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Table 2 Evolutionary analysis of the MIKCC-type MADS-box genes of peach

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 - - -2519.205 Model1 vs. M0 [11] 11.63
Site model: One ω ratio for all branches
Nested Model pairs dN/dSa Parameters estimatesb PSSc,d Model comparison [Δdf] 2ℓd
M0: one ratio 0.434 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*
  1. aAverage over all sites.
  2. bpi: proportion of sites. p, q: parameters of the β distribution.
  3. cPSS: 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.