Fig. S1 Haplotype Networks for the three loci (A) ITS, (B) GPD and (C) mtLSU. For each population, the percentage assigned to the different single-locus clusters inferred in BAPS is represented. Shading is consistent between in the maps and the haplotype networks of each locus.

Fig. S2 Profiles of Loglikelihood, second integral of likelihood (ΔK) and admixture proportion (α) infered in the serial structure runs.

Fig. S3 Mcc population tree reconstructed in *beast.

Figs. S4–S6 Mcc phylogenetic trees of ITS, GPD and mtlsu haplotypes calculated in beast.

Figs. S7–S8 Statistical summary of the stochastic map simulations, average number of transitions and average proportion of time spent in each character state per tree.

Fig. S9 (1–11) Detailed transitions through time plots resulting from the SM analyses.

Table S1 Summary statistics of the data sets, PCR settings and optimum substitution models used.

Table S2 Description of genetic polymorphism at the a population level.

Table S3 Results of the ML strict clock implemented in MEGA5.

Tables S4–S7 Nucleotide diversity, haplotype composition and measurements of genetic divergence and differentiation between MLCs and populations.

Table S8 Detailed results of the Migrate-n analyses.

Tables S9–S10 Statistical summaries of the Stochastic map simulations.

Table S11 Genbank accessions of Cetraria islandica and the haplotypes of Cetraria aculeata discussed on the manuscript.

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