Dynamic evolution of the GnRH receptor gene family in vertebrates

Table 2 Results of constrained topology tests using Bayesian and maximum likelihood methods

Model	Constraint	Topology test
		Bayes factor	AU test	SH test
Hyp 1: Type I GnRH receptors are not monophyletic	Negative	15.300**	N/A	N/A
Hyp 1a: Chimaera Type I receptor is within the monophyletic Type II subfamily	Positive	N/A	> 0.001	0.013
Hyp 1b: Chimaera Type I receptor is ancestral to vertebrate receptors	Positive	N/A	0.002	0.013
Hyp 2a: Type IIb receptors are not monophyletic	Negative	12.970**	N/A	N/A
Hyp 2b: Type IIa-2 receptors are not monophyletic	Negative	13.280**	N/A	N/A
Hyp 2c: Type IIa-3 receptors are not monophyletic	Negative	15.300**	N/A	N/A
Hyp 3a: Type IIa-1 and IIb subfamilies are monophyletic to the exclusion of all other clades	Positive	2.080**	> 0.001	> 0.001
Hyp 3b: Type IIa-1 and IIa-2 subfamilies are monophyletic to the exclusion of all other clades	Positive	(-5.660)**	0.387	0.846
Hyp 3c: Type IIa-1 and IIa-3 subfamilies are monophyletic to the exclusion of all other clades	Positive	2.000**	0.008	0.127
Hyp 4: Type IIa-3 and IIb subfamilies are monophyletic to the exclusion of all other clades	Positive	4.070 *	> 0.001	> 0.001
Hyp 5: Tunicate and vertebrate receptors are monophyletic to the exclusion of all other clades	Positive	30.900**	0.624	0.968

Hypotheses tested using topological constraint tests, which are also illustrated in Figure 7. Hypotheses were compared to the null hypothesis that vertebrate receptors are monophyletic. Specified clades for each test were either constrained to be monophyletic (positive constraint) or not allowed to be monophyletic (negative constraint; limited to Bayesian analyses). Significant results indicate rejection of the hypothesis if the values are positive and acceptance if the values are negative. Bayes Factor scores result from comparisons to a null model with a positive constraint on the vertebrate branch, using a stepping stone model [37]. The strength of the inference is * = strong or ** = very strong [40]; AU = p-values for the Approximately Unbiased test [38]; SH = p-values for the Shimodaira-Hasegawa test [39].

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