Table 2.

Detection of positive selection in codons of OXPHOS mitochondrial genes using four methods: TreeSAAP, Fubar and codeml.

OXPHOS Complex	Gene	Codon	TreeSAAP				codeml BS		codeml SM		Fubar
			From–to	Branch	Cat	Prop	Branch	PP	M2	M8
V	ATP6	28	Ala–Thr	SE + N + S	6	↓Pα	ns	ns	ns	ns	ns
		60	Thr–Ala	SE + N + S	6	↑Pα	ns	ns	ns	0.75*	ns
		181	Ala–Thr	SE	6	↓Pα	ns	ns	ns	ns	ns
I	ND1	22	Ile–Val	E	8	↑EC	SE + N + S	0.75*	ns	ns	ns
		90	Ile–Leu	N + S	8	↑EC	ns	ns	ns	ns	ns
		137	Ile–Val	E	8	↑EC	ns	ns	ns	ns	ns
I	ND2	2		ns	ns	ns	ns	ns	1***	1***	0.921
		321		ns	ns	ns	ns	ns	1***	1***	0.929
I	ND3	105	Tyr–His	E	7	↑αm	ns	ns	ns	ns	ns
I	ND4	14	Thr–Ala	E	6	↑ Pα	ns	ns	ns	ns	ns
		15	Ala–Thr	E	6	↓ Pα	ns	ns	ns	ns	ns
		29	Thr–Ala	S	6	↑ Pα	N + S	0.78*	ns	ns	ns
		191	Thr–Ala	E	6	↑ Pα	ns	ns	ns	ns	ns
		280	Thr–Ala	E	6	↑ Pα	ns	ns	ns	ns	ns
		418		ns	ns	ns	ns	ns	0.78*	0.81**	ns
I	ND5	22	Thr–Ala	SE + N + S	6	↑Pα	ns	ns	ns	ns	ns
		428	Thr–Ala	N + S	6	↑Pα	ns	ns	0.89**	0.89**	0.92
		500	Ala–Thr	SE + N + S	6	↓Pα	ns	ns	0.79*	0.81**	ns
		518		ns	ns	ns	N + S	0.96**	ns	ns	ns

Pα: α-helical tendencies; αm: Power to be at the middle of alpha-helix; EC equilibrium constant, E eastern gentoo, SE southeastern gentoo, N northern, S southern gentoo. Codeml BS (Branch-site model) and SM (site model).

Posterior probability estimates by Bayes Empirical Bayes in site and branch-site models (PP: Posterior probability; *:PP > 0.7, **:PP > 0.8, ***: PP > 0.99).