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Fig. S1 Phylogenetic tree of nuclear ITS sequences.

Fig. S2 Results of the spatial analyses of molecular variance (SAMOVA).

Fig. S3 Maximum clade credibility trees obtained from the relaxed molecular clock analysis of cpDNA sequences in beast and the coalescent-based population tree analysis in *beast.

Fig. S4 Difference between last glacial maximum (LGM) values of climate variables bio6, bio14 and bio5 under the Community Climate System Model (CCSM) and the Model for Interdisciplinary Research on Climate (MIROC) in the Iberian Peninsula.

Table S1 Point localities of L. elegans employed in species distribution modelling

Table S2 Sampled populations of L. elegans and the outgroup species, with GenBank accession numbers of cpDNA, At103 and ITS sequences

Table S3 Variable sites of the nuclear ribosomal ITS region

Table S4 Nearest-neighbour statistic (Snn) values

Table S5 Published studies analysing intraspecific divergence of plant species in a coalescent-based isolation-with-migration framework

Methods S1 Extended version of the Materials and Methods.

Notes S1 Output file of the SDM analysis in Maxent.

Notes S2 Additional Results and Discussion.