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Populations that expand their range can undergo rapid evolutionary adaptation of life-history traits, dispersal behaviour and adaptation to the local environment. Such adaptation may be aided or hindered by sexual reproduction, depending on the context. However, few empirical and experimental studies have investigated the genetic basis of adaptive evolution during range expansions. Even less attention has been given to the question how sexual reproduction may modulate such adaptive evolution during range expansions. We here studied genomic adaptation during experimental range expansions of the protist Tetrahymena thermophila in landscapes with a uniform environment or a pH gradient. Specifically, we investigated two aspects of genomic adaptation during range expansion. First, we investigated adaptive genetic change in terms of the underlying numbers of allele frequency changes from standing genetic variation and de novo variants. We focused on how sexual reproduction may alter this adaptive genetic change. Second, we identified genes subject to selection caused by the expanding range itself, and directional selection due to the presence or absence of the pH gradient. We focused this analysis on alleles with large frequency changes that occurred in parallel in more than one population to identify the most likely candidate targets of selection. We found that sexual reproduction altered adaptive genetic change both in terms of de novo variants and standing genetic variation. However, sexual reproduction affected allele frequency changes in standing genetic variation only in the absence of long-distance gene flow. Adaptation to the range expansion affected genes involved in cell divisions and DNA repair, whereas adaptation to the pH gradient additionally affected genes involved in ion balance and oxidoreductase reactions. These genetic changes may result from selection on growth and adaptation to low pH. In the absence of gene flow, sexual reproduction may have aided genetic adaptation. Gene flow may have swamped expanding populations with maladapted alleles, thus reducing the extent of evolutionary adaptation during range expansion. Sexual reproduction also altered the genetic basis of adaptation in our evolving populations via de novo variants, possibly by purging deleterious mutations or by revealing fitness benefits of rare genetic variants.

Environmental DNA (eDNA) metabarcoding is raising expectations for biomonitoring of organisms that have hitherto been neglected. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference databases, taxonomy-free approaches are proposed for biomonitoring at the level of operational taxonomic units (OTUs). This is challenging, because OTUs cannot be annotated and directly compared against classically derived taxonomic data. The application of good stringency treatments to infer the validity of OTUs and clear understanding of the consequences of such treatments is especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect eDNA diversity estimates in the statistical framework of Hill numbers. We collected water eDNA samples at 61 sites across a 740-km2 river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared when using stringency treatments with increasing weighting of the OTU abundances. Our study demonstrated the usefulness of Hill numbers for biodiversity analyses and comparisons of eDNA data sets that strongly differ in diversity. We recommend best practice for data stringency filtering for biomonitoring using eDNA.

The last decade brought a spectacular development of so-called environmental (e)DNA studies. In general, "environmental DNA" is defined as DNA isolated from environmental samples, in contrast to genomic DNA that is extracted directly from specimens. However, the variety of different sources of eDNA and the range of taxonomic groups that are targeted by eDNA studies is large, which has led to some discussion about the breadth of the eDNA concept. In particular, there is a recent trend to restrict the use of the term "eDNA" to the DNA of macro-organisms, which are not physically present in environmental samples. In this paper, we argue that such a distinction may not be ideal, because the eDNA signal can come from organisms across the whole tree of life. Consequently, we advocate that the term "eDNA" should be used in its generic sense, as originally defined, encompassing the DNA of all organisms present in environmental samples, including microbial, meiofaunal and macrobial taxa. We first suggest specifying the environmental origin of the DNA sample, such as water eDNA, sediment eDNA or soil eDNA. A second specification would then define the taxonomic group targeted through polymerase chain reaction amplification, such as fish eDNA, invertebrate eDNA and bacterial eDNA. This terminology does also not require assumptions about the specific state of the DNA sampled (intracellular or extracellular). We hope that such terminology will help better define the scope of eDNA studies, especially for environmental managers, who use them as reference in routine biomonitoring and bioassessment.

A major focus of ecology is to understand and predict ecosystem function across scales. Many ecosystem functions are measured only at local scales, while their effects occur at a landscape level. Here we investigate how landscape-scale predictions of ecosystem function depend on intraspecific competition, a fine-scale process, by manipulating intraspecific density of shredding macroinvertebrates and examining effects on leaf litter decomposition, a key function in freshwater ecosystems. For two species, we found that per capita leaf processing rates declined with increasing density following power functions with negative exponents, likely due to interference competition. To demonstrate consequences of this nonlinearity, we scaled up estimates of leaf litter processing from shredder abundance surveys in 10 replicated headwater streams. In accordance with Jensen's inequality, applying density-dependent consumption rates reduced estimates of catchment-scale leaf consumption by an order of magnitude relative to density-independent rates. Density-dependent consumption estimates aligned closely with metabolic requirements in catchments with large-but not small-shredder populations. Importantly, shredder abundance was not limited by leaf litter availability, and catchment-level leaf litter supply was much higher than estimated consumption. Thus leaf litter processing was not limited by resource supply. Our work highlights the need for scaling up, which accounts for intraspecific interactions.

Uncovering biodiversity as an inherent feature of ecosystems and understanding its effects on ecosystem processes is one of the most central goals of ecology. Studying organisms’ occurrence and biodiversity patterns in natural ecosystems has spurred the discovery of foundational ecological rules, such as the species–area relationship, and is of general scientific interest. Recent global changes add relevance and urgency to understanding the occurrence and diversity of organisms, and their respective roles in ecosystem processes. While information on ecosystem properties and abiotic environmental conditions are now available at unprecedented, highly‐resolved spatial and temporal scales, the most fundamental variable – biodiversity itself – is still often studied in a local perspective, and generally not available at a wide taxonomic breadth, high temporal scale and spatial coverage. This is limiting the capacity and impact of ecology as a field of science. In this forum article, we propose that complete biodiversity assessments should be inclusive across taxonomic and functional groups, across space, and across time to better understand emergent properties, such as ecosystem functioning. We use riverine ecosystems as a case example because they are among the most biodiverse ecosystems worldwide, but are also highly threatened, such that an in‐depth understanding of these systems is critically needed. Furthermore, their inherent spatial structure requires a multiscale perspective and consideration of spatial autocorrelation structures commonly ignored in biodiversity–ecosystem functioning studies. We show how recent methodological advances in environmental DNA (eDNA) provide novel opportunities to uncover broad biodiversity and link it to ecosystem processes, with the potential to revolutionize ecology and biodiversity sciences. We then outline a roadmap for using this technique to assess biodiversity in a complete and inclusive manner. Our proposed approach will help to get an understanding of biodiversity and associated ecosystem processes at spatial scales relevant for landscape ecology and environmental managers.

Theory predicts that the distribution of genetic diversity in a landscape is strongly dependent on the connectivity of the metapopulation and the dispersal of individuals between patches. However, the influence of explicit spatial configurations such as dendritic landscapes on the genetic diversity of metapopulations is still understudied, and theoretical corroborations of empirical patterns are largely lacking. Here, we used microsatellite data and stochastic simulations of two metapopulations of freshwater amphipods in a 28,000 km2 riverine network to study the influence of spatial connectivity and dispersal strategies on the spatial distribution of their genetic diversity. We found a significant imprint of the effects of riverine network connectivity on the local and global genetic diversity of both amphipod species. Data from 95 sites showed that allelic richness significantly increased towards more central nodes of the network. This was also seen for observed heterozygosity, yet not for expected heterozygosity. Genetic differentiation increased with instream distance. In simulation models, depending on the mutational model assumed, upstream movement probability and dispersal rate, respectively, emerged as key factors explaining the empirically observed distribution of local genetic diversity and genetic differentiation. Surprisingly, the role of site-specific carrying capacities, for example by assuming a direct dependency of population size on local river size, was less clear cut: while our best fitting model scenario included this feature, over all simulations, scaling of carrying capacities did not increase data-model fit. This highlights the importance of dispersal behaviour along spatial networks in shaping population genetic diversity.

Leaf litter processing is an essential ecosystem function in freshwater systems, since much of the carbon and nutrients moving through freshwater food webs come from the surrounding terrestrial ecosystems. Thus, it is important to understand how the species performing this function differ, especially because many native species are being replaced by non-native species in aquatic ecosystems. We used a field experiment to examine leaf consumption rates of two common shredding macroinvertebrates (the native Gammarus fossarum and the non-native Gammarus roeselii). Leaves from three species, varying in resource quality, were added both in leaf monocultures and as a three-species mixture. Biomass-adjusted daily consumption rates were similar between the two amphipod species, and each consumed nitrogen-rich alder leaves faster than oak or beech leaves. However, because adult G. roeselii are approximately twice the size of G. fossarum, this led to systematic, though nonsignificant, differences in consumption rates at the per-capita or population level. Furthermore, we found nuanced effects of decomposer identity on leaf decomposition in mixtures. Only G. roeselii showed increased consumption of the preferred resource (alder) in the mixture, while G. fossarum consumed all leaves at the same proportional rates as in monocultures. This is an important distinction, as most measures of macroinvertebrate leaf shredding are made in the laboratory with only a single leaf resource available. Our results, based on a field experiment which could control the presence of dominant macroinvertebrates while still providing natural, biologically realistic context, suggest that even functionally similar species may subtly shift ecosystem processes.

Species that successfully colonized subterranean environments are subject to two opposing selection processes. Stringent abiotic factors select for convergent adaptations, such as loss of eyes and pigments, while interspecific competition drives between-species divergence. Subterranean species can resolve opposing selection by adaptation to physically different microhabitats. Yet, species frequently co-occur in physically homogeneous subterranean habitats, like interstitial. These co-occurrences in such a narrow ecological context can be explained either by equalizing mechanisms, in which neither of the co-occurring species has a competitive advantage, or by more complex niche models that include species’ differentiation along a trophic niche axis. We tested these hypotheses using the amphipod genus Niphargus. We analysed Europe-wide co-occurrence records of Niphargus species from interstitial habitats, split into six independent large-scale regions. Firstly, we addressed whether species’ pairwise co-occurrences are random using a probabilistic model. Secondly, we tested whether species cluster into distinct functional–morphological groups and whether ecologically or phylogenetically distinct species are more likely to co-occur. We found that 68% of species co-occurrences were not different from random expectation, indicating that most species had access to most sites within each region. The remaining 32% co-occurred either significantly more or less often than expected by chance. Cluster analysis of functional morphological characters showed that interstitial species belong to two feeding types, micro- and macrofeeders, likely representing two peaks of the interstitial adaptive landscape, and hinting that niche divergence, as a mechanism allowing coexistence, is favoured. Finally, we found that the number of co-occurrences increases with increasing differentiation of functional morphology, but not phylogenetic differences. We conclude that ecological differentiation may be important in shaping such interstitial communities.

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.

International audience; Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring of organisms is becoming easier and promises a revolution in our approaches to detect changes in biodiversity over space and time. A cornerstone of eDNA approach is the development of primer pairs that allow amplifying the DNA of specific taxonomic groups, which is then used to link the DNA sequence to taxonomic identification. Here, we propose a framework for comparing primer pairs regarding (a) their capacity to bind and amplify a broad coverage of species within the target clade using in silico PCR, (b) their capacity to not only discriminate between species but also genera or families, and (c) their in situ specificity and efficiency across a variety of environments. As a case study, we focus on two mitochondrial 12S primer pairs, MiFish-U and teleo, which were designed to amplify fishes. We found that the performance of in silico PCRs were high for both primer pairs, but teleo amplified more genera acrossActinopterygii, Chondrichthyes, and Petromyzontomorphi than MiFish-U. In contrast, the discriminatory power for species, genera, and families were higher for MiFish-U than teleo, likely associated with the greater length of the amplified DNA fragments. The evaluation of their in situ efficiency showed a higher recovered species richness ,of teleo compared to MiFish-U in tropical and temperate freshwater environments, but that generally both teleo and MiFish-U primers pairs perform well to monitor fish species. Since more species were detected when used together, those primer pairs are best used in combination to increase the ability of species detection.

International audience; Intermittent rivers and ephemeral streams (IRES) – waterways in which flow ceases periodically or that dry completely – are found worldwide, and their frequency and extent are expected to increase in the future in response to global climate change and growing anthropogenic demand for fresh water. Repeated wet–dry cycles generate highly dynamic settings within river networks composed of aquatic and terrestrial habitats, which act as evolutionary triggers for aquatic and terrestrial biota. Drying also alters functions and processes within river networks, with consequences for ecosystem services. Despite the emergence of promising conceptual and methodological developments, our understanding of the occurrence and diversity of organisms in these ecosystems is limited primarily due to their coupled aquatic–terrestrial characteristics. Novel genomic tools based on high-throughput sequencing have the potential to tackle unanswered questions of pivotal importance to predict future change in IRES. Here, we outline why genomic tools are needed to assess these dynamic ecosystems from the population to the metacommunity scale, and their potential role in bridging ecological–evolutionary dynamics.

Tropical and subtropical freshwater habitats are among the most biodiverse ecosystems worldwide, containing a characteristic fauna and high numbers of endemic species. However, exploitation of organisms, global climate change, pollution and the introduction of invasive species are severely threatening this diversity. Implementation of appropriate conservation and protection measures in tropical freshwater systems depends on comprehensive knowledge of state and change in biodiversity, which however, has been barely feasible due to logistic, technical and taxonomic challenges abound in tropical and subtropical ecosystems. Here we use a single environmental DNA (eDNA) multi-site sampling campaign distributed evenly through the 200,000 km2 Chao Phraya river basin, Thailand, to provide key information on freshwater fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network with respect to alpha- and beta-diversity patterns. By using a hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. Mapping these clusters over the catchment not only accurately matched the topology of the river network, but also revealed distinct groups of sites which should each be considered of high conservation value. Our study demonstrates a key application of large-scale monitoring (via eDNA) to identify distinct areas within a catchment for conservation and habitat protection.

Current global change is associated with an increase in disturbance frequency and intensity, with the potential to trigger population collapses and to cause permanent transitions to new ecosystem states. However, our understanding of ecosystem responses to disturbances is still incomplete. Specifically, there is a mismatch between the diversity of disturbance regimes experienced by ecosystems and the one-dimensional description of disturbances used in most studies on ecological stability. To fill this gap, we conducted a full factorial experiment on microbial communities, where we varied the frequency and intensity of disturbances affecting species mortality, resulting in 20 different disturbance regimes. We explored the direct and long-term effects of these disturbance regimes on community biomass. While most communities were able to recover biomass and composition states similar to undisturbed controls after a halt of the disturbances, we identified some disturbance thresholds that had long-lasting legacies on communities. Using a model based on logistic growth, we identified qualitatively the sets of disturbance frequency and intensity that had equivalent long-term negative impacts on experimental communities. Our results show that an increase in disturbance intensity is a bigger threat for biodiversity and biomass recovery than the occurrence of more frequent but less intense disturbances.

Aim Providing a quantitative overview of ecosystem functioning in a three‐dimensional space defined by ecosystem stocks, fluxes and rates, across major ecosystem types and climatic zones. Location Global. Time period 1966–2019. Major taxa studied Ecosystem‐level measurements (all organism types). Methods We conducted a global quantitative synthesis of a wide range of ecosystem variables related to carbon stocks and fluxes. We gathered a total of 4,479 values from 1,223 individual sites (unique geographical coordinates) reported in the literature (604 studies), covering ecosystem variables including biomass and detritus stocks, gross primary production, ecosystem respiration, detritus decomposition and carbon uptake rates, across eight major aquatic and terrestrial ecosystem types and five broad climatic zones (arctic, boreal, temperate, arid and tropical). We analysed the relationships among variables emerging from the comparisons of stocks, fluxes and rates across ecosystem types and climates. Results Within our three‐dimensional functioning space, average ecosystems align along a gradient from fast rates–low fluxes and stocks (freshwater and pelagic marine ecosystems) to low rates–high fluxes and stocks (forests), a gradient that we hypothesize results mainly from variation in primary producer characteristics. Moreover, fluxes and rates decrease from warm to colder climates, consistent with the metabolic theory of ecology. However, the strength of climatic effects differs among variables and ecosystem types, resulting, for instance, in opposing effects on net ecosystem production between terrestrial and freshwater ecosystems (positive versus negative effects). Main conclusions This large‐scale synthesis provides a first quantified cross‐ecosystem and cross‐climate comparison of multivariate ecosystem functioning. This gives a basis for a mechanistic understanding of the interdependency of different aspects of ecosystem functioning and their sensitivity to global change. To anticipate responses to change at the ecosystem level, further work should investigate potential feedbacks between ecosystem variables at finer scales, which involves site‐level quantifications of multivariate functioning and theoretical developments.

International audience; Environmental change can alter species’ abundances within communities consistently; for example, increasing all abundances by the same percentage, or more idiosyncratically. Here, we show how comparing effects of temperature on species grown in isolation and when grown together helps our understanding of how ecological communities more generally respond to environmental change. In particular, we find that the shape of the feasibility domain (the parameter space of carrying capacities compatible with positive species’ abundances) helps to explain the composition of experimental microbial communities under changing environmental conditions. First, we introduce a measure to quantify the asymmetry of a community’s feasibility domain using the column vectors of the corresponding interaction matrix. These column vectors describe the effects each species has on all other species in the community (hereafter referred to as species’ multidimensional effects). We show that as the asymmetry of the feasibility domain increases the relationship between species’ abundance when grown together and when grown in isolation weakens. We then show that microbial communities experiencing different temperature environments exhibit patterns consistent with this theory. Specifically, communities at warmer temperatures show relatively more asymmetry; thus, the idiosyncrasy of responses is higher compared with that in communities at cooler temperatures. These results suggest that while species’ interactions are typically defined at the pairwise level, multispecies dynamics can be better understood by focusing on the effects of these interactions at the community level.

International audience; Ecological pyramids represent the distribution of abundance and biomass of living organisms across body‐sizes. Our understanding of their expected shape relies on the assumption of invariant steady‐state conditions. However, most of the world’s ecosystems experience disturbances that keep them far from such a steady state. Here, using the allometric scaling between population growth rate and body‐size, we predict the response of size‐abundance pyramids within a trophic guild to any combination of disturbance frequency and intensity affecting all species in a similar way. We show that disturbances narrow the base of size‐abundance pyramids, lower their height and decrease total community biomass in a nonlinear way. An experimental test using microbial communities demonstrates that the model captures well the effect of disturbances on empirical pyramids. Overall, we demonstrate both theoretically and experimentally how disturbances that are not size‐selective can nonetheless have disproportionate impacts on large species.

At species’ range edges, individuals often face novel environmental conditions that may limit range expansion until populations adapt. The potential to adapt depends on genetic variation upon which selection can act. However, populations at species’ range edges are often genetically depauperate. One mechanism increasing genetic variation is reshuffling existing variation through sex. Sex, however, can potentially limit adaptation by breaking up existing beneficial allele combinations (recombination load). The gene swamping hypothesis predicts this is specifically the case when populations expand along an abiotic gradient and asymmetric dispersal leads to numerous maladapted dispersers from the range core swamping the range edge. We used the ciliate Tetrahymena thermophila as a model for testing the gene swamping hypothesis. We performed replicated range expansions in landscapes with or without a pH-gradient, while simultaneously manipulating the occurrence of gene flow and sexual versus asexual reproduction. We show that sex accelerated evolution of local adaptation in the absence of gene flow, but hindered it in the presence of gene flow. However, sex affected adaptation independently of the pH-gradient, indicating that both abiotic gradients and the biotic gradient in population density lead to gene swamping. Overall, our results show that gene swamping alters adaptation in life-history strategies.

Environmental DNA (eDNA) metabarcoding raises expectations for biomonitoring to cover organisms that have hitherto been neglected or excluded. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference data bases, taxonomic-free approaches are proposed for biomonitoring at the level of operational taxonomic unites (OTUs). However, this is challenging, because OTUs cannot be annotated and directly compared to classically derived data. The application of good stringency treatments to infer validity of OTUs and the clear understanding of the consequences to such treatments is thus especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect diversity estimates based on Hill numbers derived from eDNA samples. We collected eDNA at 61 sites across a 740 km2 river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that the detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared between the stringency treatments with increasing weighting of the OTUs’ abundances. Our study demonstrated the usefulness of Hill numbers for comparisons between data sets with large differences in diversity, and suggests best practice for data stringency filtering for biomonitoring.

Cross-ecosystem subsidies are studied with a focus on resource exchange at local ecosystem boundaries. This perspective ignores regional dynamics that can emerge via constraints imposed by the landscape, potentially leading to spatially-dependent effects of subsidies and spatial feedbacks. Using miniaturized landscape analogues of river dendritic and terrestrial lattice spatial networks, we manipulated and studied resource exchange between the two whole networks. We found that community composition in dendritic networks depended on the resource pulse from the lattice network, with the strength of this effect declining in larger downstream patches. In turn, this spatially-dependent effect imposed constraints on the lattice network with populations in that network reaching higher densities when connected to more central patches in the dendritic network. Consequently, localized cross-ecosystem fluxes, and their respective effects on recipient ecosystems, must be studied in a perspective taking into account the explicit spatial configuration of the landscape.Statement of authorshipEH, IG, EAF and FA designed the research; EH conducted the lab experiment with support from IG, EAF and FA, processed the experimental data with methodological developments from IG, and carried out the analysis of experimental data; all authors participated in results interpretation; EH wrote the first draft of the manuscript; All authors significantly contributed to further manuscript revisions.

Several key processes in freshwater ecology are governed by the connectivity inherent to dendritic river networks. These have extensively been analyzed from a geomorphological and hydrological viewpoint, yet structures classically used in ecological modeling have been poorly representative of the structure of real river basins, often failing to capture well‐known scaling features of natural rivers. Pioneering work identified optimal channel networks (OCNs) as spanning trees reproducing all scaling features characteristic of natural stream networks worldwide. While OCNs have been used to create landscapes for studies on metapopulations, biodiversity, and epidemiology, their generation has not been generally accessible.Given the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we provide the R‐package OCNet. Owing to the stochastic process generating OCNs, multiple network replicas spanning the same surface can be built; this allows performing computational experiments whose results are irrespective of the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three‐dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the package provides functions that aggregate OCNs into an arbitrary number of nodes, calculate several descriptors of river networks, and draw relevant network features.We describe the main functionalities of the package and its integration with other R‐packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species.In conclusion, OCNet provides a powerful tool to generate realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems and enhances our knowledge on spatial processes in freshwater ecology in general., Recently, research on spatial dynamics in ecology and evolution has bloomed. However, spatial structures used in theoretical and empirical ecological studies are often not representative of realistic landscapes. This is particularly true for river networks, which are of paramount interest to ecologists owing to their wide (but currently severely declining) biodiversity. Indeed, most of ecological work has been neglecting the scaling character of real river networks, despite well‐established knowledge in the fields of geomorphology and hydrology. Here, we present a method to create optimal channel networks (OCNs, i.e., river network analogues reproducing all topographic and scaling features of natural rivers), and the respective R‐package allowing their generation and analysis. We review the theoretical background underlying the OCN concept, present the main package functionalities, discuss possible applications in the realm of ecology and evolution, and detail how the package can be integrated with other popular R‐packages in spatial ecology.

The ABCD conference format (All continents, Balanced gender, low Carbon transport, Diverse backgrounds) mixes live-streamed and pre-recorded talks with in-person ones to reflect a diverse range of viewpoints and reduce the environmental footprint of meetings while also lowering barriers to inclusiveness.

International audience; Ecology and evolution unfold in spatially structured communities, where dispersal links dynamics across scales. Because dispersal is multicausal, identifying general drivers remains challenging. In a coordinated distributed experiment spanning organisms from protozoa to vertebrates, we tested whether two fundamental determinants of local dynamics, top-down and bottom-up control, generally explain active dispersal. We show that both factors consistently increased emigration rates and use metacommunity modelling to highlight consequences on local and regional dynamics.

Human-induced global change dramatically alters individual aspects of river biodiversity, such as taxonomic, phylogenetic or functional diversity, and is predicted to lead to losses of associated ecosystem functions. Understanding these losses and dependencies are critical to human well-being. Until now, however, most studies have only looked either at individual organismal groups or single functions, and little is known on the effect of human activities on multitrophic biodiversity and on ecosystem multifunctionality in riverine ecosystem. Here we profiled biodiversity from bacteria to invertebrates based on environmental DNA (hereafter, 'eDNA') samples across a major river catchment in China, and analysed their dependencies with multiple ecosystem functions, especially linked to C/N/P-cycling. Firstly, we found a spatial cross-taxon congruence pattern of communities' structure in the network of the Shaying river, which was related to strong environmental filtering due to human land use. Secondly, human land use explained the decline of multitrophic and multifaceted biodiversity and ecosystem functions, but increased functional redundancy in the riverine ecosystem. Thirdly, biodiversity and ecosystem function relationships at an integrative level showed a concave-up (non-saturating) shape. Finally, structural equation modeling suggested that land use affects ecosystem functions through biodiversity-mediated pathways, including biodiversity loss and altered community interdependence in multitrophic groups. Our study highlights the value of a complete and inclusive assessment of biodiversity and ecosystem functions for an integrated land-use management of riverine ecosystems.

Freshwater ecosystems depend on surrounding terrestrial landscape for resources. Most important are terrestrial leaf litter subsidies, which differ depending on land use. We lack a good understanding of the variation of these inputs across spatial scales. We sought to determine: (1) the relative importance of local versus catchment-level forestation for benthic leaf litter biomass in streams, (2) how landscape configuration alters these relationships, and (3) how land use affects the quality and diversity of leaf litter subsidies. We measured biomass and identity of benthic leaf litter in 121 reaches in 10 independent catchments seasonally over the course of a year. We assessed direct and indirect effects of forestation, reach position, and seasonality on leaf litter biomass using structural equation models, and assessed how leaf litter diversity varied with land use. In catchments with forested headwaters, the degree of forestation and reach position in the catchment influenced benthic leaf litter biomass indirectly through local reach-scale forestation. In catchments where forest was only located downstream, or with minimal forest, none of these factors influenced reach-level benthic leaf litter. Leaf litter diversity peaked in fall in all land use types, but was generally lowest in forested reaches. Not only habitat amount, but its location relative to other habitats is important for ecosystem function in the context of cross-ecosystem material flows. Here, lack of upstream forest altered spatial patterns of leaf litter storage. Studies with high spatiotemporal resolution may further reveal effects of landscape configuration on other ecosystems.

Freshwater ecosystems rely on allochthonous resources. Integration of these subsidies depends on diversity of both terrestrial resources and aquatic shredder and decomposer communities, but the diversity effects on leaf litter breakdown and decomposition are less clear in aquatic than terrestrial ecosystems. We need a better understanding of this relationship because aquatic communities are rapidly changing with species invasions and anthropogenic impacts. Here, we experimentally disentangled the effects of leaf and shredder richness on leaf litter breakdown by macroinvertebrates in mesocosm experiments using three species of amphipods, a dominant guild of crustaceans in European freshwater ecosystems. Increased leaf richness led to lower-than-predicted leaf consumption by native shredders, with mixed evidence of resource-switching or prioritization of preferred food items within a leaf mix. Higher shredder species richness never promoted leaf consumption rates compared to predictions from relevant single-species experiments, and instead sometimes substantially decreased leaf consumption. We then conducted a meta-analysis of leaf litter consumption rates by seven widely distributed amphipod species (the three used in the experiments and four additional species). As expected based on our own experiments, nonnative amphipod species generally had lower biomass- adjusted leaf litter consumption rates, although their larger body size led to higher per-individual leaf consumption rates. Contamination of the water by metals, pesticides, and other chemicals additionally significantly decreased leaf litter consumption by multiple native and nonnative species compared to unpolluted systems. While the meta-analysis suggested that litter consumption, and thus breakdown, would decline if native shredders are replaced by nonnative heterospecifics, complete species replacement is not the only outcome following immigration in a meta-community context. Our experiments suggest that breakdown rates could remain reasonably high where native species coexist with nonnative arrivals. Experiments that neglect the ecological realism of species coexistence will necessarily mischaracterize effects on ecosystem functioning.

Aim: Theory and experiments strongly support the importance of interactive effects of multiple factors shaping biodiversity, although their importance rarely has been investigated at biogeographically relevant scales. In particular, the importance of higher order interactions among environmental factors at such scales is largely unknown. We investigated higher order interactions of environmental factors to explain diversity patterns in a metacommunity of aquatic invertebrates at a biogeo- graphically relevant scale and discuss the findings in an environmental management context. Location: All major drainage basins in Switzerland (Rhine, Rhone, Ticino and Inn; 41,285 km2). Methods: Riverine a-diversity patterns at two taxonomic levels (family richness of all benthic macroinvertebrates and species richness of Ephemeroptera, Plecoptera and Trichoptera) were examined at 518 sites across the basins. We applied a novel machine learning technique to detect key three-way interactions of explanatory variables by comparing the relative importance of 1,140 three-way combinations for family richness and 680 three-way combinations for species richness. Results: Relatively few but important three-way interactions were meaningful for predicting biodiversity patterns among the numerous possible combinations. Specifically, we found that interactions among elevational gradient, prevalence of forest coverage in the upstream basin and biogeoclimatic regional classification were distinctly important. Main conclusion: Our results indicated that a high prevalence of terrestrial forest generally sustains riverine benthic macroinvertebrate diversity, but this relationship varies considerably with biogeoclimatic and elevational conditions likely due to community composition of forests and macroinvertebrates changing along climatic and geographical gradients. An adequate management of riverine ecosystems at relevant biogeographical scales requires the identification of such interactions and a context-dependent implementation.

1. Rivers are spatially organised into hierarchic dendritic networks. This unique physical structure and the associated directionality of physical flows set them apart from most other environments by regulating the dispersal of resident biota and therefore the distribution of biodiversity. 2. The aim of this special issue is to highlight the importance of the river network on structuring biodiversity, particularly through metacommunity dynamics and associated dispersal processes. 3. The issue covers a wide range of topics, including disease spread, nutrient uptake, trophic dynamics, effects of anthropogenic stressors and the joint roles of dispersal and environmental filtering. Contributions employ a broad range of approaches, including field and laboratory experiments, modelling, population genetics and conceptual synthesis. 4. Although these studies represent just a sample of the research that is being per- formed on biodiversity and metacommunity dynamics in river networks, several important findings have emerged; a common theme being that the structure of the network and spatial dynamics clearly influence the dynamics of populations and communities, and their functions. By taking a broad taxonomic focus (from diatoms and protists to fish), and spanning a large geographic gradient (from the tropics to the subarctic), this special issue provides a broad look at the dynamics that occur in river networks relating to their unique makeup. We hope that this selection of studies spurs additional research on these interesting, globally impor- tant, yet severely threatened ecological systems.

Global environmental change and biodiversity loss are closely linked through different feedback mechanisms. The University of Zurich Research Priority Programme on ‘Global Change and Biodiversity’ approach is to work with interdisciplinarity and transdisciplinarity to integrate mechanisms of interactions, feedback and scale and improve our understanding of the feedbacks between global change and biodiversity effects. Such work across research disciplines is not without its challenges. Here we share some of the questions that arose from our research approach over the last five years and how we addressed these challenges. First, our transdisciplinary approach allows combining different disciplines into a more holistic perspective towards integrative research, but demands collaborative work to establish common terminology, concepts, and metrics. Second, the research theme's common perspective (biodiversity is desirable, global change is not) may also induce a confirmation bias from preconceived ideas. Third, new challenges emerge from scaling mechanisms and feedbacks at different spatial and temporal scales. Fourth, we investigate how to relate biodiversity, global change, ecosystem services and functions using interdisciplinary approaches. Fifth, we identify gaps between existing experiments and data requirements, and propose the definition of new experimental setups by linking processes and performing experiments at typical experimental scales as well as at larger scales. We conclude by emphasising the necessity to integrate theory, experiments, modelling and simulation, high performance computing and big data to understand feedbacks between biodiversity loss and processes of global change.

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.

Range expansions and biological invasions are prime examples of transient processes that are likely impacted by rapid evolutionary changes. As a spatial process, range expansions are driven by dispersal and movement behaviour. Although it is widely accepted that dispersal and movement may be context-dependent, for instance density-dependent, and best represented by reaction norms, the evolution of density-dependent movement during range expansions has received little experimental attention. We therefore tested current theory predicting the evolution of increased movement at low densities at range margins using highly replicated and controlled range expansion experiments across multiple genotypes of the protist model system Tetrahymena thermophila. Although rare, we found evolutionary changes during range expansions even in the absence of initial standing genetic variation. Range expansions led to the evolution of negatively density-dependent movement at range margins. In addition, we report the evolution of increased intrastrain competitive ability and concurrently decreased population growth rates in range cores. Our findings highlight the importance of understanding movement and dispersal as evolving reaction norms and plastic life-history traits of central relevance for range expansions, biological invasions and the dynamics of spatially structured systems in general.

River networks are hierarchical dendritic habitats embedded within the terrestrial landscape, with varying connectivity between sites depending on their positions along the network. This physical organisation influences the dispersal of organisms, which ultimately affects metacommunity dynamics and biodiversity patterns. We provide a conceptual synthesis of the role of river networks in structuring metacommunities in relation to dispersal processes in riverine ecosystems. We explore where the river network best explains observed metacommunity structure compared to other measurements of physical connectivity. We mostly focus on invertebrates, but also consider other taxonomic groups, including microbes, fishes, plants, and amphibians. Synthesising studies that compared multiple spatial distance metrics, we found that the importance of the river network itself in explaining metacommunity patterns depended on a variety of factors, including dispersal mode (aquatic versus aerial versus terrestrial) and landscape type (arid versus mesic), as well as location-specific factors, such as network connectivity, land use, topographic heterogeneity, and biotic interactions. The river network appears to be less important for strong aerial dispersers and insects in arid systems than for other groups and biomes, but there is considerable variability. Borrowing from other literature, particularly landscape genetics, we developed a conceptual model that predicts that the explanatory power of the river network peaks in mesic systems for obligate aquatic dispersers. We propose directions of future avenues of research, including the use of manipulative field and laboratory experiments that test metacommunity theory in river networks. While field and laboratory experiments have their own benefits and drawbacks (e.g. reality, control, cost), both are powerful approaches for understanding the mechanisms structuring metacommunities, by teasing apart dispersal and niche-related factors. Finally, improving our knowledge of dispersal in river networks will benefit from expanding the breadth of cost-distance modelling to better infer dispersal from observational data; an improved understanding of life-history strategies rather than relying on independent traits; exploring individual-level variation in dispersal through detailed genetic studies; detailed studies on fine-scale environmental (e.g. daily hydrology) and organismal spatiotemporal variability; and synthesising comparative, experimental, and theoretical work. Expanding in these areas will help to push the current state of the science from a largely pattern-detection mode into a new phase of more mechanistically driven research.

Leaf litter decomposition is a major ecosystem process that can link aquatic to terrestrial ecosystems by flows of nutrients. Biodiversity and ecosystem functioning research hypothesizes that the global loss of species leads to impaired decomposition rates and thus to slower recycling of nutrients. Especially in aquatic systems an understanding of diversity effects on litter decomposition is still incomplete. Here we conducted an experiment to test two main factors associated with global species loss that might influence leaf litter decomposition. Firstly, we tested whether mixing different leaf species alters litter decomposition rates compared to decomposition of these species in monoculture. Secondly, we tested the effect of the size structure of a lotic decomposer community on decomposition rates. Overall, leaf litter identity strongly affected decomposition rates, and the observed decomposition rates matched measures of metabolic activity and microbial abundances. While we found some evidence of a positive leaf litter diversity effect on decomposition, this effect was not coherent across all litter combinations and the effect was generally additive and not synergistic. Microbial communities, with a reduced functional and trophic complexity, showed a small but significant overall reduction in decomposition rates compared to communities with the naturally complete functional and trophic complexity, highlighting the importance of a complete microbial community on ecosystem functioning. Our results suggest that top-down diversity effects of the decomposer community on litter decomposition in aquatic systems are of comparable importance as bottom-up diversity effects of primary producers. This article is protected by copyright. All rights reserved.

1. Understanding the consequences of spatial structure on ecological dynamics is a central theme in ecology. Recently, research has recognised the relevance of river and river-analogue network structures, because these systems are not only highly diverse but also rapidly changing due to habitat modifications or species invasions. 2. Much of the previous work on ecological and evolutionary dynamics in metapop- ulations and metacommunities in dendritic river networks has been either using comparative approaches or was purely theoretical. However, the use of micro- cosm experiments provides the unique opportunity to study large-scale questions in a causal and experimental framework. 3. We conducted replicated microcosm experiments, in which we manipulated the spatially explicit network configuration of a landscape and addressed how linear versus dendritic connectivity affects population dynamics, specifically the spatial distribution of population densities, and movement behaviour of the protist model organism Tetrahymena pyriformis. We tracked population densities and individual-level movement behaviour of thousands of individuals over time. 4. At the end of the experiment, we found more variable population densities between patches in dendritic networks compared to linear networks, as pre- dicted by theory. Specifically, in dendritic networks, population densities were higher at nodes that connected to headwaters compared to the headwaters themselves and to more central nodes in the network. These differences follow theoretical predictions and emerged from the different network topologies per se. These differences in population densities emerged despite weakly density- dependent movement. 5. We show that differences in network structure alone can cause characteristic spatial variation in population densities. While such differences have been postu- lated by theoretical work and are the underlying precondition for differential dis- persal evolution in heterogeneous networks, our results may be the first experimental demonstration thereof. Furthermore, these population-level dynam- ics may affect extinction risks and can upscale to previously shown metacommu- nity level diversity dynamics. Given that many species in natural river systems exhibit strong spatiotemporal patterns in population densities, our work suggests that abundance patterns should not only be addressed from a local environmental perspective, but may be the outcome of processes that are inher- ently driven by the respective habitat network structure.

Eco-evolutionary dynamics are now recognized to be highly relevant for population and community dy- namics. However, the impact of evolutionary dynamics on spatial patterns, such as the occurrence of clas- sical metapopulation dynamics, is less well appreciated. Here, we analyse the evolutionary consequences of spatial network connectivity and topology for dispersal strategies and quantify the eco-evolutionary feedback in terms of altered classical metapopulation dynamics. We find that network properties, such as topology and connectivity, lead to predictable spatio-temporal correlations in fitness expectations. These spatio-temporally stable fitness patterns heavily impact evolutionarily stable dispersal strategies and lead to eco-evolutionary feedbacks on landscape level metrics, such as the number of occupied patches, the number of extinctions and recolonizations as well as metapopulation extinction risk and genetic struc- ture. Our model predicts that classical metapopulation dynamics are more likely to occur in dendritic networks, and especially in riverine systems, compared to other types of landscape configurations. As it remains debated whether classical metapopulation dynamics are likely to occur in nature at all, our work provides an important conceptual advance for understanding the occurrence of classical metapopulation dynamics which has implications for conservation and management of spatially structured populations.

Groundwater belongs to the spatially most extensive, but least explored freshwater systems. On a global scale, the species richness of several subterranean invertebrate taxa parallels species richness found in surface waters, while on a local scale species richness hardly exceeds 20 species. This results in a high contribution of groundwater ecosystems to regional β- and γ-diversity, and to a smaller degree to α-diversity, and deserves focused attention. In general, more species are to be found in large cave systems. The second largest cave system in Europe is Holloch in Switzerland. In this paper we revised the taxonomic, phylogenetic and ecological diversity of the amphipod community in the Holloch cave system. While previous records listed five geographically widespread species of the genus Niphargus for this cave system, we could not confirm the presence of any of those species, but rather found three highly distinct species new to science. In this paper we describe Niphargus styx sp. nov., Niphargus ...

Aim Biological invasions are today the second-largest global threat for biodiversity. Once introduced, exotic plant species can modify ecosystem composition, structure and dynamics, eventually driving native species to local extinction. Among the groups of organisms, most likely to be directly affected by exotic invasive plants are herbivorous insects, such as butterflies, which strongly depend on plants throughout their life cycle. However, it remains unclear whether invasive plants have a negative or a positive effect on butterfly diversity at a landscape scale. Location Switzerland. Methods Using an extensive inventory (393 sites across Switzerland) of both butterfly and invasive plants, we explore the impact of 31 invasive black listed plant species on local butterfly richness. We further identify each butterfly species’ response to invasive plants (i.e. positive, neutral or negative) and analyse the functional and phylogenetic characteristics of these different groups of species. Results Our results indicate that butterfly richness negatively correlates with an increase in invasive plant richness. When studying the individual response of each butterfly species to the number of invasive plants, we found that no single butterfly is profiting from invasive plant species, while 28 butterfly species (24%) suffer from the presence of invasive plants. We further show that the species negatively affected are on average less mobile than the unaffected species and that they are phylogenetically clustered. Main conclusions Our results present evidences of the influence of invasive species on other trophic levels and interaction networks. We further highlight that a lack of management efforts for mitigating invasive plant impacts threatens specific sections of the functional and phylogenetic diversity of butterflies.

Abiotic stress is a major force of selection that organisms are constantly facing. While the evolutionary effects of various stressors have been broadly studied, it is only more recently that the relevance of interactions between evolution and underlying ecological conditions, that is, eco-evolutionary feedbacks, have been highlighted. Here, we experimentally investigated how populations adapt to pH-stress under high population densities. Using the protist speciesTetrahymena thermophila, we studied how four different genotypes evolved in response to stressfully low pH conditions and high population densities. We found that genotypes underwent evolutionary changes, some shifting up and others shifting down their intrinsic rates of increase (r0). Overall, evolution at low pH led to the convergence ofr0and intraspecific competitive ability (α) across the four genotypes. Given the strong correlation betweenr0andα, we argue that this convergence was a consequence of selection for increased density-dependent fitness at low pH under the experienced high density conditions. Increased density-dependent fitness was either attained through increase inr0, or decrease ofα, depending on the genetic background. In conclusion, we show that demography can influence the direction of evolution under abiotic stress.

Predator-prey interactions are key for the dynamics of many ecosystems. An increasing body of evidence suggests that rapid evolution and co-evolution can alter these interactions, with important ecological implications, by acting on traits determining fitness, including reproduction, anti-predatory defense and foraging efficiency. However, most studies to date have focused only on evolution in the prey species, and the predator traits in (co-)evolving systems remain poorly understood. Here we investigated changes in predator traits after ~600 generations in a predator-prey (ciliate-bacteria) evolutionary experiment. Predators independently evolved on seven different prey species, allowing generalization of the predator’s evolutionary response. We used highly resolved automated image analysis to quantify changes in predator life history, morphology and behavior. Consistent with previous studies, we found that prey evolution impaired growth of the predator. In contrast, predator evolution did not cause a clear increase in fitness when feeding on ancestral prey. However, predator evolution affected morphology and behavior, increasing size, speed and directionality of movement, which have all been linked to higher prey search efficiency. These results show that in (co-)evolving systems, predator adaptation can occur in traits relevant to offense level without translating into an increased ability of the predator to grow on the ancestral prey type.

The persistence of ecological systems in changing environments requires energy, materials, and information. Although the importance of information to ecological function has been widely recognized, the fundamental principles of ecological science as commonly expressed do not reflect this central role of information processing. We articulate five fundamental principles of ecology that integrate information with energy and material constraints across scales of organization in living systems. We show how these principles outline new theoretical and empirical research challenges, and offer one novel attempt to incorporate them in a theoretical model. To provide adequate background for the principles, we review major concepts and identify common themes and key differences in information theories spanning physics, biology and semiotics. We structured our review around a series of questions about the role information may play in ecological systems: (i) what is information? (ii) how is information related to uncertainty? (iii) what is information processing? (iv) does information processing link ecological systems across scales? We highlight two aspects of information that capture its dual roles: syntactic information defining the processes that encode, filter and process information stored in biological structure and semiotic information associated with structures and their context. We argue that the principles of information in living systems promote a unified approach to understanding living systems in terms of first principles of biology and physics, and promote much needed theoretical and empirical advances in ecological research to unify understanding across disciplines and scales.

The metapopulation concept initiated a paradigm shift in ecology and conservation biology, recognizing the eminent role of dispersal and colonization as fundamental processes contributing to species' long-term persistence. Early models made ad hoc assumptions about a positive area dependency of dispersal (i.e., total number of emigrants), which persisted in the theoretical literature; however, numerous empirical examples of negative area dependencies of dispersal have been reported. Here, we first give a qualitative overview for different area dependencies of dispersal in empirical systems. Then, using a spatially realistic Levins model, we show that extending assumptions on the area dependence of dispersal (ADD) to include all empirically supported parameter space, specifically also negative ADD, alters predictions on several conservation-relevant patterns. Importantly, we find that small patches could be of similar importance as large ones if dispersal decreases inversely with patch area, a result contrasting with previous findings based on a positive ADD. This leads to context-dependent strategies to preserve metapopulations. If dispersal is positively correlated with patch area, efforts should be devoted to preserving large patches and the total habitat area. If dispersal is negatively correlated with patch area, the most efficient strategy is to preserve a high number of patches, including small ones. Our results have direct implications for management decisions in the context of destruction, deterioration, and protection of habitat patches.

Dispersal can strongly influence ecological and evolutionary dynamics. Besides the direct contribution of dispersal to population dynamics, dispersers often differ in their phenotypic attributes from non-dispersers, which leads to dispersal syndromes. The consequences of such dispersal syndromes have been widely explored at the population and community level; however, to date, ecosystem-level effects remain unclear. Here, we examine whether dispersing and resident individuals of two different aquatic keystone invertebrate species have different contributions to detrital processing, a key function in freshwater ecosystems. Using experimental two-patch systems, we found no difference in leaf consumption rates with dispersal status of the common native species Gammarus fossarum . In Dikerogammarus villosus , however, a Ponto-Caspian species now expanding throughout Europe, dispersers consumed leaf litter at roughly three times the rate of non-dispersers. Furthermore, this put the contribution of dispersing D. villosus to leaf litter processing on par with native G. fossarum, after adjusting for differences in organismal size. Given that leaf litter decomposition is a key function in aquatic ecosystems, and the rapid species turnover in freshwater habitats with range expansions of non-native species, this finding suggests that dispersal syndromes may have important consequences for ecosystem functioning.

Assessing individual components of biodiversity, such as local or regional taxon richness, and differences in community composition is a long-standing challenge in ecology. It is especially relevant in spatially structured and diverse ecosystems. Environmental DNA (eDNA) has been suggested as a novel technique to accurately measure biodiversity. However, we do not yet fully understand the comparability of eDNA-based assessments to previously used approaches.We sampled may-, stone-, and caddisfly genera with contemporary eDNA and kicknet methods at 61 sites distributed over a large river network, allowing a comparison of various diversity measures from the catchment to site levels and providing insights into how these measures relate to network properties. We extended our survey data with historical records of total diversity at the catchment level.At the catchment scale, eDNA and kicknet detected similar proportions of the overall and cumulative historically documented species richness (gamma diversity), namely 42% and 46%, respectively. We further found a good overlap (62%) between the two contemporary methods at the regional scale.At the local scale, we found highly congruent values of local taxon richness (alpha diversity) between eDNA and kicknet. Richness of eDNA was positively related with discharge, a descriptor of network position, while kicknet was not.Beta diversity between sites was similar for the two contemporary methods. Contrary to our expectation, however, beta diversity was driven by species replacement and not by nestedness.Although optimization of eDNA approaches is still needed, our results indicate that this novel technique can capture extensive aspects of gamma diversity, proving its potential utility as a new tool for large sampling campaigns across hitherto understudied complete river catchments, requiring less time and becoming more cost-efficient than classical approaches. Overall, the richness estimated with the two contemporary methods is similar at both local and regional scale but community composition is differently assessed with the two methods at individual sites and becomes more similar with higher discharge.

The dataset (Data File S1; DOI: 10.6084/m9.figshare.8863721) and the R code used to generate the results (Code S1; DOI: 10.6084/m9.figshare.8863655), including step by step explanations of the statistical tests, have been deposited in Figshare Digital Repository (https://figshare.com/projects/Sediment_Respiration_Pulses_in_Intermittent_Rivers_and_Ephemeral_Streams/66104)., Intermittent rivers and ephemeral streams (IRES) may represent over half the global stream network, but their contribution to respiration and carbon dioxide (CO2) emissions is largely undetermined. In particular, little is known about the variability and drivers of respiration in IRES sediments upon rewetting, which could result in large pulses of CO2. We present a global study examining sediments from 200 dry IRES reaches spanning multiple biomes. Results from standardized assays show that mean respiration increased 32–66-fold upon sediment rewetting. Structural equation modelling indicates that this response was driven by sediment texture and organic matter quantity and quality, which, in turn, were influenced by climate, land use and riparian plant cover. Our estimates suggest that respiration pulses resulting from rewetting of IRES sediments could contribute significantly to annual CO2 emissions from the global stream network, with a single respiration pulse potentially increasing emission by 0.2–0.7%. As the spatial and temporal extent of IRES increases globally, our results highlight the importance of recognizing the influence of wetting-drying cycles on respiration and CO2 emissions in stream networks., We thank Y. Etxeberria, L. Sánchez, C. Gutiérrez, G. LeGoff and B. Launay for laboratory support. DvS was supported by a Short-Term Scientific Mission of the COST Action CA15113 (SMIRES, Science and Management of Intermittent Rivers and Ephemeral Streams, www.smires.eu), supported by COST (European Cooperation in Science and Technology) and received additional funding from the EU’s 7th Framework Programme for research, technological development and demonstration under grant agreement No. 603629 (GLOBAQUA) and a Grant for Research Groups of the Basque University System (IT-951-16) funded by the Basque Government. RM and BO were supported by the Spanish Ministry of Science, Innovation and Universities through project C-HYDROCHANGE (CGL2017-86788-C3-2-P and CGL2017-86788-C3-3-P). FA was funded by the Swiss National Science Foundation grants No. PP00P3_150698 and PP00P3_179089. NC was supported by the EU project LIFE+ TRivers (LIFE13 ENV/ES/000341). SDL received funding from the EU’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 748625. PP and MP were supported by INTER-COST project LTC17017. The authors declare that they have no competing interests.

Climate change and human pressures are changing the global distribution and the extent of intermittent rivers and ephemeral streams (IRES), which comprise half of the global river network area. IRES are characterized by periods of flow cessation, during which channel substrates accumulate and undergo physico‐chemical changes (preconditioning), and periods of flow resumption, when these substrates are rewetted and release pulses of dissolved nutrients and organic matter (OM). However, there are no estimates of the amounts and quality of leached substances, nor is there information on the underlying environmental constraints operating at the global scale. We experimentally simulated, under standard laboratory conditions, rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase across 205 IRES from five major climate zones. We determined the amounts and qualitative characteristics of the leached nutrients and OM, and estimated their areal fluxes from riverbeds. In addition, we evaluated the variance in leachate characteristics in relation to selected environmental variables and substrate characteristics. We found that sediments, due to their large quantities within riverbeds, contribute most to the overall flux of dissolved substances during rewetting events (56%–98%), and that flux rates distinctly differ among climate zones. Dissolved organic carbon, phenolics, and nitrate contributed most to the areal fluxes. The largest amounts of leached substances were found in the continental climate zone, coinciding with the lowest potential bioavailability of the leached OM. The opposite pattern was found in the arid zone. Environmental variables expected to be modified under climate change (i.e. potential evapotranspiration, aridity, dry period duration, land use) were correlated with the amount of leached substances, with the strongest relationship found for sediments. These results show that the role of IRES should be accounted for in global biogeochemical cycles, especially because prevalence of IRES will increase due to increasing severity of drying events., In this study we experimentally simulated under laboratory conditions rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase from intermittent rivers and ephemeral streams covering global spatial scale. We determined the amounts and quality of the leached nutrients and dissolved organic matter, assessed their inter‐substrate and cross‐climate differences, and estimated areal fluxes from 1 m2 of riverbeds. In addition, we evaluated the variance in leachate characteristics related to selected environmental variables and substrate characteristics.

International audience; Assessing individual components of biodiversity, such as local or regional taxon richness, and differences in community composition is a long-standing challenge in ecology. It is especially relevant in spatially structured and diverse ecosystems. Environmental DNA (eDNA) has been suggested as a novel technique to detect taxa and therefore may allow to accurately measure biodiversity. However, we do not yet fully understand the comparability of eDNA-based assessments to classical morphological approaches. We assessed may-, stone-, and caddisfly genera with two contemporary methods, namely eDNA sampling followed by molecular identification and kicknet sampling followed by morphological identification. We sampled 61 sites distributed over a large river network, allowing a comparison of various diversity measures from the catchment to site levels and providing insights into how these measures relate to network properties. We extended our data with historical morphological records of total diversity at the catchment level. At the catchment scale, identification based on eDNA and kicknet samples detected similar proportions of the overall and cumulative historically documented richness (gamma diversity), 42% and 46%, respectively. We detected a good overlap (62%) between genera identified from eDNA and kicknet samples at the regional scale. At the local scale, we found highly congruent values of local taxon richness (alpha diversity) between eDNA and kicknet samples. Richness of eDNA was positively related to discharge, a descriptor of network position, while kicknet was not. Beta diversity, a measure of dissimilarity between sites, was comparable for the two contemporary methods and is driven by species replacement and not by nestedness. Although eDNA approaches are still in their infancy and optimization regarding sampling design and laboratory work is still needed, our results indicate that it can capture different components of diversity, proving its potential utility as a new tool for large sampling campaigns across hitherto understudied complete river catchments.

Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised samples (bulk DNA), 2) DNA extracted from sample preservative (fixative DNA), and 3) environmental DNA (eDNA) from water or sediment. We provide a brief overview of metabarcoding macroinvertebrate communities from each DNA source and identify challenges for their application to routine monitoring. To advance the utilisation of DNA-based monitoring for macroinvertebrates, we propose an experimental design template for a series of methodological calibration tests. The template compares sources of DNA with the goal of identifying the effects of molecular processing steps on precision and accuracy. Furthermore, the same samples will be morphologically analysed, which will enable the benchmarking of molecular to traditional processing approaches. In doing so we hope to highlight pathways for the development of DNA-based methods for the monitoring of freshwater macroinvertebrates. Copyright Rosetta C. Blackman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Global analyses of biodiversity consistently reveal recurrent patterns of species distributions worldwide. However, unveiling the specific mechanisms behind those patterns remains logistically challenging, yet necessary for reliable biodiversity forecasts. Here, we combine theory and experiments to investigate the processes underlying spatial biodiversity patterns in dendritic, river-like landscapes, iconic examples of highly threatened ecosystems. We used geometric scaling properties, common to all rivers, to show that the distribution of biodiversity in these landscapes fundamentally depends on how ecological selection is modulated across space: while uniform ecological selection across the network leads to higher diversity in downstream confluences, this pattern can be inverted by disturbances when population turnover (i.e. local mortality) is higher upstream than downstream. Higher turnover in small headwater patches can slow down ecological selection, increasing local diversity in comparison to large downstream confluences. Our results show that disturbance-mediated slowing down of competitive exclusion can generate a specific transient signature in terms of biodiversity distribution when applied over a spatial gradient of disturbance, which is a common feature of many river landscapes.

Aim Globally, the geographical distributions of species are dynamic and strongly influenced by dispersal. At the same time, range dynamics feed back and may select for increased dispersal at expanding range fronts. This interplay between macroecological and evolutionary dynamics happens almost universally across environmental gradients and such gradients can have a direct impact on the fitness of organisms due to the match or mismatch between an individual's environmental optimum and the current conditions along the gradient. Importantly, gradients also provide individuals with information on environmental changes because dispersing individuals may sense whether environmental conditions improve or deteriorate. However, the ability of organisms to use this information on the environment and to subsequently adjust dispersal decisions plastically, that is, deciding to further disperse into the gradient or not, has been largely ignored and the macroecological consequences remain unclear. We here aim to demonstrate the impact of informed dispersal on the eco-evolutionary dynamics of ranges. Location Laboratory and theoretical. Methods We used individual-based simulations and controlled experiments in replicated microcosm landscapes. Range expansions of the protist model organism Tetrahymena were tracked using video recording and analysis. Results We show that information on environmental gradients had a severe impact on range dynamics and inverted the spatial distribution of population densities in comparison with controls where this information was not provided. Additionally, the use of information on gradients prevented evolutionary changes in dispersal rates and an acceleration of range expansion. Main conclusions We demonstrate the strong impact of informed dispersal and subsequent behavioural changes on range dynamics in environmental gradients. More generally, our findings highlight the importance of informed dispersal for spatial ecological and evolutionary dynamics.

Summary Species and genetic diversity patterns are predicted to co-vary due to similar mechanistic processes. Previous studies assessing species and genetic diversity correlations (SGDCs) have focused primarily on local diversity patterns or island-like systems and ignore the underlying dispersal network. Here we assessed local and regional SGDCs using freshwater macroinvertebrates sampled across the Rhine river network, a spatially large and highly connected system, in Switzerland. We utilised a set of polymorphic microsatellite markers to assess the genetic diversity of two amphipod species of the Gammarus fossarum complex, which were compared to species level diversities of Amphipoda, Ephemeroptera, Plecoptera, Trichoptera and family level macroinvertebrate diversity across 217 randomly selected sites. All sites were selected based on a representative and standardised species-sampling scheme. We analysed within site (α-SGDC) and between-site SGDC (β-SGDC). Against our expectation, we generally found negative or null α-SGDCs and β-SGDCs. However, we did find genetic diversity to be spatially structured, whereas species richness was related to local environmental factors. These findings suggest that the genetic and species levels of diversity observed are driven by different mechanisms (e.g., environment versus demography), or operate across different temporal or spatial scales (e.g., colonisation history or dendritic river network structure), and may be attributed to differences in the species' ecology or life history. Overall, conservation measures in riverine systems aiming at only one level of diversity may not necessarily benefit other levels of diversity.