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

^(a) Probability associated with the LRT between the model M8 and the model M8a

^(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)

^(c) ns not significant, no no sites validated after manual curation, - no partition tested