Table 4

Test of alternative phylogenetic hypotheses for continental cichlid groups

Topological constraint

pKH

pSH

2 ln Bayes factor

Best as in Fig. 1

1.000

1.000

Constraint 1: monophyly of Madagascar and Indo/Sri Lanka (Tree 1)

0.006**

0.043*

65.4*

Constraint 2: monophyly of Africa, Madagascar and Indo/Sri Lanka (Tree 2)

0.001**

0.002**

125.1*

Constraint 3: monophyly of Africa and Indo/Sri Lanka (Tree 3)

0.000**

0.000**

297.2*

Probabilities for constrained trees were assessed using the Kishino-Hasegawa (pKH) and Shimodaira-Hasegawa (pSH) tests and the Bayes factor. Single asterisks indicate significant rejection (p < 0.05) and double asterisks indicate highly significant rejection (p < 0.01) of the corresponding hypothesis. We used the traditional criterion of 2 ln Bayes factor over 10 (with an asterisk), indicating very strong evidence against an alternative hypothesis [39]. Constrained trees are the following: Tree 1: ((((Oreochromis sp., (Tropheus duboisi, Neolamprologus brichardi)), Tylochromis polylepis),(Astronotus ocellatus, Hypselecara temporalis)),((Etroplus maculatus, Paretroplus maculatus),(Ptychochromoides katria, Paratilapia polleni))); Tree 2: ((((Oreochromis sp.,(Tropheus duboisi, Neolamprologus brichardi)), Tylochromis polylepis),((Etroplus maculatus, Paretroplus maculatus),(Ptychochromoides katria, Paratilapia polleni))),(Astronotus ocellatus, Hypselecara temporalis)); and Tree 3: (((((Oreochromis sp.,(Tropheus duboisi, Neolamprologus brichardi)), Tylochromis polylepis), Etroplus maculatus),((Astronotus ocellatus, Hypselecara temporalis),(Ptychochromoides katria, Paratilapia polleni))), Paretroplus maculatus).

Azuma et al. BMC Evolutionary Biology 2008 8:215   doi:10.1186/1471-2148-8-215