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Table 1 Evolutionary analysis of the MIKCC-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/dSa Parameters estimatesb PSSc,d Model comparison [Δdf] 2ℓd
M: free ratio several - - -17495.098 Model1 vs. M0 [169] 590.92***
Site model: One ω ratio for all branches
Nested Model pairs dN/dSa Parameters estimatesb PSSc,d Model comparison [Δdf] 2ℓd
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/dSa Parameters estimatesb PSSc,d Model comparison [Δdf] 2ℓd
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/dSa Parameters estimatesb PSSc,d Model comparison [Δdf] 2ℓd
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
  1. aAverage over all sites.
  2. bpi: proportion of sites. p, q: parameters of the β distribution.
  3. cPSS: Number of positively selected sites. Naïve empirical Bayes was used in M3 and Bayes empirical Bayes in M2a and M8.
  4. dAsterisks indicate significance: * P < 0.05, ** P < 0.01, *** P < 0.001.