High Altitudes as Reservoirs of Unique Genetic Diversity: A Case Study on Aquatic Beetles in Glacial Lakes of Tatra Mountains

Mountains play a crucial role in global biodiversity, serving as refugia for many endemic and endangered species. This extends to high‐altitude freshwater habitats, such as glacial lakes and ponds, which support unique communities of cold‐adapted invertebrates. However, their remoteness, short ice‐free periods and difficult accessibility pose challenges for research, leaving key ecosystem aspects poorly understood. This is particularly true for population genetic diversity and structure, which are essential for developing effective conservation strategies, especially in the context of climate change adaptation and biodiversity preservation. This study aims to (i) assess the community composition and genetic diversity and structure of aquatic beetles in the (sub)alpine lakes and ponds of the Tatra Mountains, (ii) compare these populations with conspecifics from lower elevations and (iii) evaluate the role of this mountain system in maintaining unique genetic diversity. Macroinvertebrate samples were collected from 215 sites, and a target barcoding fragment was amplified from ~500 aquatic beetles. Furthermore, our dataset was expanded with > 1700 sequences from the BOLD database (Barcode of Life Data Systems) and used for species delimitation with RESL, ASAP and mPTP, as well as for assessing key genetic parameters, including haplotype and nucleotide diversity, intraspecific variation and genetic differentiation. Phylogenetic relationships among haplotypes recorded within the study area were inferred using maximum likelihood analyses, and time‐calibrated Bayesian phylogenies were conducted to assess cryptic taxa. Aquatic beetles were recorded at 106 sites, yielding 387 DNA barcodes and identifying 68 species from 27 genera and eight families. Of these, 29 species were newly recorded in the region. The expanded dataset comprised 657 haplotypes representing 106 BINs (barcode index numbers), with species delimitation yielding 81 (ASAP) and 92 (mPTP) MOTUs (molecular operational taxonomic units). For species recorded in the Tatra Mountains, approximately 75% of their globally recognised BINs/MOTUs were also present within the region, and three Linnean species were confirmed to include cryptic complexes likely originating in the Pleistocene. Notably, 68% of the 179 haplotypes found in the studied area were unique to this region, with significant genetic differentiation from non‐Tatra populations, as shown by AMOVA analyses. The study demonstrates that highly diverse (sub)alpine lakes distributed in a geographically small area can harbour substantial species and genetic diversity and serve as important reservoirs of unique genetic diversity. These lakes likely also act as secondary contact sites for the cryptic complexes identified in this study. In contrast, the first recorded findings of some thermophilic and eurytopic species, along with the absence of several previously reported cold‐adapted taxa, suggest a potential shift in species composition, likely driven by climate change. This research significantly contributes to expanding the regional DNA barcode library and enhancing general understanding of genetic diversity in mountain freshwater ecosystems. The findings are also relevant for biodiversity monitoring efforts and conservation strategies, especially in the context of climate change‐driven shifts in community composition, as evidenced by some of the newly recorded species in the Tatra Mts.