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Table S1 Sampling sites. Nμ: number of individuals genotyped with microsatellite loci; NM: number of individuals genotyped for the MITE insertion. *: populations collected in localities where wild and domesticated forms are both present.

Table S2 Primers used for the study of the MITE insertion.

Table S3 Microsatellite multiplexes. LG: linkage group on the pearl millet genetic map; Labelling: fluorescent dye used for each forward primer; Ta: annealing temperature; Na: number of alleles identified in this study. u: unknown, (imp): imperfect repeats.

Table S4 Origin of the sequences used for the study of the nucleotide polymorphism in the region surrounding the MITE insertion.

Table S5 Pairwise FST values. All values are significant (P < 0.01) except when underlined.

Table S6 Standardized FST values for the microsatellite loci.

Fig. S1 DIC analysis for the whole data set (A), the domesticated group (B) and the wild group (C), with the maximum numbers of clusters K ranging from 2 to 15, for the model with (CAR) and without (NoSpatial) spatiality (error bars: 95% CIs).

Fig. S2 Population structure estimated by the tess analysis for the whole data set assuming 10 clusters (K = 10). All solutions among the 10 best replicates are displayed. Numbers on the right show how many times a solution was observed. Each individual is represented by a vertical line divided into K colored segments representing the individuals estimated membership to each cluster.

Fig. S3 Population structure estimated by the tess analysis for pearl millet in Sahel for the domesticated populations when K = 7 (A) and the wild populations when K = 7 (B). All solutions among the 10 best replicates are displayed. Numbers on the right show how many times a solution was observed. Each individual is represented by a vertical line divided into K colored segments representing the individuals estimated membership to each cluster.

Fig. S4 Isolation by distance tested on the basis of microsatellite markers in domesticated populations when taking into account (A) or not (B) KAN-D and TAN-D, and in wild populations (C).

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