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Appendix S1. Current spatial distribution and recent distribution changes.

Figure S1. Map of the Garonne river basin (South–Western France) representing (1) sites where P. toxostoma was unsuccessfully sampled for genetic analyses (white circles); and (2) sites where P. toxostoma was successfully sampled for genetic analyses (green circles).

Figure S2. Maps representing sites where the occurrence of P. toxostoma was recorded (A) from 1 to 19 times during the 1980–1992 period and (B) from 1 to 14 times during the 2003–2009 period.

Table S1. Information on microsatellite loci and multiplexed PCR used in this study

Table S2. Observed number of alleles (na), expected (He) and observed (Ho) heterozygosities and departures from Hardy–Weinberg equilibrium (Fis) for all loci and populations of P. toxostoma. No significant departures from Hardy–Weinberg equilibrium were found after applying Benjamini and Hochberg (1995) false discovery rate corrections.

Table S3. Mean observed (Ho) and expected (He) heterozygosities, mean number of alleles over loci (NA), allelic richness (AR8 for a minimum sample size of 8 individuals; AR18 for a minimum sample size of 18 individuals) and departures from Hardy–Weinberg equilibrium (Fis) for each P. toxostoma population.

Table S4. P-values for the linkage disequilibrium test for each pair of loci and population.

Table S5. Results for the Wilcoxon's sign rank test computed by BOTTLENECK for each river and for the TPM and SMM microsatellite mutation models.

Table S6. Median, 5 and 95% quartile values calculated for N0 (the current effective population size), N1 (the past effective population size), Ta (the time of the beginning of the demographic change, in years backwards from the present) and Log10 (N0/N1; the magnitude of the demographic change) for each river, through the posterior distributions obtained with MSVAR 1.3.

Table S7. Values for the Mann–Kendall's S statistic, variance in S (Var[S]), mean densities and P-values obtained for the twelve time series with the modified Mann–Kendall trend test.

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