In the present thesis, using midges (Diptera Chironomidae) as flagship taxa of freshwater ecology, I am focusing on the interesting research model represented by the Skadar Lake system. It is a well-known hot-spot of freshwater biodiversity consisting of the geologically young lake Skadar (originated ca. 1200 years BP) and by its ancient system of springs (originated in the Pliocene). The main aim of my thesis was to reveal and compare the morphological and molecular species diversity of non-biting midges (Diptera, Chironomidae) inhabiting Skadar Lake and its spring system. Using a taxonomy-based approach for adult males and pupal exuviae, I identified 164 Chironomidae taxa providing the first insight into species diversity of the Skadar Lake basin. Results presented in my thesis extending the existing checklist with 152 taxa newly found in the Skadar Lake basin. DNA barcoding of larvae and mature males revealed a total of 168 Operational Taxonomic Units which is a higher result than the number of morphotypes obtained during morphological identification. Pursuing this goal, I additionally compared the level of species diversity with other central and southern European lakes. A comparison of species checklists from 13 other well-studied European lakes resulted that Lake Constance (Switzerland/Germany/ Austria) is the richest in species number, followed by the Skadar Lake.
The second aim was to investigate the influence of physical-chemical conditions on composition and distribution of chironomid assemblages in Skadar Lake basin. The obtained results suggest that shallow, coastal parts of the lake covered with macrophytes are inhabited by a higher number of species.
As a third aim, I developed and evaluated the first reference barcode library for Chironomidae from Skadar Lake basin. Moreover, using an expanded reference library and records deposited in Barcode of Life Database (BOLD), I estimated DNA barcoding efficiency for the European Chironomidae. My study provides COI barcodes for 770 Chironomidae individuals assigned, based on morphology, to 75 species collected in the Skadar Lake basin (all records from this area are new for online repositories) and confirms the usefulness of DNA barcoding for the identification of non-biting midges.
My fourth aim was to explore chironomid species distribution patterns in Europe using universal Barcode Index Number (BIN) with a discussion of problematic species groups, both for traditional taxonomy and DNA barcoding. The results of my PhD thesis provide the first insight into the factual chironomid species diversity of the Lake Skadar basin, in comparison with chironomid fauna at the European scale. The results fill a significant gap in knowledge of biodiversity in the Balkan region. Based on the results of Chironomidae fauna investigation, I can conclude that the Skadar Lake basin is now well sampled and such a high representation of species from various sampling sites provides reliable estimation of the local chironomid fauna. Based on obtained results it is hard to predict the origin of the chironomids inhabiting the Skadar Lake basin based on the sequences uploaded so far to BOLD and on their known geographic distribution. The still insufficient number of sequences is distributed between the well-studied European regions and Skadar Lake basin. Additionally, the Skadar Lake basin could be recognized as a hot-spot of freshwater biodiversity but without species-level endemism
