Table 1.

Migration edges inferred by TreeMix during the Maximum Likelihood (ML) searches carried out fitting eight gene flow events.

Migration edge	Origin	Destination	N	$\overline{w}$	${\overline{w}}_j$	${\overline{SE}}_j$	p-value	MS	MSE
A	(V. labrusca)	(V. x novae-angliae)	40	0.492	0.492	0.020	< < 1.000 E-10	69	–
B	(V. x novae-angliae)	(V. x slavinii)	40	0.444	0.444	0.025	< < 1.000 E-10	63	–
C	Euvitis group	(V. x champinii, V. x doaniana, V. mustangensis, V. shuttleworthii)	40	0.154	0.154	0.064	0.008	26	62 §
D	(V. acerifolia, V. arizonica, V. blancoi, V. bloodworthiana, V. girdiana, V. x novae-angliae, V. riparia, V. rupestris)	(V. tiliifolia)	40	0.431	0.431	0.025	< < 1.000 E-10	16	23 #
E	(V.girdiana)	(V. californica)	40	0.347	0.347	0.055	1.333 E-10	74	–
F	(V. rupestris)	(V. x champinii, V.x doaniana)	40	0.488	0.487	0.018	< < 1.000 E-10	35	36 *
G	(V. acerifolia)	(V. x doaniana)	40	0.358	0.358	0.023	< < 1.000 E-10	32	–
H	(V. californica)	(V. bloodworthiana)	40	0.140	0.140	0.035	3.843 E-05	10	–

Migration edges are labelled with capital letters from A to H. For each migration the number of independent runs (N) used to calculate mean values, the mean weight on the edge ($\overline{w}$), the jackknife estimate of the weight averaged over the N independent runs (${\overline{w}}_j$) and the jackknife estimate of the standard error averaged over the N independent runs (${\overline{SE}}_j$) are shown in the table. The least significant p-value (p-value) recovered by TreeMix during the independent runs is also shown. Overall, results were found to be very stable across different runs (see Supplementary Tables S3 and S4 ). Origin, the set of species found in the subtree below the origin of the migration edge; Destination, the set of species found in the subtree below the destination of the migration edge; MS, migration support; MS_E, extended migration support. Both MS and MS_E are defined in Supplementary file S1 . §, MS_E value is computed considering as valid destination of migration the set of species shown in the column ‘Destination’ as well as any of its proper subsets with at least 2 elements. #, MS_E value is computed considering as valid origin of migration the set of n species specified in the column ‘Origin’ as well as its proper subsets with at least n-3 elements. *, MS_E value is computed considering as valid origin of migration the set of species shown in the column ‘Destination’ as well as any of its proper subsets.