Table 1.

Log-likelihood values and RELL BPs (%) for trees for the small dataset. The number of parameters excluding branch lengths is shown in parentheses. The log-likelihood values for the ML tree are shown, while those for other trees are shown as a difference from that for the ML tree. The unrooted trees including the outgroup pygmy right whale are used in the likelihood calculation while they are shown as rooted trees for A, B, F and G. The BPs are approximated using the RELL method, evaluating all 15 trees. The MLEs for the substitution parameters are not shown. The log-likelihood values under the nucleotide and codon models are not comparable with those under the amino acid models, as different data are analysed.

	tree	JC (0)		HKY+Γ5 (5)		HKY+C+Γ5 (13)		codon.M0 (11)		mtmam (0)		mtmam+Γ5 (1)
1	(A((FB)G))	−29 522.9	40	−26 154.4	78	−0.7	34	−0.2	41	−7.5	16	−0.1	26
2	(G((FB)A))	−47.5	2	−3.7	4	−23 935.3	35	−23 643.2	41	−12 245.4	56	−12 166.7	30
3	((AG)(FB))	−81.4		−3.7	5	−7.3	1	−15.5	1	−13.0	3	−1.7	13
4	(A(F(BG)))	−2.6	34	−5.0	7	−14.0	2	−22.2	5	−18.8	9	−6.7	14
5	(A((FG)B))	−15.2	12	−5.2	2	−19.1		−36.1		−38.7		−16.6
6	((BG)(FA))	−77.5		−9.0	1	−11.1	4	−31.7	1	−24.8	2	−8.7	9
7	((FG)(BA))	−123.2		−9.0	1	−26.3		−57.0		−50.3		−22.0
8	(F((BA)G))	−90.5		−9.0		−24.5		−48.2		−42.1		−20.7
9	(G((BA)F))	−85.5		−9.0	1	−18.2		−32.4		−26.3		−16.3
10	(F((BG)A))	−55.4	1	−9.1		−19.4		−37.2		−25.6	3	−10.9	2
11	(B((FA)G))	−55.1	2	−9.2		−10.3	8	−34.0	1	−31.1	1	−15.0
12	(B(F(AG)))	−64.7	1	−9.2		−19.9		−41.8		−32.6	1	−14.9
13	(G((FA)B))	−47.6	5	−9.2		−7.2	14	−18.9	10	−15.4	9	−10.7	4
14	(F(B(AG)))	−62.7	2	−9.3		−22.5		−40.9		−31.7	1	−14.5	1
15	(B((FG)A))	−72.3		−9.4		−22.3		−53.0		−46.4		−21.4