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Table 3 Branch-site models: estimated parameters and log-likelihood ratio tests

From: Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicagogenus (L.)

  Model (k) np LogL LRT P-value prop clade ω
  M3 (2) 58 −2375.94       
Lax2/Lax4 MD (2) 59 −2369.54 vs. M3 (2) 12.8** 3.47 10-4 0.76   0.00
        0.24 Lax2 0.15
         Lax4 0.52
  M3 (3) 60 −2375.94       
  MD (3) 61 −2361.85 vs. M3 (3) 28.17** 1.11 10-7 0.77   0.005
        0.03   0.97
        0.20 Lax2 0.55
         Lax4 0.97
  M3 (2) 61 −3411.03       
Pg11/Pg3 MD (2) 62 −3407.95 vs. M3 (2) 6.16* 0.01 0.68   0.09
        0.32 Pg3 0.74
         Pg11 1.35
  M3 (3) 63 −3400.58       
  MD (3) 64 −3399.59 vs. M3 (3) 1.98 1.16    
  M3 (2) 40 −2216.23       
Pg11a/Pg11c MD (2) 41 −2214.01 vs. M3 (2) 4.45* 0.03 0.79   0.12
        0.21 Pg11a 1.54
         Pg11c 3.13
  M3 (3) 42 −2210.38       
  MD (3) 43 −2209.37 vs. M3 (3) 2.01 0.16    
  1. Note. Models: for M3 (discrete model), ω is free to take the number of values indicated in brackets (k); these values are homogenous in all branches of the tree; for MD, as explained in Figure 1 (b), one category of ω is allowed to differ between the two paralogous genes clades of the tree [33]. np: number of free parameters; logL: log-likelihood; LRT: likelihood ratio test statistic between indicated models; one (respectively two) asterisk indicates that the probability of observing such an LRT or higher under the compared model is <0.05 (respectively <0.01), assuming that the LRT follows a χ2 distribution with the difference of free parameters between the compared models as the number of degrees of freedom.