Table 1: Formal tests of the common ancestry between cytb and nd2 based on the nucleotide sequence data sets aligned with various values of gap penalties (GOP and GEP).
(a)

  ModelNo alignment (1038 bp)(GOP, GEP) = (100, 100) (1026 bp)(GOP, GEP) = (50, 6.66) (1029 bp)
IndependentCommonIndependentCommonIndependentCommon

JC11043.811005.510876.910844.510935.010862.9
K8010820.810821.210669.310662.210727.610684.4
HKY10398.610414.710255.310266.610309.710294.4
GTR10307.510320.410186.510192.110242.410224.3
K80+Γ10789.510723.410637.510562.710695.710650.4
HKY+Γ10329.810274.810186.410119.410239.710228.4
GTR+Γ10271.910216.4 10129.510066.6 10184.110168.6

Homology*0.3140.3170.349

(b)

  Model(GOP, GEP) = (30, 6.66) (1025 bp)(GOP, GEP) = (15, 6.66) (999 bp)(GOP, GEP) = (3, 6.66) (974 bp)
IndependentCommonIndependentCommonIndependentCommon

JC10890.610802.210592.410409.2 10262.19865.7
K8010684.610623.310395.010221.3 10056.99613.1
HKY10271.810241.09991.19875.0 9645.89283.2
GTR10204.910170.39921.19820.4 9585.09234.3
K80+Γ10652.510577.510363.010188.2 10028.19595.4
HKY+Γ10202.410162.09920.59817.6 9580.99249.5
GTR+Γ10146.310099.7 9863.69768.5 9531.19201.7

Homology*0.3600.4190.504

AICs of each model comparing the independent and common origin hypotheses were shown. In the comparison between the two hypotheses, the hypothesis with lower AIC was indicated by . The substitution model with the minimal AIC in each data set was indicated by an underline. Default values of GOP and GEP were indicated in bold fonts.
*Homology between cytb and nd2 alignments, which is defined by 1–(average 𝑝 -distance between cytb and nd2).