Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes

Table 3 Tests of significance for conflicting phylogenetic hypotheses

			P-values
Hypotheses	intact BP	RELL BP	KH	AU	BPP	MRBAYES	TREE-PUZZLE
1. Basal jawed vertebrate
A. Cartilaginous fishes	0.93	0.88	ML	ML	1.00	1.00	0.69
B. Tetrapods	0.00	0.01	≤ 0.03	≤ 0.06	0.00	0.00	0.00
2. Phylogenetic relationship among ray-finned fishes
A. ((Teleostei, (bowfin, gar)), Chondrostei)	0.90	0.89	ML	ML	1.00	1.00	0.34
B. (((Teleostei, bowfin), gar), Chondrostei)	0.06	0.07	≤ 0.11	≤ 0.21	0.00	0.00	0.00
C. (((Teleostei, gar), bowfin), Chondrostei)	0.03	0.01	≤ 0.05	≤ 0.08	0.00	0.00	0.00
D. (Teleostei, ((bowfin, gar), Chondrostei))	0.01	0.01	≤ 0.03	≤ 0.05	0.00	0.00	0.37
3. Phylogenetic position of bichir
A. Bichir is the basal ray-finned fish	0.99	0.99	ML	ML	1.00	1.00	0.71
B. Bichir and Chondrostei form a monophyletic group	0.00	0.01	≤ 0.02	≤ 0.08	0.00	0.00	0.16
4. Phylogenetic relationship among tetrapods, lobe-finned fishes and ray-finned fishes
A. ((tetrapods, lobe-finned fishes), ray-finned fishes)	0.55	0.52	ML	ML	0.89	0.93	0.37
B. ((tetrapods, ray-finned fishes), lobe-finned fishes)	0.40	0.39	≤ 0.42	≤ 0.81	0.11	0.07	0.51

Hypotheses 1 A and B and hypotheses 2 A-D correspond to those shown in Figure 1A and 1B and Figure 2A,2B,2C,2D, respectively. Hypotheses supported in this study are shown in bold letters. Two types of bootstrap probabilities (intact and RELL, see Materials and Methods for their differences), P-values by the Kishino-Hasegawa (KH) test and the approximately unbiased (AU) test, the Bayesian posterior probability (BPP) and support values by the MRBAYES and TREE-PUZZLE programs are shown.

ISSN: 1741-7007