Table 2.

Comparison of topologies.

		Log likelihood	Branch lengths
Topology	No. genes	Super gene	Pig	Human	Mouse	Internal	Fugu
Amino Acids
A	245	-921354	0.0227	0.0280	0.0554	0.0083	0.3294
B	440	-920090	0.0292	0.0281	0.0403	0.0171	0.3229
C	180	-921703	0.0292	0.0241	0.0555	0.0055	0.3304
1. codon pos.
A	215	-570181	0.0189	0.0235	0.0524	0.0088	0.2692
B	386	-568900	0.0265	0.0237	0.0341	0.0195	0.2600
C	208	-570504	0.0264	0.0190	0.0525	0.0058	0.2708
2. codon pos.
A	215	-498689	0.0124	0.0156	0.0323	0.0053	0.1680
B	545	-498005	0.0167	0.0157	0.0229	0.0102	0.1642
C	175	-498925	0.0167	0.0130	0.0324	0.0034	0.1687

Top (A-C) refers to the three different topologies shown in Figure 3a–c. No. genes is the number of individual genes that favour each topology. The likelihood and the branch lengths shown are based on the concatenated super gene of the 988 individual four-species alignments; the average values of the branch lengths from the individual genes are highly similar to these results. Branch lengths are shown in number of substitutions per site.