Strong small-scale differentiation but no cryptic species within the two isopod species Asellus aquaticus and Proasellus coxalis in a restored urban river system (Emscher, Germany)

Worldwide, humans have strongly altered river networks. Key changes resulted in modified hydromorphology, poor habitat quality and availability, migration barriers, and pollution. Restoration measures aim at mitigating anthropogenic stressors and to restore connectivity, but the biological success of the measures is not guaranteed. Analyzing genetic diversity and population structure of target species in the river network with genetic markers can help understanding recolonization processes and identifying persisting gene flow barriers. Here, we studied the population genetic structure of two pollution-tolerant detritivorous isopod species in the former heavily degraded and polluted, but now mostly restored Emscher catchment in Germany: the native Asellus aquaticus and the non-native Proasellus coxalis. For both species, we analyzed mitochondrial cytochrome c oxidase I (COI) gene sequences and nuclear genome-wide single nucleotide polymorphism (SNP) data. Surprisingly, we found a strong population structure for both species with several isolated populations on a small-scale of few kilometers, but a still high genetic diversity, especially in the COI gene. Both species consisted of two known possible cryptic species, while our SNP data showed, that they represent only one species, each. This highlights the importance of integrating high-resolution nuclear markers into species identification, because species diversity may otherwise be greatly overestimated. While we could identify some migration barriers and found indication for passive dispersal by birds or humans, these factors could not fully explain the population structure, suggesting that also other drivers, such as isolation by adaptation, priority effects or biotic interactions play a role in shaping the local population structure.