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Table S1. Specimen and haplotype informationdata set with locality of origin (the name of the water body, thenearest town/place and country), 16S, COI with number (n) ofanalysed individuals, and concatenated sequences identity code,phylogroup, and the GenBank accession numbers. GenBank accessionnumbers for outgroups: Austropotamobius pallipes s. lato(JF293367, AY667106 for 16S and COI respectively), Astacusastacus (DQ320033, AY667146 for 16S and COI respectively),Orconectes limosus (JF293366, DQ882096for 16S and COI respectively). ZV, Zeleni Vir; GK, Gorski Kotar; ŽPB, Žumberak, Plitvice and Bjelolasica; LD, Lika and Dalmatia; BAN, Banovina; SB, southern Balkans; CSE, central and south-eastern Europe; AT, Austria; BA, Bosnia and Herzegovina; BG, Bulgaria; CH, Switzerland; DE, Deutschland; FR, France; GR, Greece; HR, Croatia; IT, Italy; LU, Luxemburg; ME, Montenegro; MK, Macedonia; RO, Romania; SR, Serbia; SI, Slovenia; TR, Turkey.

Table S2. Estimation of divergence times according to different approaches (see Methods). Mean posterior divergence times estimates and 95% HPD values (in brackets) are given in Ma. Nodes (see Fig. 5) with posterior probability <0.50 have no HPD values.

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