Data from: Molecular diversity of Germany’s freshwater fishes and lampreys assessed by DNA barcoding

This study represents the first comprehensive molecular assessment of freshwater fishes and lampreys from Germany. We analyzed COI sequences of more than 80% of the species mentioned in the current German Red List. In total, 1056 DNA barcodes belonging to 93 species from all major drainages were used to i) build a reliable DNA barcode reference library, ii) test for phylogeographic patterns, iii) check for the presence of barcode gaps between species, and iv) evaluate the performance of the barcode index number (BIN) system, available on the Barcode of Life Database. For 76.6% of all analysed species DNA barcodes are a reliable means for identification, indicated by the presence of barcode gaps. An overlap between intra- and interspecific genetic distances was present in 16 species, seven of which belonging to the genus Coregonus. The Neighbour-Joining phenogram showed 60 non-overlapping species clusters and six singletons, which were related to 66 separate BIN numbers. Furthermore Barbatula barbatula, Leucaspius delineates, Phoxinus phoxinus and Squalius cephalus exhibited remarkable levels of cryptic diversity. The assignment of at least two BIN numbers to each of these species indicates the occurrence of cryptic species. In contrast, eleven clusters showed haplotype sharing, or low levels of divergence between species, hindering successful identification. The analysis of our barcode library together with public data resulted in 89 BINs, of which 56% showed taxonomic conflicts. Most of these conflicts were caused by synonymities, inadequate taxonomy or misidentifications, and may only exceptionally have a biological reason (introgression, recent speciation). Moreover, our study increased the number of potential alien species in Germany from 14 to 21 and is therefore a valuable groundwork for further faunistic investigations.