Table S1. Characteristics of microsatellite loci applied in the study. Column abbreviations: Reference -Genbank accession number or publication of the locus; Locus -Common name of the locus; Panel -Set of loci run in the same capillary; MP -Multiplex group or single locus PCR amplification; Primer ??M -Primer concentration in the PCR-mix, PCR prog. -Annealing temperature profile of the PCR program used; Forward Primer 5'-3' - Sequence of the labeled primer; Reverse Primer 5'-3' -Sequence of the non-labeled primer; #A -Number of alleles found in the locus; A-range -Range of the length (bp) of alleles; HE -Expected heterozygosity in the locus.

Table S2. Diversity indices for 32 microsatellite loci used in the study. Sampling site abbreviations as in table 1.

Table S3. Pairwise FST between the samples (above diagonal) and inferred populations (below diagonal). Full names of the samples (rightmost column and top row) and inferred populations (leftmost column and bottom row) corresponding to abbreviations are listed in table 1 for the samples and in table 3 for the inferred populations. Statistically not significant pairwise FST values are denoted in bold. Location of the sample site /population is denoted in brackets; LM -lower mainstem, UM -upper mainstem, HW -headwater and T -tributary.

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