Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from peach

BMC Plant Biology

Table 2 Evolutionary analysis of the MIKC^C-type MADS-box genes of peach

Site model: One ω ratio for each branch
Nested Model pairs	dN/dS^a	Parameters estimates^b	PSS^c,d	ℓ	Model comparison [Δdf]	2ℓ^d
M: free ratio	several	-	-	-2519.205	Model1 vs. M0 [11]	11.63
Site model: One ω ratio for all branches
Nested Model pairs	dN/dS^a	Parameters estimates^b	PSS^c,d	ℓ	Model comparison [Δdf]	2ℓ^d
M0: one ratio	0.434	ω = 0.434		-2525.019
M3: discrete (k = 3)	0.611	p₀ = 0.51, p₁ = 0.46, p₂ = 0.03 ω₀ = 0.10, ω₁ = 0.90, ω₂ = 4.66	62, 79, 185, 218, 228, 239*	-2486.684	M3 vs. M0 [4]	76.67***
M1a: nearlyneutral	0.509	p₀ = 0.55, p₁ = 0.45 ω₀ = 0.11, ω₁ = 1.00	Not allowed	-2489.546
M2a: positive selection	0.632	p₀ = 0.54, p₁ = 0.43, p₂ = 0.03 ω₀ = 0.12, ω₁ = 1.00, ω₂ = 5.15	62, 79, 185, 218, 228, 239	-2486.782	M2a vs. M1a [2]	5.53
M7: beta	0.476	p = 0.36, q = 0.40	Not allowed	-2491.716
M8: beta & ω > 1	0.593	p₀ = 0.96, p₁ = 0.04 p = 0.44, q = 0.55, ω = 3.94	62, 79, 81, 83, 185, 218, 228, 239*	-2487.434	M8 vs. M7 [2]	8.56*

^aAverage over all sites.
^bp_i: proportion of sites. p, q: parameters of the β distribution.
^cPSS: positively selected sites. Naïve empirical Bayes was used in M3 and Bayes empirical Bayes in M2a and M8.
^dAsterisks indicate significance: * P < 0.05, ** P < 0.01, *** P < 0.001.

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