Phylogeography of a freshwater crustacean species complex reflects a long‐gone archipelago

Aim The Carpathian Mountains are an important European biodiversity hotspot and are characterized by a dynamic geological history. Their freshwater amphipod fauna is ubiquitous and diverse, consisting of micro‐endemic lineages that apparently reflect historical geological events. In this study, we propose that the complementary distribution of two widespread morphotypes belonging to the Gammarus balcanicus species complex reflects two chronologically distinct uplift episodes of the Carpathian Archipelago during the Miocene. Location Southeastern Europe. Methods We sequenced two mitochondrial (COI and 16S) and three nuclear (28S, 18S and EF1α) markers from 68 localities (n = 171) across the Carpathian Arc. Distance and phylogenetic‐based methods were used to quantify cryptic diversity from the mitochondrial markers. We examined phylogenetic relationships, estimated divergence times and reconstructed ancestral geographical distributions of the Carpathian lineages within a wider geographical and phylogenetic context. Results Our results revealed that one morphotype, Gammarus cf. balcanicus, is a highly diverse and polyphyletic entity (consisting of at least 20 cryptic lineages), mostly inhabiting the areas corresponding to old Carpathian palaeo‐islands. We estimated that this morphotype originated and diversified on this archipelago throughout the Miocene. In contrast, a distinct morph, previously described as G. balcanicus dacicus (elevated here to species rank as G. dacicus [new status]), is monophyletic and comprises only two lineages that likely originated and diversified on younger landmasses at the onset of the Late Miocene. Furthermore, it appears that the Pleistocene glaciations did not have a significant effect on the observed distribution and diversity patterns. Each cryptic lineage detected by mitochondrial markers was also supported by at least one nuclear marker. Main conclusions The different timings of landmass uplifts of the Carpathian palaeo‐archipelago seem to have played a central role in the evolution and diversification of local lineages of the G. balcanicus species complex. This indicates that the genetic legacy of long‐gone archipelagos can persist for millions of years in contemporaneous continental biotas.