Long‐term within‐basin isolation patterns, different conservation units, and interspecific mitochondrial DNA introgression in an amphipod endemic to the ancient Lake Skadar system, Balkan Peninsula

Investigation of biodiversity, including genetic diversity within species, is crucial for rational planning of nature conservation and species protection. Endemics or narrow‐ranged taxa, sensitive to alteration of physical and chemical conditions, may serve as local bioindicators. Homoeogammarus scutarensis is an endemic, cold‐adapted amphipod crustacean, inhabiting fragmented spring habitats, within a relatively small area of the Lake Skadar basin. The basin is recently under heavy anthropogenic influence leading to habitat deterioration. Genetic diversity within H. scutarensis was investigated using the mitochondrial cytochrome c oxidase subunit I and the nuclear 28S ribosomal RNA markers. Genetic diversity within the mitochondrial (mt)DNA appeared to be surprisingly high as for the limited spatial scale. The history of within‐species divergence dates back at least to the Pliocene. A case of interspecific mtDNA introgression from the endemic H. scutarensis to the widespread and partly sympatric Homoeogammarus thoni was observed in one of the studied populations. Demographic analysis showed that the demography of H. scutarensis population has been stable, without evidence of expansion. Thus, we believe that H. scutarensis, responsive to environmental changes, is a proper model mirroring the conditions in sensitive habitats of the Lake Skadar basin. To protect ongoing evolutionary processes, the conservation measures for this species should take into account the complex fine‐scale lineage endemism patterns. This case study may also provide a hint for planning conservation strategies in other geologically old spring systems. Most of the localities where H. scutarensis occurs provide refugia for divergent mtDNA lineages, suggesting prolonged isolation between sites and independent evolutionary histories. We conclude that H. scutarensis is composed of two or three conservation units. One of them occupies the headwaters of the Crnojevica River and spring in its valley. The other is widespread throughout the sub‐lacustrine springs and the Zeta Plain; however, a group of unique haplotypes is found in springs in the Podhum Bay. Their presence and distribution should be considered while planning any investments or conservation strategies.