 1 1 1 1
 E4 288.35 0 0 0 0 0 1.3e-75 2.8e-07
 E7 904.92 0 0 0 0 0 3.4e-299 6.7e-97
 L1 273.21 0 0 0 0 0 5.9e-70 5.7e-44
 L2 224.96 0 0 0 0 0 1.8e-60 5.1e-07
E4 as reference tree
 Tree deltaL bp-RELL p-KH p-SH p-WKH p-WSH c-ELW p-AU
 E1 79.74 0 0 0.012 0 0.004 0.000433 0.0217
 E2 64.99 0.02 0.003 0.02 0.003 0.016 0.00211 0.104
 E4 0 0.998 0.997 1 0.997 1 0.997 0.992
 E7 311.86 0 0 0 0 0 8.7e-85 5.8e-114
 L1 130.15 0 0 0 0 0 1.2e-23 6.4e-35
 L2 84.83 0 0 0.004 0 0 1.1e-10 0.00483
E7 as reference tree
 Tree deltaL bp-RELL p-KH p-SH p-WKH p-WSH c-ELW p-AU
 E1 59,374 0.004 0.016 0.017 0.016 0.064 0.00429 0.0117
 E2 71.02 0.001 0.007 0.007 0.007 0.031 0.000919 0.00182
 E4 138.43 0 0 0 0 0 1.78e-20 0.014
 E7 0 0.946 0.952 1 0.952 0.991 0.944 0.945
 L1 39.42 0.0041 0.048 0.119 0.048 0.189 0.043 0.118
 L2 59.86 0.008 0.022 0.025 0.022 0.063 0.00759 0.0321
L1 as reference tree
Tree deltaL bp-RELL p-KH p-SH p-WKH p-WSH c-ELW p-AU
 E1 188.69 0 0 0 0 0 1.3e-25 7.6e-05
 E2 218.51 0 0 0 0 0 4.1e-40 6.6e-48
 E4 473.21 0 0 0 0 0 1.6e-133 0.000267
 E7 899.66 0 0 0 0 0 3.5e-301 5.98e-65
 L1 0 1 1 1 1 1 1 1
 L2 149.83 0 0 0.005 0 0 9.9e-301 1.23e-10
L2 as reference tree
 Tree deltaL bp-RELL p-KH p-SH p-WKH p-WSH c-ELW p-AU
 E1 226.34 0 0 0 0 0 2.4e-51 1.3e-52
 E2 220.29 0 0 0 0 0 1.8e-50 8.4e-12
 E4 478.78 0 0 0 0 0 1.5e-149 4.2e-06
 E7 1087.1 0 0 0 0 0 0 0.00124
 L1 229.72 0 0 0 0 0 1.3e-42 2.01e-13
 L2 0 1 1 1 1 1 1 1
  1. deltaL: logL difference from the maximal logl in the set
  2. bp-RELL: bootstrap proportion using RELL method [38]
  3. p-KH: p-value of one sided [29]
  4. p-SH: p-value of Shimodaira-Hasegawa test [22]
  5. p-WKH: p-value of weighted KH test
  6. p-WSH: p-value of weighted SH test
  7. c-ELW: Expected Likelihood Weight [39]
  8. p-AU: p-value of approximately unbiased (AU) test [30]