Abstract
Temporal monitoring of genetic diversity within species is crucial for incorporating intraspecific genetic variation into global change monitoring. This pilot study aims to establish and validate a methodology for long-term genetic monitoring of aquatic insects in the Bavarian Forest National Park. Over seven years, the genetic diversity and spatiotemporal population structure of the mayfly Baetis alpinus, the stonefly Brachyptera seticornis, and the caddisfly Drusus discolor were investigated within three rivers in the national park. Utilising nuclear microsatellite analysis across nine loci for each species, 735 B. alpinus, 295 B. seticornis, and 193 D. discolor individuals were genotyped to assess local population structures in space and time. Our results revealed distinct spatial genetic patterns in B. alpinus, while B. seticornis and D. discolor lacked spatial genetic structure, indicating maintained gene flow throughout the populations within the national park. B. alpinus exhibited site-specific temporal changes, while B. seticornis and D. discolor showed stable genetic structures over the study period. These findings demonstrate the ability of this system to detect subtle genetic shifts over time. Furthermore, the results emphasise that environmental changes act species-specifically, highlighting the importance of species-level approaches in ecological studies. Continued monitoring and expanded analyses will further our understanding of ecological and population dynamics in changing environments. In light of our preliminary data, it is posited that neutral intraspecific genetic variation is a key indicator of the impacts of global change on freshwater species as it is often among the first aspects of biodiversity to reflect the consequences of changing environmental conditions in a species.