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

Jiménez, Sergio; Lawton-Rauh, Amy L; Reighard, Gregory L; Abbott, Albert G; Bielenberg, Douglas G

doi:10.1186/1471-2229-9-81

BMC Plant Biology

Table 1 Evolutionary analysis of the MIKC^C-type MADS-box Arabidopsis, poplar and peach genes

From: Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from 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	-	-	-17495.098	Model1 vs. M0 [169]	590.92***
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	0.137	ω = 0.14		-17790.560
M3: discrete (k = 3)	0.155	p₀ = 0.28, p₁ = 0.46, p₂ = 0.26 ω₀ = 0.02, ω₁ = 0.12, ω₂ = 0.36	None	-17165.244
M3: discrete (k = 2)	0.151	p₀ = 0.47, p₁ = 0.53 ω₀ = 0.04, ω₁ = 0.25	None	-17319.365	M3 vs. M0 [4]	1250.63***
M1a: nearlyneutral	0.341	p₀ = 0.76, p₁ = 0.24 ω₀ = 0.13, ω₁ = 1.00	Not allowed	-17592.704
M2a: positive selection	0.341	p₀ = 0.76, p₁ = 0.05, p₂ = 0.19 ω₀ = 0.13, ω₁ = 1.00, ω₂ = 1.00	None	-17592.704	M2a vs. M1a [2]	0
M7: beta	0.166	p = 0.61, q = 2.76	Not allowed	-17168.752
M8: beta & ω>1	0.166	p₀ = 1.00, p₁ = 0.00 p = 0.61, q = 2.76, ω = 1.00	None	-17168.752	M8 vs. M7 [2]	0
Branch-specific model: ancestral SVP/StMADS11 clade
Nested Model pairs	dN/dS^a	Parameters estimates^b	PSS^c,d	ℓ	Model comparison [Δdf]	2ℓ^d
Model A1	-	p₀ = 0.68, p₁ = 0.22, p₂+ p₃ = 0.10 ω₀ = 0.13, ω₁ = 1.00, ω₂ = 27.63	16*, 26, 124, 125**, 139, 151, 169	-17582.792	A1 vs M1a [2]	19.82***
Model A2	-	p₀ = 0.59, p₁ = 0.19, p₂+ p₃ = 0.17 ω₀ = 0.13, ω₁ = 1.00, ω₂ = 1.00	N/A	-17586.128	A1 vs A2 [1]	6.67**
Model B	-	p₀ = 0.41, p₁ = 0.45, p₂+ p₃ = 0.14 ω₀ = 0.04, ω₁ = 0.25, ω₂ = 9.54	4, 7, 16, 26, 50, 124, 125, 127, 139, 169, 172, 173	-17312.590	B vs M3(k = 2) [2]	13.55**
Branch-specific model: ancestral DAM clade
Nested Model pairs	dN/dS^a	Parameters estimates^b	PSS^c,d	ℓ	Model comparison [Δdf]	2ℓ^d
Model A1	-	p₀ = 0.67, p₁ = 0.22, p₂+ p₃ = 0.11 ω₀ = 0.13, ω₁ = 1.00, ω₂ = 1.00	N/A	-17592.339	A1 vs M1a [2]	0.73
Model A2	-	p₀ = 0.67, p₁ = 0.22, p₂+ p₃ = 0.11 ω₀ = 0.13, ω₁ = 1.00, ω₂ = 1.00	N/A	-17592.339	A1 vs A2 [1]	0
Model B	-	p₀ = 0.39, p₁ = 0.44, p₂+ p₃ = 0.17 ω₀ = 0.04, ω₁ = 0.25, ω₂ = 0.40	N/A	-17318.615	B vs M3(k = 2) [2]	1.5

^aAverage over all sites.
^bp_i: proportion of sites. p, q: parameters of the β distribution.
^cPSS: Number of 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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ISSN: 1471-2229

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