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Table 1 Branch models: estimated parameters and log-likelihood ratio tests

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

Paralog pair Model logL np Branchs ω LRT p-value
  M0 −2847.12 58 OG 0.05    
     Lax 0.08    
     OG 0.05    
  MP −2846.50 59 Lax2 0.07 vs. M0 1.24 0.26
     Lax4 0.10    
     OG 0.05    
Lax2/Lax4 MA −2840.62 59 Lax early 0.14 vs. M0 13.0** 0.00031
     Lax late 0.05    
     OG 0.05    
     Lax2 early 0.19 vs. MP 13.8** 0.001
  MPA −2839.60 61 Lax4 early 0.11    
     Lax2 late 0.04 vs. MA 2.04 0.36
     Lax4 late 0.06    
  M0 −4127.20 62 OG 0.06    
     Pg 0.33    
     OG 0.06    
  MP −4125.06 63 Pg3 0.25 vs. M0 4.28* 0.04
     Pg11 0.41    
     OG 0.06    
Pg3/Pg11 MA −4124.78 63 Pg early 0.22 vs. M0 4.84* 0.03
     Pg late 0.38    
     OG 0.06    
     Pg3 early 0.24 vs. MP 3.68 0.16
  MPA −4123.22 65 Pg11 early 0.21    
     Pg3 late 0.29 vs. MA 3.12 0.21
     Pg11 late 0.44    
  M0 −3604.36 40 OG 0.27    
     Pg11 0.44    
     OG 0.27    
  MP −3603.75 41 Pg11a 0.38 vs. M0 1.22 0.27
     Pg11c 0.50    
     OG 0.27    
Pg11a/Pg11c MA −3604.19 41 Pg11 early 0.50 vs. M0 0.34 0.57
     Pg11 late 0.42    
     OG 0.27    
     Pg11a early 0.50 vs. MP 0.72 0.70
  MPA −3603.39 43 Pg11c early 0.54    
     Pg11a late 0.35 vs. MA 1.60 0.45
     Pg11c late 0.49    
  1. *Note. Models: for M0, ω is allowed to take a different value only in the branch of the outgroup (OG); for MP, MA and MPA ω is allowed to take a different values according to the tested effect, i.e. “paralogs”, “age” or combined as explained in Figure 1. 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.