Summary 1. This study examines phylogeography and phylogeny of the threatened stone crayfish, Austropotamobius torrentium, in order to elucidate the role of the Dinaric Karst geology in shaping the evolutionary history and genetic diversity of aquatic fauna in the western Balkans. Mitochondrial 16S rRNA and COI genes were partially sequenced from 188 and 159 crayfish, respectively, sampled from 70 localities. Phylogenetic relationships were reconstructed using four methods of phylogenetic inference. Divergence times between phylogroups were estimated in a Bayesian framework, and their demographic history was examined using neutrality tests and mismatch distribution analysis. 2. Seven geographically localised phylogroups separated by pronounced genetic gaps were found. Five of them have a distribution range within the northern‐central Dinaric (NCD) region, while the remaining two include populations from the southern Balkans (SB) and central and south‐eastern Europe (CSE). The oldest divergence event separated two NCD lineages from the rest of populations in the Late Miocene or Early Pliocene. Divergences amongst the five NCD phylogroups and SB + CSE occurred in the Pliocene. The most recent split separated SB and CSE phylogroups during the Late Pliocene. For both genes, uncorrected pairwise divergences between most of the phylogroups (4.1–8.7% for COI and 1.6–4.8% for 16S rRNA) were of the same range as, or higher than, some of the interspecific distances previously reported for the genus Austropotamobius. 3. Geographically isolated and deeply divergent cryptic monophyletic phylogroups within A. torrentium in the NCD region arose in the course of intensification of Neotectonic movements during the Pliocene and the beginning of the Pleistocene and the development of karstification that has heavily fragmented the palaeohydrography of the area. The results confirm a gradual north–south expansion of stone crayfish during the pre‐Pleistocene that preceded the rapid northward post‐glacial re/colonisation of central Europe (CSE phylogroup) through the Danube drainage. 4. Austropotamobius torrentium comprises morphologically cryptic but molecularly distinct taxa. Considering the relatively small geographical areas they inhabit, the NCD phylogroups of stone crayfish should be given the highest conservation priority.

Summary Reconstructing the phylogeographic history of a species can aid in defining areas of conservation priority. For freshwater species, historical river structure plays a significant role in explaining genetic differentiation and population structure. However, human‐induced translocations can erase the natural genetic structure, especially for species of commercial interest such as the noble crayfish (Astacus astacus). Our aim was to reconstruct the current genetic structure of the endangered noble crayfish in central Europe to identify refugial areas that are hotspots of genetic diversity. We analysed a fragment of the mitochondrial cytochrome oxidase subunit I, and the 16S rRNA from 540 noble crayfish specimens from 156 sampling sites distributed around five European sea basins. Additionally, we conducted a microsatellite analysis of 289 individuals from 22 sites. Both mitochondrial and nuclear markers revealed genetically relatively homogenous populations in central Europe that had been influenced by anthropogenic translocations. However, some areas (Eider catchment in northern Germany and Rhineland‐Palatinate in south‐western Germany) show a distinct genetic structure with endemic haplotypes and private alleles indicating (i) that these areas were refugia for A. astacus in central Europe and (ii) that these populations have not been subject to anthropogenic translocations. Further, we found the highest genetic diversity in the Black Sea basin and particularly high differentiation between populations from the western Balkans and the remaining Black Sea populations. The split between Western Balkan and the remaining European populations is estimated to have occurred approximately 700 k years before present, whereas remaining differentiations occurred within the last 450 k years. Using migration modelling, we detected that the North Sea basin and the Baltic Sea basin were colonised independently via different colonisation paths from the eastern Black Sea basin, while the western Balkans did not contribute to this colonisation. Our results suggest the existence of at least two refugial areas in south‐eastern Europe. To conserve maximum genetic diversity, conservation priorities for noble crayfish should focus on the south‐eastern European genetic hotspots and on populations in central Europe that hold an autochthonous genetic structure (e.g. Langsee in the Eider catchment area). We further propose that each river catchment should form a separate management unit to reduce anthropogenic genetic homogenisation.

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In order to improve our general knowledge on the distribution of the various species of freshwater cray sh of the family Astacidae in Croatia, we gathered all the available unpublished data, as well as data from the literature and those of our own investigations. Our research con rmed the presence of three cray sh species in Croatia: Astacus astacus (Linnaeus, 1758), Austropotamobius torrentium (Schrank, 1803), and Austropotamobius pallipes (Lereboullet, 1858), and we of cially recorded the presence of Astacus leptodactylus Eschscholtz, 1823 and Orconectes limosus (Ra nesque, 1817). Biogeographical data suggest the following distribution pattern: A. astacus is distributed in the continentalpart of Croatia, forming both river and lake populations. A. pallipes is distributed in south and southwest Croatia (Lika, Istria, Dalmatia, and on some islands in the Adriatic Sea). A. torrentium can be found in streams at higher altitudes in the continental part of Croatia. Finally, A. leptodactylus is found in the rivers of eastern and central Croatia (Slavonia and Posavina), while O. limosus was discovered recently in marshes of the Nature Park Kopa † cki rit (Slavonia). Some mixed populations of A. astacus and A. torrentium were detected. Some specimens of A. pallipes and A. torrentium were found in underground habitats. Research on the distribution of freshwater cray sh should be more intensive, and will be continued in the future. RÉSUMÉA n d'améliorer notre connaissance sur la répartition des différentes espèces d'Astacidae de Croatie, nous avons rassemblé toutes les données non publiées disponibles, les données de la littérature et les résultats de nos propres investigations. Nos recherches ont con rmé la présence de trois espèces d'écrevisses en Croatie: Astacus astacus (Linnaeus, 1758), Austropotamobius torrentium (Schrank, 1803), et Austropotamobius pallipes (Lereboullet, 1858), et nous avons enregistré la présence d'Astacus leptodactylus Eschscholtz, 1823 et d'Orconectes limosus (Ra nesque, 1817). Les données biogéographiques suggèrent le modèle de répartition suivant: A. astacus est répartie dans la partie continentale de la Croatie, formant des populations à la fois de rivières et de lacs. A. pallipes est présente dans le sud et le sud-ouest de la Croatie (Lika, Istrie, Dalmatie, et dans quelques îles de la mer Adriatique). A. torrentium peut être trouvée dans les cours d'eau, à des altitudes plus élevées, dans la partie continentale de la Croatie. En n, A. leptodactylus se rencontre dans les rivières de la Croatie orientale et centrale (Slavonie et Posavina) tandis que O. limosus a été découverte récemment dans les marais du Parc Naturel Kopa † cki rit (Slavonie). Quelques populations mixtes d'A. astacus et A. torrentium ont été détectées. Quelques spécimens d'A. pallipes et d'A. torrentium ont été trouvés dans les habitats souterrains. Les recherches sur la répartition des écrevisses devraient être plus intensives, et seront poursuivies dans le futur.

Key-words:non-indigenous crayfish species, dispersal rate, impact