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Table 2 Results of selection footprints analysis (PAML site, branch, and branch-site models). Clusters are defined in the general Medicago-only phylogenetic analysis described in Fig. 3. A further subdivision of cluster 3 and 6 into two internal sub-clusters (denoted a and b) was defined for site models tests. Branch tested are colour-coded in red in Fig. 3. In each table cell are reported the significance of the model comparison (p value), position and ω values of the amino-acid found to be under positive selection in the ‘site’ and ‘branch-site’ analyses after manual curation (see Additional file 4: Table S4 for global alignment positioning)

From: Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

Cluster Site model (a)   Branch model (b) Branch-site model (b)
cluster_1 p = 1.4 10−4   ns (c) ns  
  pos = 83 ω =3.02 +/− 0.78    
  pos = 179 ω =2.97 +/− 0.83    
cluster_2 no (c)   - (c) -  
cluster_3 p = 1.99 10−13   ns p = 1.02 10−4  
  pos = 27 ω =3.27 +/− 0.59   pos = 74 ω =19.02
     pos = 82 ω =19.02
cluster_3a p = 1.01 10−3     
cluster_3b p = 1.24 10−6     
  pos = 27 ω =5.54 +/− 1.89    
  pos = 82 ω =5.66 +/− 1.79    
cluster_4 ns   - -  
cluster_5 no   - -  
cluster_6 p = 1.09 10−44   ns p = 6.07 10−14  
  pos = 43 ω =8.42 +/− 0.95   pos = 43 ω =19.23
  pos = 76 ω =8.39 +/− 1.07   pos = 92 ω =19.23
  pos = 120 ω =8.42 +/− 0.95   pos = 128 ω =19.23
     pos = 183 ω =19.23
cluster_6a p = 8.04 10−10     
  pos = 43 ω =7.074 +/− 1.62    
cluster_6b p = 5.13 10−15     
  pos = 92 ω =10.11 +/− 1.25    
  pos = 94 ω =10.20 +/− 0.86    
  1. (a) Probability associated with the LRT between the model M8 and the model M8a
  2. (b) Probability associated with the LRT between the model for which branches in red are considered as foreground branches and the null model (cf. Fig. 3 for branch partition and Method section for models details)
  3. (c) ns not significant, no no sites validated after manual curation, - no partition tested