Data from: The south-western Carpathians as a centre of ancient diversity of freshwater gammarid amphipods: insights from the Gammarus fossarum species complex

Gammarus fossarum is a diverse species complex of epigean freshwater amphipods throughout Europe. Due to their poor dispersal capabilities and ubiquity, these crustaceans may serve as a model for investigating the influence of historical factors on the contemporary distribution and diversity patterns of freshwater macrozoobenthos. Here, we investigate the fine-scale phylogeographic structure of this complex across its range in the southwestern Carpathian Mountains, which comprises two areas that are geographically isolated from its main European distribution area as well as from each other. Given the Tertiary age of many freshwater Gammarus species, we hypothesize that the southwestern Carpathian populations reflect a relict distribution pattern. We used two mitochondrial and three nuclear markers from 32 localities to reconstruct phylogenetic relationships and estimate the timings of divergence among southwestern Carpathian and non-Carpathian lineages. Cryptic diversity was evaluated from mitochondrial markers by employing phylogenetic and distance-based methods. We distinguished at least 16 cryptic microendemic taxa, some of them coexisting, distributed in the southwestern Carpathians in a mosaic-like pattern. These lineages form a monophyletic group together with several lineages from southeastern Europe. Estimated divergence times indicate a Middle Miocene origin of this clade, with many deep splits dating back to more than 10 Ma. This time frame corresponds with a period of intense geological subsidence in the region that gave birth to the Pannonian Basin. We conclude that subsidence could have been an important driver of diversification in freshwater Gammarus and that the southwestern Carpathians represent an ancient centre of diversity for these crustaceans

A substantial range expansion of alien Ponto-Caspian amphipods along the eastern Baltic Sea coast

We report a considerable range expansion of four Ponto-Caspian amphipod species in transitional waters along the southeastern Baltic Sea coast. Chaetogammarus warpachowskyi and Dikerogammarus haemobaphes were found for the first time in Latvia, the former being common along the coast, while the latter was encountered only in the port of Riga. This indicates a 400 to 600 km expansion along the coast, assuming an origin from the Curonian or Vistula lagoons. We also officially document an expansion for Chelicorophium curvispinum in Latvia of ca. 300 km until Riga, confirming recent unpublished records. Moreover, we document a second invasion route of Pontogammarus robustoides into Estonia from nearby Latvian waters by uncovering a population at the port of Pärnu. This species was previously known in Estonia only from the Gulf of Finland (>500 km from Pärnu). With the exception of D. haemobaphes, all newly recorded species were represented by various life-stages and ovigerous females, indicating viable populations. Overall, our findings reveal that Ponto-Caspian amphipods are much more widespread in the Baltic area than previously known and highlight the need for more stringent monitoring

Copilas-Ciocianu&Petrusek_Gammarus_fossarum_SW_Carpathians_alignments&trees

The archive contains alignments (fasta format) and maximum likelihood trees (newick format) for each of the markers used in this study as well as a concatenated supermatrix

Comparative mitogenomics of native European and alien Ponto-Caspian amphipods

European inland surface waters are home to a rich diversity of native amphipod crustaceans, many of which face threats from invasive Ponto-Caspian counterparts. In this study, we analyse mitochondrial genomes to deduce phylogenetic relationships and compare gene order and nucleotide composition between representative native European and invasive Ponto-Caspian taxa across five families, ten genera and 20 species (with 13 newly sequenced herein). We observe various gene rearrangement patterns in the phylogenetically diverse native species pool. Pallaseopsis quadrispinosa and Synurella ambulans exhibit notable deviations from the typical organisation, featuring extensive translocations of tRNAs and the nad1 gene, as well as a tRNA-F polarity switch in the latter. The monophyletic invasive Ponto-Caspian gammarids display a conserved gene order, primarily differing from native species by a tRNA-E and tRNA-R translocation, which reinforces previous findings. However, Chaetogammarus warpachowskyi shows extensive rearrangement with translocations of six tRNAs. The invasive corophiid, Chelicorophium curvispinum, maintains a highly conserved gene order despite its distant phylogenetic position. We also discover that native species have a significantly higher GC and lower AT content compared to invasive species. The mitogenomic differences observed between native and invasive amphipods warrant further investigation and could provide insights into the mechanisms underlying invasion success

Locomotion of Niphargus amphipods from cave lakes and streams

Locomotion is a complex trait directly linked to different fitness components such as foraging, mate-finding, and escaping from predators. In a food-limited subterranean environment a strong selection for an energetically optimal strategy of locomotion is expected and should lead to different strategies among closely related species adapted to different microhabitats. Due to its taxonomic and ecological diversity, the amphipod genus Niphargus is an ideal model system for studying locomotion strategies of species affiliated with different subterranean aquatic microhabitats. Such species differ from each other morphologically, and we predicted that they also evolved alternative strategies of locomotion. In this study, we examined three species from cave lakes and five species from cave streams or springs. After collection all species were first acclimated in a cave laboratory. Then, we video-recorded behaviour in a rectangular open-field arena of approximately 10 individuals per species. A single individual at a time was recorded under red light for 20 minutes. Videos were used to construct ethograms of distinct locomotor behaviours such as swimming, crawling, and walking. A video-tracking analysis was performed to extract variables like total path covered, time spent moving, average and maximal speed. Individuals were euthanized and measured for several morphological traits likely related to locomotion. Additionally, we measured activities of enzymes acetylcholinesterase and glutathione S-transferase, which are likely related to animals’ locomotor and metabolic activity, respectively. Preliminary analyses suggest that species from lakes and streams differ in locomotor behaviour. Interestingly, variation in locomotor behaviour was larger among lake species, possibly implying that selection for the optimal locomotion strategy is stronger and more uniform in streams than in lakes

A DNA barcode reference library for endemic Ponto-Caspian amphipods

The Ponto-Caspian region is an endemicity hotspot that harbours several crustacean radiations, among which amphipods are the most diverse. These poorly known species are severely threatened in their native range, while at the same time they are invading European inland waters with significant ecological consequences. A proper taxonomic knowledge of this fauna is paramount for its conservation within the native region and monitoring outside of it. Here, we assemble a DNA barcode reference library for nearly 60% of all known Ponto-Caspian amphipod species. We use several methods to define molecular operational taxonomic units (MOTUs), based on two mitochondrial markers (COI and 16S), and assess their congruence with current species-level taxonomy based on morphology. Depending on the method, we find that 54–69% of species had congruent morpho-molecular boundaries. The cases of incongruence resulted from lumping distinct morphospecies into a single MOTU (7–27%), splitting a morphospecies into several MOTUs (4–28%), or both (4–11%). MOTUs defined by distance-based methods without a priori divergence thresholds showed the highest congruence with morphological taxonomy. These results indicate that DNA barcoding is valuable for clarifying the diversity of Ponto-Caspian amphipods, but reveals that extensive work is needed to resolve taxonomic uncertainties. Our study advances the DNA barcode reference library for the European aquatic biota, paving the way towards improved taxonomic knowledge needed to enhance monitoring and conservation efforts

Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda)

Traditional morphological diagnoses of taxonomic status remain widely used while an increasing number of studies show that one morphospecies might hide cryptic diversity, i.e. lineages with unexpectedly high molecular divergence. This hidden diversity can reach even tens of lineages, i.e. hyper cryptic diversity. Even well-studied model-organisms may exhibit overlooked cryptic diversity. Such is the case of the freshwater crustacean amphipod model taxon Gammarus fossarum. It is extensively used in both applied and basic types of research, including biodiversity assessments, ecotoxicology and evolutionary ecology. Based on COI barcodes of 4926 individuals from 498 sampling sites in 19 European countries, the present paper shows (1) hyper cryptic diversity, ranging from 84 to 152 Molecular Operational Taxonomic Units, (2) ancient diversification starting already 26 Mya in the Oligocene, and (3) high level of lineage syntopy. Even if hyper cryptic diversity was already documented in G. fossarum, the present study increases its extent fourfold, providing a first continental-scale insight into its geographical distribution and establishes several diversification hotspots, notably south-eastern and central Europe. The challenges of recording hyper cryptic diversity in the future are also discussed