Abstract

Niphargus is the largest genus of freshwater amphipods. Its systematics from the species to the family level has always been problematic. This study is the first comprehensive phylogenetic treatment of the chiefly subterranean group in 160 years of its taxonomic history. It includes 103 niphargid species plus outgroups, representing about one-third of all nominal species. The samples originated mainly from type localities or adjacent sites and covered most of the morphological variability of the genus. Character sampling included nuclear 28S and mitochondrial 12S rDNA sequences, and 122 morphological characters. Quantitative morphological traits were coded using two alternative methods. The first one searches for gaps in the variability range of each character, while the second one uses absolute differences between the standardized raw data as weights. Different data sets yielded alternative topologies. All data support the monophyly of Niphargidae, while Niphargopsis— another niphargid genus — was consistently nested within Niphargus, loosing justification for its separate status. We predict a similar fate for all or most of the remaining six small niphargid genera, which were not yet scrutinized phylogenetically. Different topologies agreed in species composition of five large, well-supported clades, although the hierarchic relationships between them remain unresolved. These clades reject all previously proposed taxonomic subdivisions of Niphargus, implying a high degree of morphological homoplasy that renders any morphology-based groups questionable. The clade members are distributed within well-established zoogeographical regions that do not exceed 1300 km across the longest diagonal. These results provide a framework for future studies on niphargid systematics, the evolution of endemism and cryptic diversity in subterranean environments, the mechanisms leading to exceptional morphological heterogeneity, historical biogeography, and applied ecological issues.