Chironomids as Indicators of Biodiversity and Isolation Patterns in a Balkan Karst Biodiversity Hotspot

ABSTRACT Aim Our research aimed to assess the beta diversity of Chironomidae (Diptera) and faunal connections across springs, streams, and rivers within the Skadar Lake basin, a Mediterranean biodiversity hotspot, using DNA barcoding. Location Skadar Lake basin—a Mediterranean biodiversity hotspot. Methods We analysed mitochondrial cytochrome c oxidase subunit I sequences from larvae collected at 56 sites, employing Barcode Index Numbers (BINs) as proxies for species. Results Our analysis revealed high overall diversity (224 BINs) along high site heterogeneity and a large proportion of rare BINs. Nearly two‐thirds of BINs were represented by fewer than four specimens, and 84% occurred at three or fewer sites. We observed extremely low faunal overlap between ecosystems, with only nine BINs shared among springs, streams, and rivers. Springs had the highest richness (169 BINs) and exceptional uniqueness, hosting 126 exclusive BINs (ca. 56%). No significant large‐scale geographical or altitudinal diversity gradients were detected, suggesting local factors override broader patterns. Main Conclusions The major conclusion is that hydrogeological isolation within the karst landscape profoundly shapes chironomid diversity, creating unique and isolated spring communities. These distinct, often rare assemblages indicate that chironomids are a sensitive indicator of habitat fragmentation and the vulnerability of these unique Mediterranean freshwater ecosystems to environmental change and localised impacts.