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Metabarcoding is often presented as an alternative identification tool to compensate for coarse taxonomic resolution and misidentification encountered with traditional morphological approaches. However, metabarcoding comes with two major impediments which slow down its adoption. First, the picking and destruction of organisms for DNA extraction are time and cost consuming and do not allow organism conservation for further evaluations. Second, current metabarcoding protocols include a PCR enrichment step which induces errors in the estimation of species diversity and relative biomasses. In this study, we first evaluated the capacity of capture enrichment to replace PCR enrichment using controlled freshwater macrozoobenthos mock communities. Then, we tested if DNA extracted from the fixative ethanol (etDNA) of the same mock communities can be used as an alternative to DNA extracted from pools of whole organisms (bulk DNA). We show that capture enrichment provides more reliable and accurate representation of species occurrences and relative biomasses in comparison with PCR enrichment for bulk DNA. While etDNA does not permit to estimate relative biomasses, etDNA and bulk DNA provide equivalent species detection rates. Thanks to its robustness to mismatches, capture enrichment is already an efficient alternative to PCR enrichment for metabarcoding and, if coupled to etDNA, is a time‐saver option in studies where presence information only is sufficient. [ABSTRACT FROM AUTHOR]

Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species‐rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large‐scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade‐offs during groundwater colonization. [ABSTRACT FROM AUTHOR]

Ecologists increasingly rely on molecular delimitation methods (MMs) to identify species boundaries, thereby potentially increasing the number of putative species because of the presence of morphologically cryptic species. It has been argued that cryptic species could challenge our understanding of what determine large‐scale biodiversity patterns which have traditionally been documented from morphology alone. Here, we used morphology and three MMs to derive four different sets of putative species among the European groundwater crustaceans. Then, we used regression models to compare the relative importance of spatial heterogeneity, productivity and historical climates, in shaping species richness and range size patterns across sets of putative species. We tested three predictions. First, MMs would yield many more putative species than morphology because groundwater is a constraining environment allowing little morphological changes. Second, for species richness, MMs would increase the importance of spatial heterogeneity because cryptic species are more likely along physical barriers separating ecologically similar regions than along resource gradients promoting ecologically‐based divergent selection. Third, for range size, MMs would increase the importance of historical climates because of reduced and asymmetrical fragmentation of large morphological species ranges at northern latitudes. MMs yielded twice more putative species than morphology and decreased by 10‐fold the average species range size. Yet, MMs strengthened the mid‐latitude ridge of high species richness and the Rapoport effect of increasing range size at higher latitudes. Species richness predictors did not vary between morphology and MMs but the latter increased the proportion of variance in range size explained by historical climates. These findings demonstrate that our knowledge of groundwater biodiversity determinants is robust to overlooked cryptic species because the latter are homogeneously distributed along environmental gradients. Yet, our findings call for incorporating multiple species delimitation methods into the analysis of large‐scale biodiversity patterns across a range of taxa and ecosystems. [ABSTRACT FROM AUTHOR]

The hyporheic zone of rivers potentially acts as a dispersal corridor for groundwater organisms because it provides a spatially continuous interstitial habitat between isolated aquifers. Yet, the degree to which it can facilitate the movement of organisms has been hypothesized to vary in response to change in sediment regime, which determines channel morphology., In this study, we used microsatellite markers to test for a relationship between the genetic structure and diversity of the minute interstitial isopod Proasellus walteri and channel morphology along three nearby hyporheic corridors differing widely in their sediment regime. We predicted that genetic diversity would decrease and genetic structuring would increase as sediment supply-limited channels would become prominent features in the river corridor. The reason is that such channels have fewer and less suitable sedimentary habitats for migration because they lack large depositional bedforms such as gravel bars., Using genotypic data from seven microsatellite loci for a total of 713 individuals distributed among 25 demes, we found that demes had on average more alleles and were less differentiated in the river showing the most extensive alluvial deposits and shortest length of sediment supply-limited channels. Population clusters were also of greater size, reaching up to 30 km in length. The longitudinal pattern of genetic differentiation in this sediment-rich river was best explained by hydrologic distance and the longitudinal pattern of allelic richness was bell-shaped, as expected under a stepping-stone model with symmetrical migration., The length of sediment supply-channels was more important than hydrologic distance in explaining the longitudinal distribution of genetic differentiation in the two other corridors facing a sediment shortage. Allelic richness decreased monotonically upstream in the most sediment-poor river. This correlates with the expansion further downstream of sediment supply-limited channels in this river, which is likely to decrease animal movement and hence gene flow among demes., This study provides the first evidence that the degree to which the hyporheic zone facilitates the movement of groundwater organisms varies greatly among rivers of contrasted geomorphology. Extending the application of riverscape genetics across a range of interstitial taxa and geomorphic settings holds much promise for assessing the contribution of the hyporheic zone to the dispersal of groundwater organisms. [ABSTRACT FROM AUTHOR]

Aim Disentangling the roles of the interacting processes that shape species' ranges requires independent measurements of dispersal, physiological traits and habitat use. Multifaceted approaches of range determinants are, however, still rare, despite the widespread recognition that correlative modelling approaches alone are not sufficient to understand and predict species' distributions. Here, we combined genetic, distributional and physiological data to reveal the processes that cause the disjunct distribution of the groundwater isopod Proasellus valdensis in isolated Alpine mountains previously covered by Pleistocene glaciers. Location The Alps and Jura Mountains, France. Methods Phylogenetic/phylogeographical methods based on mitochondrial and nuclear genes were used to test for recent dispersal between mountains. A logistic regression on presence-absence data was performed to quantify variation in the probability of occurrence with temperature. Variation in survival and respiration over a range of temperatures was measured within four populations to test for a causal effect of temperature on species distribution. Results Despite the disjunct distribution, genetic analyses supported recent dispersal between mountains, as indicated by weak divergence among sequences of cytochrome c oxidase subunit I ( COI), a single haplotype network showing no spatial structuring, and a small proportion of molecular variance distributed between mountains. The probability of occurrence of P. valdensis decreased significantly with increasing temperature, although physiological experiments indicated that occurrence in warmer habitats was probably restricted by thermally dependent biotic interactions rather than by temperature itself. All populations maintained a high survival rate over a wide range of temperatures (3-15 °C), with a weak but detectable tendency for local adaptation. Main conclusions Combining phylogeographical, physiological and habitat modelling methods reveals the interacting processes that drive range dynamics. A broad thermal tolerance helps P. valdensis to colonize vacant habitats during the onset of glacial melting, but range fragmentation and local adaptation, leading to thermal niche narrowing, proceed during warmer interglacials as biotic interactions progressively intensify. [ABSTRACT FROM AUTHOR]