Genetic diversity among populations of the endangered European weatherfish Misgurnus fossilis in the Czech Republic, Austria and adjacent areas

The European weatherfish Misgurnus fossilis is a freshwater fish species specialised at inhabiting shallow, stagnant water bodies with dense vegetation. Owing to the widespread loss and degradation of such habitats through human-induced landscape alteration, the species has undergone a severe decline and is currently considered endangered across much of Europe. To support future conservation and management strategies, we analysed the intraspecific genetic diversity of weatherfish populations from the Czech Republic, Austria and adjacent regions. Both genetic markers, the mitochondrial cytochrome oxidase I gene ( COI ) and the nuclear recombination-activating gene ( RAG1 ), revealed a remarkably low genetic diversity and shallow population structure compared with most other European freshwater fish species. Across 170 specimens from 35 populations, two common mitochondrial haplotypes and two common nuclear alleles were identified. All specimens from Austria and Bavaria exclusively carried the most common mitochondrial haplotype and the most common nuclear allele. This marker combination was also dominant in most Czech populations. However, locally restricted populations displayed rarer haplotypes and alleles. Notably, two populations from the Czech part of the Oder basin were dominated by a combination of a rare mitochondrial haplotype and rare nuclear alleles, indicating the presence of a genetically distinct lineage in the Oder basin relative to the Danube and Elbe basins. This geographic pattern was independently recovered by both mitochondrial and nuclear markers, strongly suggesting that it reflects genuine historical population structure. The observed geographic structure implies the importance of considering regional genetic units in conservation planning for this endangered species.