Translating Niphargus barcodes from Switzerland into taxonomy with a description of two new species (Amphipoda, Niphargidae)

Integrating citizen science and environmental DNA metabarcoding to study biodiversity of groundwater amphipods in Switzerland

Groundwater is the physically largest freshwater ecosystem, yet one of the least explored habitats on earth, both because of accessing difficulties and the scarcity of the organisms inhabiting it. Here, we demonstrate how a two-fold approach provides complementary information on the occurrence and diversity of groundwater amphipods. Firstly, we used a citizen science approach in collaboration with municipal water providers who sampled groundwater organisms in their spring catchment boxes over multiple weeks, followed by DNA barcoding. Secondly, we collected four 10 L water samples at each site, in one sampling event, for environmental DNA (eDNA) metabarcoding. We found that citizen science was very effective in describing the distribution and abundance of groundwater amphipods. Although the single time-point of eDNA sampling did not detect as many amphipods, it allowed the assessment of the entire groundwater community, including microorganisms. By combining both methods, we found different amphipod species co-occurring with distinct sequences from the eDNA-metabarcoding dataset, representing mainly micro-eukaryotic species. We also found a distinct correlation between the diversity of amphipods and the overall biodiversity of groundwater organisms detected by eDNA at each site. We thus suggest that these approaches can be used to get a better understanding of subterranean biodiversity.

Not the Last Piece of the Puzzle: Niphargus Phylogeny in Hungary

The Palaearctic genus Niphargus is a promising model system to understand subterranean fauna genesis in Europe. The Pannonian Plain (mainly covered by Hungary) in Central Europe, once being the area of the Paratethys, is a key area for Niphargus diversification. However, our knowledge on Hungarian species of Niphargus is primarily based on sporadic taxonomical works from the pre-molecular era. Here, we studied 14 localities, covering the eight valid Hungarian species of Niphargus and including nine previously unstudied populations. Based on sequences of three gene fragments, we reconstructed their phylogeny using maximum likelihood and Bayesian approaches. We found that not all Hungarian species of Niphargus are closely related, and even species sampled at the same localities can belong to different clades. Some Hungarian species form monophyletic clades, while others are nested in various non-Hungarian lineages. The new populations are all genetically distinct from the known species. Our results suggest that the Hungarian Niphargus fauna has originated from seven unrelated clades and its diversity is underestimated due to unknown populations and cryptic species. The detection of genetically distinct species of Niphargus from non-carbonate regions calls for further research efforts. The high diversity and the number of putative new species in the N. tatrensis clade warrants further, high-resolution phylogenetic studies.

A New Species of the Genus Niphargus Schiödte, 1849 (Crustacea: Amphipoda: Niphargidae) from Groundwater Habitats of the Tarkhankut Upland, Crimean Peninsula

A new species of the genus Niphargus Schiödte, 1849 (Crustacea: Amphipoda), co-occurring with water louse Asellus cf. aquaticus (Linnaeus, 1758) (Crustacea: Isopoda) in deep wells, is described from the Tarkhankut Upland, located in the northwestern part of the Crimean Peninsula. Niphargus tarkhankuticus sp. nov. corresponds to a separate phylogenetic lineage (the “tarkhankuticus” ingroup), also including several undescribed species from the coastal habitats of the Black Sea (the Crimean Peninsula, the southern Caucasus and the northern coast of Turkey), which is related to the paraphyletic European “stygius-longicaudatus” group. The divergence of the “tarkhankuticus” ingroup from the related European species probably appeared in the Late Miocene age, about 11–10 Mya, related to the separation of the Eastern Paratethys for different basins (Euxinian, Alpine and Pannopian). At the same time, the speciation within the ingroup started in Pliocene, about 5.76–3.6 Mya, and correlated with the Black Sea leveling and the drainage of coastal marine carbonate accumulations, including the Tarkhankut Upland. Intraspecific values of COI mtDNA gene markers (p-distances) for N. tarkhankuticus sp. nov. are about 2%, showing that the division into a number of isolated subpopulations, probably associated with local tectonic movements, the active formation of the river network, and further karst processes in the Tarkhankut Upland occurred during the Pleistocene (since 2.58 Mya). Analysis of stable isotopes (δ13C/δ15N) revealed that only discovered macrocrustaceans in the studied wells of the Tarkhankut Upland have non-overlapping trophic niches, with A. cf. aquaticus possibly feeding on algae/periphyton, while the trophic position of N. tarkhankuticus sp. nov. is close to predators.

A subterranean adaptive radiation of amphipods in Europe

Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.

Citizen science approach reveals groundwater fauna in Switzerland and a new species of Niphargus (Amphipoda, Niphargidae)

Knowledge on the diversity and distribution of subterranean organisms is still scattered, even in faunistically relatively well-researched countries such as Switzerland. This is mostly due to the restricted access to these subterranean habitats. Better knowledge on these organisms is needed, because they contribute substantially to overall biodiversity of a region, often contain unique elements of biodiversity, and can potentially be indicative of the ecological status of subterranean ecosystems that are providing important ecosystem services such as drinking water. Past research on subterranean organisms has often used highly specialised sampling techniques and expert knowledge. Here, we show that inclusion of non-professionals can be an alternative and highly promising sampling strategy. We retrieved citizen science-based samples from municipal groundwater wells across Switzerland, mainly from the Swiss Plateau. Opportunistic samples from 313 sites revealed a previously undocumented groundwater fauna including organisms from different major invertebrate groups, with a dominance of crustaceans. Here, we studied amphipods of the genus Niphargus. Among all 363 individuals sampled, we found in total eight nominal species. Two of them, namely N. fontanus and N. kieferi, are reported for Switzerland for the first time. We also found four further phylogenetic lineages that are potentially new species to science. One of them is here formally described as Niphargus arolaensissp. nov. The description is based on molecular and morphometric data. Our study proves the suitability of citizen science to document subterranean diversity, supports groundwater conservation efforts with data, and raises awareness for the relevance and biodiversity of groundwater amphipods among stakeholders.

The galaxy of the non-Linnaean nomenclature

Contrary to the traditional claim that needs for unambiguous communication about animal and plant species are best served by a single set of names (Linnaean nomenclature) ruled by international Codes, I suggest that a more diversified system is required, especially to cope with problems emerging from aggregation of biodiversity data in large databases. Departures from Linnaean nomenclature are sometimes intentional, but there are also other, less obvious but widespread forms of not Code-compliant grey nomenclature. A first problem is due to the circumstance that the Codes are intended to rule over the way names are applied to species and other taxonomic units, whereas users of taxonomy need names to be applied to specimens. For different reasons, it is often impossible to refer a specimen with certainty to a named species, and in those cases an open nomenclature is employed. Second, molecular taxonomy leads to the discovery of clusters of gene sequence diversity not necessarily equivalent to the species recognized and named by taxonomists. Those clusters are mostly indicated with informal names or formulas that challenge comparison between different publications or databases. In several instances, it is not even clear if a formula refers to an individual voucher specimen, or is a provisional species name. The use of non-Linnaean names and formulas must be revised and strengthened by fixing standard formats for the different kinds of objects or hypotheses and providing permanent association of 'grey names' with standardized source information such as author and year. In the context of a broad-scope revisitation of aims and scope of scientific nomenclature, it may be worth rethinking if natural objects like plant galls and lichens, although other than the 'single-entity' objects traditionally covered by biological classifications, may nevertheless deserve taxonomic names.