Search

Water temperature is recognized as an important driver of aquatic ecosystems and is of increasing interest because of global warming. However, to date, no studies have disentangled the contribution of annual thermal variability from the contributions of annual thermal mean and other environmental variables to spatiotemporal patterns of macroinvertebrate assemblages in mountain streams. In this study, we explored patterns of macroinvertebrate biodiversity within and among 5 mountain stream sites in the Serio watershed (Orobic Alps, Northern Italy) along a gradient of annual water thermal variability (annual range: ~1–16°C) but with similar means. At each site, macroinvertebrates were sampled; physicochemical variables, flood disturbance, and resource availability were measured monthly over a year; and water temperature was monitored continuously. The relationship between macroinvertebrate assemblages and environmental conditions was described by separating time and space through co-inertia analyses. Results showed a strong temporal co-inertia, with floods and mean monthly temperature most associated with within-site macroinvertebrate temporal patterns (70% of total variance) and with the greatest effects on the abundance of stoneflies. Synchronous floods occurred in all sites and promoted changes in macroinvertebrate community composition through a loss of taxa and individuals, whereas monthly water temperature variations were associated with the replacement of individuals among taxa. Spatial differences (30% of the total variance) were mainly linked to geographical proximity, although annual thermal variability covaried with annual temporal dissimilarity in taxonomic composition, suggesting that temporal patterns also explain spatial differences. Overall, the study indicates that even when accounting for the overall environmental setting, the thermal regime remains an important driver of macroinvertebrate spatiotemporal patterns. Mountain streams are particularly subject to thermal variation, and an increase in mean water temperature and thermal variability will substantially influence community composition, with the strongest effects on cold stenothermal taxa. Large-scale research across mountain ranges is essential to properly assess how spatiotemporal thermal heterogeneity influences the distribution of macroinvertebrates, as well as to guide conservation strategies in the context of increasing global warming. [ABSTRACT FROM AUTHOR]

The analysis of phylogeographic patterns has often been based on mitochondrial DNA variation, but recent analyses dealing with nuclear DNA have in some instances revealed mito-nuclear discordances and complex evolutionary histories. These enigmatic scenarios, which may involve stochastic lineage sorting, ancestral hybridization, past dispersal and secondary contacts, are increasingly scrutinized with a new generation of genomic tools such as RADseq, which also poses additional analytical challenges. Here, we revisited the previously inconclusive phylogeographic history, showing the mito-nuclear discordance of an endemic groundwater amphipod from Iceland, Crangonyx islandicus, which is the only metazoan known to have survived the Pleistocene beneath the glaciers. Previous studies based on three DNA markers documented a mitochondrial scenario with the main divergence occurring between populations in northern Iceland and an ITS scenario with the main divergence between the south and north. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to clarify this mito-nuclear discordance by applying several statistical methods while estimating the sensitivity to different analytical approaches (data-type, differentiation indices and base call uncertainty). A majority of nuclear markers and methods support the ITS divergence. Nevertheless, a more complex scenario emerges, possibly involving introgression led by male-biased dispersal among northern locations or mitochondrial capture, which may have been further strengthened by natural selection. [ABSTRACT FROM AUTHOR]

Understanding and predicting the geographic distribution of taxa in hierarchical stream landscapes is a cornerstone of river ecology. A central issue is to tease apart the unique and shared effects of local and catchment predictors over species distributions. Here, we tested Hynes's influential hypothesis (1975, Baldi Memorial Lecture) that 'In every respect, the valley rules the stream'. We predicted that if catchment features exert a major control on in‐stream local conditions, the shared effect of local and catchment predictors should largely surpass their unique effects. To test this prediction, we used logistic regression models and variation partitioning to quantify the unique and shared effects of local and catchment predictors on the distribution of two hyporheic crustacean taxa (Bogidiellidae, Amphipoda and Anthuridae, Isopoda) in streams of New Caledonia. We sampled the two taxa at 228 sites. At each site, we quantified nine local predictors related to habitat area and stability, sediment metabolism and water origin, and eight catchment predictors related to geology, area, primary productivity, land use and specific discharge. When analyzed separately, the two predictor types explained the same amount of model variation in occurrence in both taxa. When analyzed jointly, the shared effects of the two predictor types explained twice as much model variation as the unique effect of each. The overriding contribution of shared effects was notably due to controls exerted by catchment area and geology on local habitat size and sediment metabolism, respectively. For both taxa, a model with only these two catchment predictors provided occurrence distribution as reliable as models containing only local predictors or both predictor types. Our findings pave the way for predicting reliably from catchment predictors alone the geographic distribution in local occurrence of taxa in difficult‐to‐access habitats and landscapes, such as here the hyporheic zone of tropical streams. [ABSTRACT FROM AUTHOR]

Changes in the functional structures of communities are rarely examined along multiple large‐scale environmental gradients. Here, we describe patterns in functional beta diversity for New Zealand marine fishes versus depth and latitude, including broad‐scale delineation of functional bioregions. We derived eight functional traits related to food acquisition and locomotion and calculated complementary indices of functional beta diversity for 144 species of marine ray‐finned fishes occurring along large‐scale depth (50–1200 m) and latitudinal gradients (29°–51°S) in the New Zealand Exclusive Economic Zone. We focused on a suite of morphological traits calculated directly from in situ Baited Remote Underwater Stereo‐Video (stereo‐BRUV) footage and museum specimens. We found that functional changes were primarily structured by depth followed by latitude, and that latitudinal functional turnover decreased with increasing depth. Functional turnover among cells increased with increasing depth distance, but this relationship plateaued for greater depth distances (>750 m). In contrast, functional turnover did not change significantly with increasing latitudinal distance at 700–1200 m depths. Shallow functional bioregions (50–100 m) were distinct at different latitudes, whereas deeper bioregions extended across broad latitudinal ranges. Fishes in shallow depths had a body shape conducive to efficient propulsion, while fishes in deeper depths were more elongated, enabling slow, energy‐efficient locomotion, and had large eyes to enhance vision. Environmental filtering may be a primary driver of broad‐scale patterns of functional beta diversity in the deep sea. Greater environmental homogeneity may lead to greater functional homogeneity across latitudinal gradients at deeper depths (700–1200 m). We suggest that communities living at depth may follow a 'functional village hypothesis', whereby similar key functional niches in fish communities may be maintained over large spatial scales. [ABSTRACT FROM AUTHOR]

Aim: Phylogenies are increasingly used in community ecology, biogeography and macroecology. However, sourcing a phylogeny comprising the entire species pool for a focal region can be difficult. Typically, a bespoke phylogeny must be created requiring considerable data manipulation and the use of many standalone software packages. Here we present a suite of methodological tools within the popular R environment that help to build molecular phylogenies appropriate for ecological studies with a regional focus. Innovation: Our R package regPhylo provides a pipeline to construct a Bayesian posterior distribution of time‐calibrated trees suitable to address ecological questions. The novel contributions of regPhylo include options to: use prior phylogenetic knowledge through flexible topological constraints; include spatial metadata in sourcing DNA sequences; and include taxa without DNA sequences and then infer consequent phylogenetic uncertainty. Specifically, regPhylo helps researchers: retrieve DNA sequences; enhance available metadata; select DNA sequences based on their length or spatial proximity to the region of study; align sequences; and perform quality control. Output from the pipeline is a file ready to run in the Bayesian tree reconstruction software beast2, appropriate for estimating time‐calibrated trees and including phylogenetic uncertainty for downstream analyses. Main conclusions: Overall, regPhylo improves the integration of popular standalone phylogenetic software into the flexible R environment. It provides a novel approach to include topological constraints based on prior knowledge, include taxa without DNA sequences, and select spatially appropriate DNA sequences. When coupled with a Bayesian tree‐building process, our approach provides estimates of uncertainty in both topology and branch lengths. We demonstrate the utility of the package by constructing a posterior distribution of time‐calibrated phylogenies for the New Zealand marine ray‐finned fishes (Actinopterygii) providing the unprecedented opportunity to include phylogenetic information in downstream ecological analyses for marine fishes in this region. [ABSTRACT FROM AUTHOR]

The global biodiversity crisis due to anthropogenic pressures jeopardizes marine ecosystem functioning and services. Community responses to these environmental changes can be assessed through functional diversity, a biodiversity component related to organism–environment interactions, and estimated through biological traits related to organism functions (locomotion, feeding mode, and reproduction). Fish play a key role in marine systems functioning and supply proteins for billions of humans worldwide, yet most of the knowledge is limited to several commercial species and little is known about the intraspecific variability of their functional traits. The data provided here consist of 867 records of individuals from 85 species of ray‐finned (Actinopterygii) and cartilaginous (Chondrichthyes) fish sampled in the Bay of Biscay (Atlantic, France) between autumn 2017 and 2019. We provided for each individual the taxonomic classification, 16 ecomorphological measures (5 directly made on fresh individuals and 11 realized using individual pictures) that were converted into nine ecomorphological traits classically documented in the literature (biomass, protrusion, oral gape shape, surface and position, eye size and position, body transversal shape and surface, pectoral fin position and caudal peduncle throttling) and eight life history traits obtained from FishBase (maximum length, average depth, depth range, trophic level, reproduction mode, fertilization mode, parental care, vertical position in the water column). These traits document several functions such as dispersion, feeding mode, habitat use, position in the food web, and reproduction. To improve the development of new traits, we provided a picture of each individual with an ROI file containing the different morpho‐anatomical measures made using "ImageJ" software and an R function to extract them. In addition, we provided the metadata from each sampling site (years, dates, stations, sampling hours, strata, gears, latitudes, longitudes, and depths) and environmental variables measured in situ (conductivity, salinity, water temperature, water density, and air temperature). This data set accounting for the intraspecific variability among 85 fish species is of interest to better understand the effects of environmental forcing in a global change context as in the Bay of Biscay, a highly fished transition zone harboring mixed assemblages of boreal, temperate, and subtropical fish species that are susceptible to display variability in functional trait to adapt to changing conditions. The data set is freely available without copyright restrictions; users should cite this paper in research products (publications, presentations, reports, etc.) derived from the data set. [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]

[Display omitted] • The spatiotemporal dynamics of demersal fish communities were investigated in the Bay of Biscay (BoB) and Celtic Sea (CS). • Two decades of changes in temperature, trophic resources, habitat and fishing pressure on community were assessed. • Diversity patterns showed greater variability in space than in time and species richness and abundance weakly changed. • Communities are becoming more spatially similar (homogeneous) in the CS and differentiated in the BoB. • Such patterns are best explained by the dynamics of trophic resources mediated by small pelagic species. Climate change and resource exploitation represent strong selection pressure affecting the spatio-temporal dynamics of marine assemblages that ensure food provision for humans. However, such dynamics remain poorly documented, and their drivers unclear. Here, we investigate changes in fish assemblages of two key European fishing areas, the Bay of Biscay (BoB) and the Celtic Sea (CS), during the last two decades. We quantify the relative contribution of change in energy (i.e. temperature and trophic resources), habitat (depth, substrate, oxygen) and fishing pressure to explaining observed spatial and temporal variations in fish diversity. We used long-term scientific surveys to evaluate the spatio-temporal changes in species richness (SR), abundance and composition of demersal fish (Actinopterygii) assemblages at different spatial scales combined with a range of regression models and variance partitioning. Diversity patterns showed greater variability in space than in time: SR weakly changed over time, while compositional dissimilarity showed local patterns of taxonomic homogenization in the CS and differentiation in the southern BoB, where local assemblages were becoming more similar and dissimilar over time, respectively. Energy funnelled through small pelagic species as a potential trophic link affecting the dynamics of demersal assemblages was the most important driver, while habitat and fishing pressure had limited importance. Our study revealed contrasted dynamics of demersal fish assemblages at a regional scale that were best explained by the dynamics of small pelagic species. Direct effects of environmental forcing and fishing pressure were limited in both regions which have a long history of fishing and still remain relatively buffered from global warming effects. This research paved the way to combine methods inspired by biogeography with scientific monitoring surveys to detect spatio-temporal dynamics of fish assemblages and their drivers in marine ecosystems under multiple pressures. [ABSTRACT FROM AUTHOR]

The recognition of multi-causality and spatial non-stationarity in the determinants of large-scale biodiversity patterns requires to consider the role of multiple mechanisms, their interactions, and how these mechanisms vary in strength relative to each other across geographical space. Here, we challenge the view that historical climate stability primarily drives European patterns of groundwater crustacean diversity by testing also the role of spatial heterogeneity and productive energy. First, we predicted that the three mechanisms would be equally important at continental scale when analyzed separately, but that the importance of historical climate variability would weaken in joint analyses due to co-variation with the two other mechanisms. Second, we predicted that the three mechanisms would exhibit predictable latitudinal changes in their relative strength. To test these predictions, we selected predictors representing each mechanism and analyzed separately and jointly their effects and interactions using global regression models. We further mapped the independent and overlapping effects of mechanisms across Europe using partial geographically weighted regressions. When analyzed separately, the three mechanisms explained the same amount of variation in species richness, but in the joint analysis, the influence of historical climate stability became hidden in the variation shared with the other mechanisms. Topographic heterogeneity interacted synergistically with actual evapotranspiration and habitat heterogeneity on species richness. Spatial non-stationarity in the independent and overlapping effects of the three mechanisms was the most plausible explanation for the hump-shaped latitudinal pattern of crustacean species richness. Productive energy and spatial heterogeneity were important predictors at mid and southern latitudes, whereas historical climate stability overlapped with the two other mechanisms in northern Europe and productive energy in southern Europe. Multi-causality and spatial non-stationarity provide a broader perspective of groundwater biodiversity determinants that revives the importance of spatial heterogeneity and the strong dependence of subterranean communities on food supply from the surface. [ABSTRACT FROM AUTHOR]

Aim Three broad mechanisms have been proposed to explain geographic variation in species range size: habitat area/heterogeneity, climate seasonality and long-term climate variability. However, it has proved difficult to disentangle their relative role, particularly as temperature seasonality often covaries with the amplitude of long-term temperature oscillations. Here, we shed new light onto this debate by providing the first continental-scale analysis of range size and beta diversity in groundwater habitats, where taxa are not exposed to latitudinal variation in temperature seasonality. Location Europe. Methods We compiled and mapped occurrence data for 1570 groundwater crustacean species. Generalized regression models were used to test for latitudinal variation in geographic range size and to assess the relative role of the three broad mechanisms in shaping present-day patterns of range size. We partitioned beta diversity into its spatial turnover and nestedness components and analysed their latitudinal variation across Europe. Results Median range size increases with latitude above 43° N and the range size of individual species is positively correlated to latitude, even after accounting for phylogenetic effects. Long-term temperature variability accounted for a substantially higher variation in median range size of groundwater crustaceans across Europe than precipitation seasonality and habitat heterogeneity, including aquifer area, elevation range, climatic rarity and productive energy. Spatial turnover contributes significantly more to beta diversity in southern regions characterized by stable historic climates than it does in northern Europe. Main conclusions Our findings add support to the historic climate hypothesis which suggests that patterns of increasing range size and decreasing species turnover at higher latitudes in the Palaearctic region are primarily driven by long-term temperature oscillations rather than by climatic seasonality and the availability and heterogeneity of habitats. [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]

Globalization and planetary environmental changes have stimulated the inventory of groundwater resources and biodiversity at continental and global scales but there has been no concurrent attempt to map the distribution of groundwater habitats even at continental scale. A vector version of the areal information contained in the international hydrogeological map of Europe (IHME) was produced, and thematic indicators for assessing its accuracy were established. Then, groundwater flow type, permeability and pore size were extracted from the vector IHME to define and map the distribution of 13 habitat types. The habitat map was used to test for latitudinal variations in habitat diversity (HD) and whether these variations might in part account for the latitudinal gradient of regional species richness. The HD of river catchments decreased significantly with increasing latitude after correcting for the effect of catchment area. HD decreased by half the amount of deviance attributed to latitude in a regression model of regional species richness, although the explanatory power of HD was probably limited by the coarse resolution of biogeographical regions. The groundwater habitat map of Europe represents a major step for the understanding, assessment and conservation of groundwater biodiversity and for incorporating ecological perspectives in groundwater management policy. [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]

Understanding patterns and processes governing biodiversity along broad‐scale environmental gradients, such as depth or latitude, requires an assessment of not just taxonomic richness, but also morphological and functional traits of organisms. Studies of traits can help to identify major selective forces acting on morphology. Currently, little is known regarding patterns of variation in the traits of fishes at broad spatial scales.The aims of this study were (a) to identify a suite of key traits in marine fishes that would allow assessment of morphological variability across broad‐scale depth (50–1200 m) and latitudinal (29.15–50.91°S) gradients, and (b) to characterize patterns in these traits across depth and latitude for 144 species of ray‐finned fishes in New Zealand waters.Here, we describe three new morphological traits, namely fin‐base‐to‐perimeter ratio, jaw‐length‐to‐mouth‐width ratio, and pectoral‐fin‐base‐to‐body‐depth ratio. Four other morphological traits essential for locomotion and food acquisition that are commonly measured in fishes were also included in the study. Spatial ecological distributions of individual fish species were characterized in response to a standardized replicated sampling design, and morphological measurements were obtained for each species from preserved museum specimens.With increasing depth, fishes, on average, became larger and more elongate, with higher fin‐base‐to‐perimeter ratio and larger jaw‐length‐to‐mouth‐width ratio, all of which translates into a more eel‐like anguilliform morphology. Variation in mean trait values along the depth gradient was stronger at lower latitudes for fin‐base‐to‐perimeter ratio, elongation and total body length. Average eye size peaked at intermediate depths (500–700 m) and increased with increasing latitude at 700 m.These findings suggest that, in increasingly extreme environments, fish morphology shifts towards a body shape that favours an energy‐efficient undulatory swimming style and an increase in jaw‐length vs. mouth width for opportunistic feeding. Furthermore, increases in eye size with both depth and latitude indicate that changes in both the average ambient light conditions as well as seasonal variations in day‐length can act to select ecomorphological adaptations in fishes. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) metabarcoding is a method to detect taxa from environmental samples. It is increasingly used for marine biodiversity surveys. As it only requires water collection, eDNA metabarcoding is less invasive than scientific trawling and might be more cost effective. Here, we analysed data from both sampling methods applied in the same scientific survey targeting Northeast Atlantic fish in the Bay of Biscay. We compared the methods regarding the distribution of taxonomic, phylogenetic, and functional diversity. We found that eDNA captured more taxonomic and phylogenetic richness than bottom trawling and more functional richness at the local scale. eDNA was less selective than trawling and detected species in local communities spanning larger phylogenetic and functional breadths, especially as it detected large pelagic species that escaped the trawl, even though trawling detected more flat fish. eDNA indicated differences in fish community composition that were comparable to those based on trawling. However, consistency between abundance estimates provided by eDNA metabarcoding and trawl catches was low, even after accounting for allometric scaling in eDNA production. We conclude that eDNA metabarcoding is a promising method that can complement scientific trawling for multi-component biodiversity monitoring based on presence/absence, but not yet for abundance. [ABSTRACT FROM AUTHOR]

Land use effects are considered among the main stressors on freshwater biodiversity, with up to 80% of land in Europe under intensive use. Here, we address the impact of arable and urban landscapes on taxon richness, Shannon–Wiener diversity, taxon rareness and taxonomic distinctness of eleven organism groups encompassing vertebrates, invertebrates and plants, occurring in five freshwater ecosystem types across Europe: rivers, floodplains, lakes, ponds and groundwater. In addition, nine geo-climatic descriptors (e.g. latitude, longitude, precipitation) were used to disentangle land use effects from those of natural drivers of biodiversity. Using a variance partitioning scheme based on boosted regression trees and generalised linear regression modelling, we sought: (i) to partition the unique, shared and unexplained variation in the metrics explained by both groups of descriptor variables, (ii) to quantify the contribution of each descriptor variable to biodiversity variation in the most parsimonious regression model and (iii) to identify interactions of land use and natural descriptors. The variation in biodiversity uniquely described by land use was consistently low across both ecosystem types and organism groups. In contrast, geo-climatic descriptors uniquely, and jointly with land use, explained significantly more variance in all 39 biodiversity metrics tested. Regression models revealed significant interactions between geo-climatic descriptors and land use for a third of the models, with interactions accounting for up to 17% of the model's deviance. However, no consistent patterns were observed related to the type of biodiversity metric and organism group considered. Subdividing data according to the strongest geo-climatic gradient in each dataset aimed to reduce the strength of natural descriptors relative to land use. Although data sub-setting can highlight land use effects on freshwater biodiversity, sub-setting our data often failed to produce stronger land use effects. There was no increase in spatial congruence in the subsets, suggesting that the observed land use effects were not dependent on the spatial extent of the subsets. Our results confirm significant joint effects of, and interactions between, land use and natural environmental descriptors on freshwater biodiversity, across ecosystem types and organism groups. This has implications for biodiversity monitoring. First, the combined analysis of anthropogenic and natural descriptors is a prerequisite for the analysis of human threats to biodiversity. Second, geo-climatically, but not necessarily geographically more homogeneous datasets can help unmask the role of anthropogenic descriptors. And third, whole community-based biodiversity metrics (including taxon richness) are not ideal indicators of anthropogenic effects on biodiversity at broad scales. [ABSTRACT FROM AUTHOR]

Variation in both inter‐ and intraspecific traits affects community dynamics, yet we know little regarding the relative importance of external environmental filters versus internal biotic interactions that shape the functional space of communities along broad‐scale environmental gradients, such as latitude, elevation, or depth. We examined changes in several key aspects of functional alpha diversity for marine fishes along depth and latitude gradients by quantifying intra‐ and interspecific richness, dispersion, and regularity in functional trait space. We derived eight functional traits related to food acquisition and locomotion and calculated seven complementary indices of functional diversity for 144 species of marine ray‐finned fishes along large‐scale depth (50–1200 m) and latitudinal gradients (29°–51° S) in New Zealand waters. Traits were derived from morphological measurements taken directly from footage obtained using Baited Remote Underwater Stereo‐Video systems and museum specimens. We partitioned functional variation into intra‐ and interspecific components for the first time using a PERMANOVA approach. We also implemented two tree‐based diversity metrics in a functional distance‐based context for the first time: namely, the variance in pairwise functional distance and the variance in nearest neighbor distance. Functional alpha diversity increased with increasing depth and decreased with increasing latitude. More specifically, the dispersion and mean nearest neighbor distances among species in trait space and intraspecific trait variability all increased with depth, whereas functional hypervolume (richness) was stable across depth. In contrast, functional hypervolume, dispersion, and regularity indices all decreased with increasing latitude; however, intraspecific trait variation increased with latitude, suggesting that intraspecific trait variability becomes increasingly important at higher latitudes. These results suggest that competition within and among species are key processes shaping functional multidimensional space for fishes in the deep sea. Increasing morphological dissimilarity with increasing depth may facilitate niche partitioning to promote coexistence, whereas abiotic filtering may be the dominant process structuring communities with increasing latitude. [ABSTRACT FROM AUTHOR]

All organisms on Earth are exposed to low doses of natural radioactivity but some habitats are more radioactive than others. Yet, documenting the influence of natural radioactivity on the evolution of biodiversity is challenging. Here, we addressed whether organisms living in naturally more radioactive habitats accumulate more mutations across generations using 14 species of waterlice living in subterranean habitats with contrasted levels of radioactivity. We found that the mitochondrial and nuclear mutation rates across a waterlouse species' genome increased on average by 60% and 30%, respectively, when radioactivity increased by a factor of three. We also found a positive correlation between the level of radioactivity and the probability of G to T (and complementary C to A) mutations, a hallmark of oxidative stress. We conclude that even low doses of natural bedrock radioactivity influence the mutation rate possibly through the accumulation of oxidative damage, in particular in the mitochondrial genome. [ABSTRACT FROM AUTHOR]

Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well‐established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation, evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top‐priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis‐driven studies likely to resonate broadly from the traditional boundaries of this field. [ABSTRACT FROM AUTHOR]

Ecological criteria are needed for a comprehensive evaluation of groundwater ecosystem health by including biological components with the physical and chemical properties that are already required by European directives. Two methodological approaches to assess the ecological status of groundwater ecosystems were combined in two alluvial plains (the Ariège and Hers Rivers, southwestern France) varying in agriculture intensity (from grassland to crop rotation including maize and sunflower, and to maize monoculture). In the first approach, the composition of invertebrate assemblages (only obligate-groundwater crustaceans, i.e. stygobionts) sampled in 28 wells differing in their land use contexts was analysed. Abundance, species richness, and assemblage composition significantly changed with agricultural land use or urbanization around the wells. In the second approach, we tested an in situ exposure of sentinel organisms to quantify their response to the environmental pressures. The epigean and native amphipod species Gammarus cf. orinos was used as the sentinel species. Amphipods (30 individuals in each of 10 wells) were exposed for one week to the in situ conditions at two seasons with contrasted concentrations of pollutants. The Ecophysiological Index (EPI) synthetizing the survival rates and energetic storage decreased in wells with low oxygen and high nitrate concentrations, but only during the highest contamination period. Atrazine-related compounds negatively impacted sentinel health whatever the season. The combination of these two approaches may have major applications for orientating groundwater ecosystem management. [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]

Species distribution models (SDM) are commonly used to identify potential habitats. When fitting them to heterogeneous, opportunistically collated presence/absence data, imbalance in the number of presence and absence observations often occurs, which could influence results. To robustly identify potential habitats for blackspot seabream (Pagellus bogaraveo) throughout its distribution area in the Northeast Atlantic and the western Mediterranean Sea, we used an ensemble species distribution modelling (eSDM) approach, modelling gridded presence–absence data with environmental predictors for two types of occurrence data sets. The first data set displayed the observed unbalanced spatially heterogeneous presence/absence ratio and the second a balanced presence/absence ratio. The data covered the full distribution area, including the European Atlantic shelf, the Azorean region and the Western Mediterranean Sea. Across these regions, populations display variable status. The main environmental predictors for potential habitats were bathymetry and annual maximum SST. The fitted ensemble compromise (eSDM) was projected over the whole grid to create a habitat suitability map. This map exhibited higher probabilities of presence for the balanced-ratio data set. A binary presence–absence map was then generated using optimized presence probability thresholds for four validation indices. Using the true skill statistic to optimize the threshold, the surface areas of the binary presence–absence map was 53% smaller for the balanced data set than for the observed unbalanced data set. However, the choice of validation index had an even greater impact (up to 15 000%). This indicates that studies using opportunistic data for SDM fitting need to pay attention to the effects of presence/absence data imbalance and the choice of validation index to fully evaluate uncertainty. • Ensemble species distribution modelling to identify potential habitat of rare fish. • Comparison of two occurrence data sets: imbalanced and balanced presence–absence. • Main predictors: bathymetry and sea surface temperature. • Higher presence probabilities for the balanced data set. • Effect of validation index on habitat map larger than data imbalance effect. [ABSTRACT FROM AUTHOR]