Boreal and Lusitanian species display trophic niche variation in temperate waters.

Climate change has non-linear impacts on species distributions and abundance that have cascading effects on ecosystem structure and function. Among them are shifts in trophic interactions within communities. Sites found at the interface between two or more biogeographical regions, where species with diverse thermal preferenda are assembled, are areas of strong interest to study the impact of climate change on communities' interactions. This study examined variation in trophic structure in the Celtic Sea, a temperate environment that hosts a mixture of cold-affiliated Boreal species and warm-affiliated Lusitanian species. Using carbon and nitrogen stable isotope ratios, trophic niche area, width, and position were investigated for 10 abundant and commercially important demersal fish species across space and time. In general, the niches of Boreal species appear to be contracting while those of Lusitanian species expand, although there are some fluctuations among species. These results provide evidence that trophic niches can undergo rapid modifications over short time periods (study duration: 2014-2021) and that this process may be conditioned by species thermal preferenda. Boreal species displayed spatial variation in trophic niche width and seem to be facing increased competition with Lusitanian species for food resources. These findings underscore the need to utilize indicators related to species trophic ecology to track the ecosystem alterations induced by climate change. Such indicators could reveal that the vulnerability of temperate ecosystems is currently being underestimated.

Gadiform species display dietary shifts in the Celtic Sea.

Global changes, through their impacts on ecosystem trophic structures, are behind regime shifts and cascading effects, and could result in the reorganization of whole ecosystems. The Celtic Sea is a temperate sea at risk of the above because of the interplay between climate change and fisheries. This sea has only displayed slight changes in species diversity between the late 20th century and the present day. However, this apparent stability in species diversity could be hiding structural transformations, including the rearrangement of trophic relationships. Historical stomach content database offers the opportunity to investigate changes in ecosystem trophic structure. Based on such database, this study explored shifts in the feeding habits of gadiform species in the Celtic Sea in the 1980s, 1990s, and 2010s. To this end, it examined dietary generalism and composition for four top predator fish species. During the target period, generalists maintained their diets, while specialists adopted more generalist diets. There were also decreases in frequencies of occurrence of certain fishes within the diets of gadiform species. These recent changes in trophic structure organization have likely been caused by the influence of global changes on both top-down and bottom-up processes that occurred in the Celtic Sea.

Marine spatial planning to solve increasing conflicts at sea: A framework for prioritizing offshore windfarms and marine protected areas.

Direct and indirect anthropogenic pressures on biodiversity and ecosystems are expected to lower the provided ecosystem services (ES) in the near future. To limit these impacts, protected areas will be implemented as part of the Post-2020 Global Biodiversity Framework. Simultaneously, as an answer to climate change, renewable energies are being rapidly developed on a worldwide scale, leading to a significant increase in space use in the coming decades. Sharing space is an increasingly complex task, especially because of the high rate of emergence of such competitors for space. In fisheries-dominated socio-ecosystems, acceptability of offshore windfarms (OWFs) and marine protected areas (MPAs) is usually very low, partly due to an underrepresentation of fisheries in spatial plans and poor attention to equity in the spatial distribution of restrictive areas. Here we developed a framework with a marine spatial planning case study in the Bay of Biscay represented by the socio-ecosystem of the Grande Vasière, a mid-shelf mud belt spanning over 21,000 km2. We collected biological, environmental, and anthropogenic data to model the distribution of 62 bentho-demersal species, 7 regulating ES layers related to nutrient cycling, life cycle maintenance and food web functioning, as well as provisioning ES of 18 commercial species and 82 fisheries subdivisions. We used these spatial layers and a prioritization algorithm to explore siting scenarios of OWFs and two types of MPAs (benthic and total protection), aimed at conserving species, regulating and provisioning ES, while also ensuring that fisheries are equitably impacted. We demonstrate that equitable scenarios are not necessarily costlier and provide alternative spatial prioritizations. We emphasize the importance of exploring multiple targets with a Shiny app to visualize results and stimulate dialogue among stakeholders and policymakers. Overall, we show how our flexible, inclusive framework with particular attention to equity could be an ideal discussion tool to improve management practices.

Assessing the diet and trophic level of marine fauna in a fishing ground subject to discarding activity using stable isotopes.

Discarding practices have become a source of concern for the perennation of marine resources, prompting efforts of discard reduction around the globe. However, little is known about the fate of discards in marine environments. Discarding may provide food for various marine consumers, potentially affecting food web structure and stability. Yet, quantifying reliance upon discards is difficult because identity and frequency of discards may change according to multiple factors, and most previously used diet assessment techniques do not allow to assume consistency of feeding strategies over time. One currently untested hypothesis is that significant contribution of discards over time should reflect in increased trophic level (TL) of marine fauna, particularly in low TL consumers. Here, we explored this hypothesis by modeling the TL and assimilated diet of consumers living in fishing grounds subject to important discarding activity using stable isotope analysis. We found indications that benthic invertebrates and Chondrichthyes may depict a higher than expected TL, while other fish tend to depict similar to lower TL compared to global averages from the literature. Based on prior knowledge of discard consumption in the same area, stable isotope mixing models congruently revealed that discards may represent substantial portions of the assimilated diet of most benthic invertebrate macrofauna, cephalopods and Chondrichthyes. We highlight limitations and challenges of currently used diet assessment techniques to study discard consumption and stress that understanding their reintegration in marine food webs is crucial in the context of an ecosystem approach to fisheries management and to better understand the functioning of marine ecosystems subject to fishing.

Advancing biological invasion hypothesis testing using functional diversity indices.

Pioneering investigations on the effects of introduced populations on community structure, ecosystem functioning and services have focused on the effects of invaders on taxonomic diversity. However, taxonomic-based diversity metrics overlook the heterogeneity of species roles within and among communities. As the homogenizing effects of biological invasions on community and ecosystem processes can be subtle, they may require the use of functional diversity indices to be properly evidenced. Starting from the listing of major functional diversity indices, alongside the presentation of their strengths and limitations, we focus on studies pertaining to the effects of invasive species on native communities and recipient ecosystems using functional diversity indices. By doing so, we reveal that functional diversity of the recipient community may strongly vary at the onset of the invasion process, while it stabilizes at intermediate and high levels of invasion. As functional changes occurring during the lag phase of an invasion have been poorly investigated, we show that it is still unknown whether there are consistent changes in functional diversity metrics that could indicate the end of the lag phase. Thus, we recommend providing information on the invasion stage under consideration when computing functional diversity metrics. For the existing literature, it is also surprising that very few studies explored the functional difference between organisms from the recipient communities and invaders of the same trophic levels, or assessed the effects of non-native organism establishment into a non-analogue versus an analogue community. By providing valuable tools for obtaining in-depth diagnostics of community structure and functioning, functional diversity indices can be applied for timely implementation of restoration plans and improved conservation strategies. To conclude, our work provides a first synthetic guide for their use in hypothesis testing in invasion biology.

Functional representativeness and distinctiveness of reintroduced birds and mammals in Europe.

Reintroduction, the human-mediated movement of organisms to re-establish locally extinct populations, has become a popular conservation tool. However, because reintroductions often focus on local or national conservation issues, their contribution to the conservation of biodiversity at large scale remains unclear. While taxonomic biases have already been identified in reintroduction programs at regional scales, studies have stressed the need to account for other facets of biodiversity when assessing the relevance of the allocation of conservation efforts. In particular, it may be very fruitful to discriminate if and how such taxonomic biases may influence the functional complementarity of reintroduction targets, and to which extent reintroduction practitioners may have focused on species performing more singular functions than others. Here, we investigate the diversity of functional traits supported by reintroduced species of terrestrial birds and mammals in Europe. For each taxonomic group, we explored the functional representativeness of reintroduction targets at the European scale, i.e., whether species involved in reintroduction programs collectively represent the range of functional trait variation observed in the regional assemblage. Because additional conservation value could have been given by practitioners to species performing singular functions, we also measured the functional distinctiveness of reintroduced species. We found that reintroductions of birds did not focus on functionally distinct species, and that the subset of reintroduced birds is representative of the functional diversity at a continental scale. However, reintroductions of mammals involved more functionally distinct species than expected, even though reintroduced mammals are not collectively representative of the functional diversity of the continental assemblage.

Species richness and food-web structure jointly drive community biomass and its temporal stability in fish communities.

Biodiversity-ecosystem functioning and food-web complexity-stability relationships are central to ecology. However, they remain largely untested in natural contexts. Here, we estimated the links among environmental conditions, richness, food-web structure, annual biomass and its temporal stability using a standardised monitoring dataset of 99 stream fish communities spanning from 1995 to 2018. We first revealed that both richness and average trophic level are positively related to annual biomass, with effects of similar strength. Second, we found that community stability is fostered by mean trophic level, while contrary to expectation, it is decreased by species richness. Finally, we found that environmental conditions affect both biomass and its stability mainly via effects on richness and network structure. Strikingly, the effect of species richness on community stability was mediated by population stability rather than synchrony, which contrasts with results from single trophic communities. We discuss the hypothesis that it could be a characteristic of multi-trophic communities.

Biomass of slow life history species increases as local bottom trawl effort decreases in the Celtic sea.

Due to its selective removal, fishing pressure has long influenced the dynamics of species based on their life history traits. Sensitivity to fishing increases along a "fast-to-slow" gradient of life history strategies, and the "slow" species (large, long-lived, late-maturing, giving birth to few large offspring) require the most time to recover from fishing. In the North East Atlantic, after having reached extreme levels, fishing pressure has decreased since the 1980's due to management measures such as total allowable catch (TAC) or area closure. An effect on the distribution of species as well as a potential recovery could be expected. However, temporal patterns of life history strategies are rarely linked to management measures. In addition, a larger emphasis is often put on exploited or emblematic sensitive species but rarely on assembly processes at the ecosystem scale (both commercial and non-commercial species). Based on a 17-year time series of 101 taxa (fishes, elasmobranchs, bivalves, cephalopods and crustaceans), we observed a negative relationship between the biomass of taxa sensitive to fishing and bottom trawling pressure, as well as an increase in their total biomass in the Celtic Sea. Over the whole area, stochasticity appeared as the dominant assembly process. Deterministic assembly processes were at play in the centre of the area where significant overdispersion (caused by the presence of both slow and fast taxa) were observed. The absence of sensitive taxa from the rest of the Celtic Sea appeared to be caused mainly by a historical effect of environmental filtering when fishing was high. At the local scale, we related the decrease in fishing pressure to the increase in biomass of five of the most sensitive taxa. This local decrease in fishing pressure, resulting from the implementation of an area closure, highlights the positive effect of such management measures in less than two decades.

Environment outweighs the effects of fishing in regulating demersal community structure in an exploited marine ecosystem.

Global climate change has already caused bottom temperatures of coastal marine ecosystems to increase worldwide. These ecosystems face many pressures, of which fishing is one of the most important. While consequences of global warming on commercial species are studied extensively, the importance of the increase in bottom temperature and of variation in fishing effort is more rarely considered together in these exploited ecosystems. Using a 17 year time series from an international bottom trawl survey, we investigated covariations of an entire demersal ecosystem (101 taxa) with the environment in the Celtic Sea. Our results showed that over the past two decades, biotic communities in the Celtic Sea were likely controlled more by environmental variables than fisheries, probably due to its long history of exploitation. At the scale of the entire zone, relations between taxa and the environment remained stable over the years, but at a local scale, in the center of the Celtic Sea, dynamics were probably driven by interannual variation in temperature. Fishing was an important factor structuring species assemblages at the beginning of the time series (2000) but decreased in importance after 2009. This was most likely caused by a change in spatial distribution of fishing effort, following a change in targeted taxa from nephrops to deeper water anglerfish that did not covary with fishing effort. Increasing bottom temperatures could induce additional changes in the coming years, notably in the cold-water commercial species cod, hake, nephrops, and American plaice. We showed that analyzing covariation is an effective way to screen a large number of taxa and highlight those that may be most susceptible to future simultaneous increases in temperature and changes in exploitation pattern by fisheries. This information can be particularly relevant for ecosystem assessments.

Vulnerability to climate change of islands worldwide and its impact on the tree of life.

Island systems are among the most vulnerable to climate change, which is predicted to induce shifts in temperature, rainfall and/or sea levels. Our aim was: (i) to map the relative vulnerability of islands to each of these threats from climate change on a worldwide scale; (ii) to estimate how island vulnerability would impact phylogenetic diversity. We focused on monocotyledons, a major group of flowering plants that includes taxa of important economic value such as palms, grasses, bananas, taro. Islands that were vulnerable to climate change were found at all latitudes, e.g. in Australia, Indonesia, the Caribbean, Pacific countries, the United States, although they were more common near the equator. The loss of highly vulnerable islands would lead to relatively low absolute loss of plant phylogenetic diversity. However, these losses tended to be higher than expected by chance alone even in some highly vulnerable insular systems. This suggests the possible collapse of deep and long branches in vulnerable islands. Measuring the vulnerability of each island is a first step towards a risk analysis to identify where the impacts of climate change are the most likely and what may be their consequences on biodiversity.

Using a trait-based approach to understand the efficiency of a selective device in a multispecific fishery.

Improving the selectivity of a fishing gear is one technical management measure to significantly reduce by-catch of non-commercial species or undersized individuals. The efficiency of selective device is mainly estimated by comparing species composition, the biomass and length spectrum of caught individuals and escapees while the functional traits of species are rarely accounted for. Using an innovative technical device to reduce catches of undersized individuals in a multispecific bottom trawl fishery in the Bay of Biscay, namely a T90 mesh cylinder, we measured functional traits on both caught and escaped individuals of 18 species. Using a Principal Component Analysis and K-means partitioning, we clustered species into 6 groups illustrating 6 different locomotion strategies. We identified functional traits related to body size, visual ability and locomotion, differing between caught individuals and escapees using Linear Mixed-effects Models. As expected, escapees were smaller on average but also tended to be more streamlined, with a high position of the eyes and fin features characteristic of manoeuvrability and propulsion. Here, we present how a trait-based approach can shed light on the biological characteristics influencing the efficiency of selective devices.

Distribution and relative age of endemism across islands worldwide.

Islands have remarkable levels of endemism and contribute greatly to global biodiversity. Establishing the age of island endemics is important to gain insights into the processes that have shaped the biodiversity patterns of island biota. We investigated the relative age of monocots across islands worldwide, using different measures of phylogenetic endemism tested against null models. We compiled a species occurrence dataset across 4,306 islands, and identified 142 sites with neo-, paleo-, mixed and super-endemism. These sites were distributed across the world, although they tended to be more common at low latitudes. The most frequent types of endemism were mixed and super-endemism, which suggests that present-day island biodiversity has frequently been shaped by processes that took place at different points in times. We also identified the environmental factors that contributed most to different types of endemism; we found that latitude, habitat availability and climate stability had a significant impact on the persistence of ancient taxa and on recent diversification events. The islands identified here are irreplaceable both for the uniqueness and the evolutionary history of their flora, and because they are a source of "option values" and evolutionary potential. Therefore, our findings will help guide biodiversity conservation on a global scale.

Reintroductions of birds and mammals involve evolutionarily distinct species at the regional scale.

Reintroductions offer a powerful tool for reversing the effects of species extirpation and have been increasingly used over recent decades. However, this species-centered conservation approach has been criticized for its strong biases toward charismatic birds and mammals. Here, we investigated whether reintroduced species can be representative of the phylogenetic diversity within these two groups at a continental scale (i.e., Europe, North and Central America). Using null models, we found that reintroduced birds and mammals of the two subcontinents tend to be more evolutionarily distinct than expected by chance, despite strong taxonomic biases leading to low values of phylogenetic diversity. While evolutionary considerations are unlikely to have explicitly driven the allocation of reintroduction efforts, our results illustrate an interest of reintroduction practitioners toward species with fewer close relatives. We discuss how this phylogenetic framework allows us to investigate the contribution of reintroductions to the conservation of biodiversity at multiple geographic scales. We argue that because reintroductions rely on a parochial approach of conservation, it is important to first understand how the motivations and constraints at stake at a local context can induce phylogenetic biases before trying to assess the relevance of the allocation of reintroduction efforts at larger scales.

Functional diversity and redundancy across fish gut, sediment and water bacterial communities.

This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (ß) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.

Fixism and conservation science.

The field of biodiversity conservation has recently been criticized as relying on a fixist view of the living world in which existing species constitute at the same time targets of conservation efforts and static states of reference, which is in apparent disagreement with evolutionary dynamics. We reviewed the prominent role of species as conservation units and the common benchmark approach to conservation that aims to use past biodiversity as a reference to conserve current biodiversity. We found that the species approach is justified by the discrepancy between the time scales of macroevolution and human influence and that biodiversity benchmarks are based on reference processes rather than fixed reference states. Overall, we argue that the ethical and theoretical frameworks underlying conservation research are based on macroevolutionary processes, such as extinction dynamics. Current species, phylogenetic, community, and functional conservation approaches constitute short-term responses to short-term human effects on these reference processes, and these approaches are consistent with evolutionary principles.

Testing the Effectiveness of Environmental Variables to Explain European Terrestrial Vertebrate Species Richness across Biogeographical Scales.

We compared the effectiveness of environmental variables, and in particular of land-use indicators, to explain species richness patterns across taxonomic groups and biogeographical scales (i.e. overall pan-Europe and ecoregions within pan-Europe). Using boosted regression trees that handle non-linear relationships, we compared the relative influence (as a measure of effectiveness) of environmental variables related to climate, landscape (or habitat heterogeneity), land-use intensity or energy availability to explain European vertebrate species richness (birds, amphibians, and mammals) at the continental and ecoregion scales. We found that dominant land cover and actual evapotranspiration that relate to energy availability were the main correlates of vertebrate species richness over Europe. At the ecoregion scale, we identified four distinct groups of ecoregions where species richness was essentially associated to (i) seasonality of temperature, (ii) actual evapotranspiration and/or mean annual temperature, (iii) seasonality of precipitation, actual evapotranspiration and land cover) and (iv) and an even combination of the environmental variables. This typology of ecoregions remained valid for total vertebrate richness and the three vertebrate groups taken separately. Despite the overwhelming influence of land cover and actual evapotranspiration to explain vertebrate species richness patterns at European scale, the ranking of the main correlates of species richness varied between regions. Interestingly, landscape and land-use indicators did not stand out at the continental scale but their influence greatly increased in southern ecoregions, revealing the long-lasting human footprint on land-use-land-cover changes. Our study provides one of the first multi-scale descriptions of the variability in the ranking of correlates across several taxa.

Plant trait-based models identify direct and indirect effects of climate change on bundles of grassland ecosystem services.

Land use and climate change are primary causes of changes in the supply of ecosystem services (ESs). Although the consequences of climate change on ecosystem properties and associated services are well documented, the cascading impacts of climate change on ESs through changes in land use are largely overlooked. We present a trait-based framework based on an empirical model to elucidate how climate change affects tradeoffs among ESs. Using alternative scenarios for mountain grasslands, we predicted how direct effects of climate change on ecosystems and indirect effects through farmers' adaptations are likely to affect ES bundles through changes in plant functional properties. ES supply was overall more sensitive to climate than to induced management change, and ES bundles remained stable across scenarios. These responses largely reflected the restricted extent of management change in this constrained system, which was incorporated when scaling up plot level climate and management effects on ecosystem properties to the entire landscape. The trait-based approach revealed how the combination of common driving traits and common responses to changed fertility determined interactions and tradeoffs among ESs.

A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales.

Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (α), regional (γ) and the overall difference between local communities (ß). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the ß component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically explicit relationship among the α, ß and γ components. We propose a unified quantitative framework based on the Rao quadratic entropy, to obtain an additive decomposition of diversity (γ = α + ß), so the three components can be compared, and that integrate the relationship (phylogenetic or functional) among Microbial Diversity Units that compose a microbial community. We show how this framework is adapted to all types of molecular data, and we highlight crucial issues in microbial ecology that would benefit from this framework and propose ready-to-use R-functions to easily set up our approach.

Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints.

Considering the major involvement of gut microflora in the digestive function of various macro-organisms, bacterial communities inhabiting fish guts may be the main actors of organic matter degradation by fish. Nevertheless, the extent and the sources of variability in the degradation potential of gut bacterial communities are largely overlooked. Using Biolog Ecoplate™ and denaturing gradient gel electrophoresis (DGGE), we explored functional (i.e. the ability to degrade organic matter) and genetic (i.e. identification of DGGE banding patterns) diversity of fish gut bacterial communities, respectively. Gut bacterial communities were extracted from fish species characterized by different diets sampled along a salinity gradient in the Patos-Mirim lagoons complex (Brazil). We found that functional diversity was surprisingly unrelated to genetic diversity of gut bacterial communities. Functional diversity was not affected by the sampling site but by fish species and diet, whereas genetic diversity was significantly influenced by all three factors. Overall, the functional diversity was consistently high across fish individuals and species, suggesting a wide functional niche breadth and a high potential of organic matter degradation. We conclude that fish gut bacterial communities may strongly contribute to nutrient cycling regardless of their genetic diversity and environment.

Decomposing phylogenetic entropy into α, ß and γ components.

Measuring the phylogenetic diversity of communities has become a key issue for biogeography and conservation. However, most diversity indices that rely on interspecies phylogenetic distances may increase with species loss and thus violate the principle of weak monotonicity. Moreover, most published phylogenetic diversity indices ignore the abundance distribution along phylogenetic trees, even though lineage abundances are crucial components of biodiversity. The recently introduced concept of phylogenetic entropy overcomes these limitations, but has not been decomposed across scales, i.e. into α, ß and γ components. A full understanding of mechanisms sustaining biological diversity within and between communities needs such decomposition. Here, we propose an additive decomposition framework for estimating α, ß and γ components of phylogenetic entropy. Based on simulated trees, we demonstrate its robustness to phylogenetic tree shape and species richness. Our decomposition fulfils the requirements of both independence between components and weak monotonicity. Finally, our decomposition can also be adapted to the partitioning of functional diversity across different scales with the same desirable properties.