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)
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 | ||||