Phylogeography of noble crayfish (Astacus astacus) reveals multiple refugia

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 700k years before present, whereas remaining differentiations occurred within the last 450k 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.