Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth

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)

Model	No alignment (1038 bp)		(GOP, GEP) = (100, 100) (1026 bp)		(GOP, GEP) = (50, 6.66) (1029 bp)
	Independent	Common	Independent	Common	Independent	Common
JC	11043.8	11005.5^†	10876.9	10844.5^†	10935.0	10862.9^†
K80	10820.8^†	10821.2	10669.3	10662.2^†	10727.6	10684.4^†
HKY	10398.6^†	10414.7	10255.3^†	10266.6	10309.7	10294.4^†
GTR	10307.5^†	10320.4	10186.5^†	10192.1	10242.4	10224.3^†
K80+Γ	10789.5	10723.4^†	10637.5	10562.7^†	10695.7	10650.4^†
HKY+Γ	10329.8	10274.8^†	10186.4	10119.4^†	10239.7	10228.4^†
GTR+Γ	10271.9	10216.4 ^†	10129.5	10066.6 ^†	10184.1	10168.6 ^†
Homology*	0.314		0.317		0.349

(b)

Model	(GOP, GEP) = (30, 6.66) (1025 bp)		(GOP, GEP) = (15, 6.66) (999 bp)		(GOP, GEP) = (3, 6.66) (974 bp)
	Independent	Common	Independent	Common	Independent	Common
JC	10890.6	10802.2^†	10592.4	10409.2 ^†	10262.1	9865.7^†
K80	10684.6	10623.3^†	10395.0	10221.3 ^†	10056.9	9613.1^†
HKY	10271.8	10241.0^†	9991.1	9875.0 ^†	9645.8	9283.2^†
GTR	10204.9	10170.3^†	9921.1	9820.4 ^†	9585.0	9234.3^†
K80+Γ	10652.5	10577.5^†	10363.0	10188.2 ^†	10028.1	9595.4^†
HKY+Γ	10202.4	10162.0^†	9920.5	9817.6 ^†	9580.9	9249.5^†
GTR+Γ	10146.3	10099.7 ^†	9863.6	9768.5 ^†	9531.1	9201.7 ^†
Homology*	0.360		0.419		0.504

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).