Table 2: Formal tests of the common ancestry between cytb and nd2 based on the amino acid sequence data sets aligned with various values of gap penalties (GOP and GEP).

  Model No alignment (346 aa) (GOP, GEP) = (100, 100) (338 aa) (GOP, GEP) = (15, 6.66) (342 aa) (GOP, GEP) = (10, 0.1) (330 aa) (GOP, GEP) = (1, 0.1) (313 aa)
IndependentCommonIndependentCommonIndependentCommonIndependentCommonIndependentCommon

Poisson5934.35933.55748.65745.85856.95838.65664.9 5638.0 5403.15288.6
Poisson+Γ5922.05933.55735.95740.65843.95832.35651.7 5639.0 5392.75288.5
JTT5591.55586.15420.35414.05515.85495.65335.5 5276.4 5080.24879.8
mtmam5247.45252.55083.15090.85174.75176.04995.4 4989.9 4754.34688.6
JTT+F+Γ5304.35325.85133.75152.85226.85231.75044.8 5034.2 4809.54682.4
mtmam+F+Γ5248.1 5272.35082.6 5107.75174.6 5185.44995.0 4995.6 4759.74678.7

Homology*0.0770.0830.1070.123 0.216

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).