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Fig. S1 Posterior probability densities for the mutation-scaled effective population sizes during plague (A, B) and remission (C, D) periods, when considering log-uniform distributions of the effective population size priors.

Fig. S2 Allele frequency distributions for the 24 microsatellites.

Fig. S3 Inbreeding coefficient distributions.

Fig. S4 Hierarchical Structure clustering analyses based on the Coulon et al.'s (2008) approach.

mec12687-sup-0002-TableS1-S7.docxWord document76K

Table S1 Prior distributions for diyabc demographic and mutational parameters.

Table S2 Bias and precision of effective population size estimation using diyabc.

Table S3 Mean, median and 2.5 and 97.5% quantile estimates from diyabc posterior distribution samples of demographic parameters, when considering log-uniform distributions of the effective population size priors.

Table S4 Genetic diversity for 23 S. gregaria population samples at all 24 microsatellite markers.

Table S5 Pairwise FST values (Weir 1996) for 23 S. gregaria population samples (above the diagonal) and confidence intervals based on 2000 bootstrap samples (below diagonal) for all 24 microsatellite markers.

Table S6 Pairwise FST values (Weir 1996) 23 S. gregaria population samples for the 21 microsatellite markers at selective neutrality (above the diagonal) and confidence intervals based on 2000 bootstrap samples (below diagonal).

Table S7 Robustness of diyabc inferences on the intensity of the population size decline associated with the end of plagues (α) to rejection and estimation procedures.

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