@article{Barneche2014, title = {Scaling metabolism from individuals to reef-fish communities at broad spatial scales}, volume = {17}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.12309}, doi = {10.1111/ele.12309}, abstract = {Abstract Fishes contribute substantially to energy and nutrient fluxes in reef ecosystems, but quantifying these roles is challenging. Here, we do so by synthesising a large compilation of fish metabolic-rate data with a comprehensive database on reef-fish community abundance and biomass. Individual-level analyses support predictions of Metabolic Theory after accounting for significant family-level variation, and indicate that some tropical reef fishes may already be experiencing thermal regimes at or near their temperature optima. Community-level analyses indicate that total estimated respiratory fluxes of reef-fish communities increase on average ∼2-fold from 22 to 28 °C. Comparisons of estimated fluxes among trophic groups highlight striking differences in resource use by communities in different regions, perhaps partly reflecting distinct evolutionary histories, and support the hypothesis that piscivores receive substantial energy subsidies from outside reefs. Our study demonstrates one approach to synthesising individual- and community-level data to establish broad-scale trends in contributions of biota to ecosystem dynamics.}, number = {9}, journal = {Ecology Letters}, author = {Barneche, Diego R. and Kulbicki, Michel and Floeter, Sergio R. and Friedlander, Alan M. and Maina, J. and Allen, A. P.}, year = {2014}, note = {tex.mendeley-tags: GASPAR}, keywords = {acclimation, Allometry, climate change, coral reef, ecosystem function, food web, GASPAR, metabolic theory of ecology}, pages = {1067--1076}, annote = {pubid: e9bUPLv0EjcC}, } @article{Yancovitch2020, title = {A closer examination of the 'abundant center' hypothesis for reef fishes}, volume = {47}, doi = {10.1111/jbi.13920}, journal = {Journal of Biogeography}, author = {Yancovitch Shalom, Hagar and Granot, Itai and Blowes, Shane A. and Friedlander, Alan M. and Mellin, Camille and Leite Ferreira, Carlos Eduardo and Arias-González, Jesus Ernesto and Kulbicki, Michel and Floeter, Sergio R. and Chabanet, Pascale and Parravicini, Valeriano and Belmaker, Jonathan}, year = {2020}, pages = {2194--2209}, annote = {pubid: nj26e0utjpAC}, } @article{DAgata2016b, title = {Marine reserves lag behind wilderness in the conservation of key functional roles}, volume = {7}, issn = {20411723}, doi = {10.1038/ncomms12000}, abstract = {Although marine reserves represent one of the most effective management responses to human impacts, their capacity to sustain the same diversity of species, functional roles and biomass of reef fishes as wilderness areas remains questionable, in particular in regions with deep and long-lasting human footprints. Here we show that fish functional diversity and biomass of top predators are significantly higher on coral reefs located at more than 20[thinsp]h travel time from the main market compared with even the oldest (38 years old), largest (17,500[thinsp]ha) and most restrictive (no entry) marine reserve in New Caledonia (South-Western Pacific). We further demonstrate that wilderness areas support unique ecological values with no equivalency as one gets closer to humans, even in large and well-managed marine reserves. Wilderness areas may therefore serve as benchmarks for management effectiveness and act as the last refuges for the most vulnerable functional roles.}, journal = {Nature Communications}, author = {D'agata, Stéphanie and Mouillot, David and Wantiez, Laurent and Friedlander, Alan M. and Kulbicki, Michel and Vigliola, Laurent}, year = {2016}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {12000--12009}, annote = {pubid: DPO9WFcz7UcC}, } @article{Bender2017, title = {Isolation drives taxonomic and functional nestedness in tropical reef fish faunas}, volume = {40}, issn = {16000587}, doi = {10.1111/ecog.02293}, abstract = {Taxonomic nestedness, the degree to which the taxonomic composition of species-poor assemblages represents a subset of richer sites, commonly occurs in habitat fragments and islands differing in size and isolation from a source pool. However, species are not ecologically equivalent and the extent to which nestedness is observed in terms of functional trait composi- tion of assemblages still remains poorly known. Here, using an extensive database on the functional traits and the distribu- tions of 6316 tropical reef fish species across 169 sites, we assessed the levels of taxonomical vs functional nestedness of reef fish assemblages at the global scale. Functional nestedness was considerably more common than taxonomic nestedness, and generally associated with geographical isolation, where nested subsets are gradually more isolated from surrounding reef areas and from the center of biodiversity. Because a nested pattern in functional composition implies that certain combina- tions of traits may be represented by few species, we identified these groups of low redundancy that include large herbivore- detritivores and omnivores, small piscivores, and macro-algal herbivores. The identified patterns of nestedness may be an outcome of the interaction between species dispersal capabilities, resource requirements, and gradients of isolation among habitats. The importance of isolation in generating the observed pattern of functional nestedness within biogeographic regions may indicate that disturbance in depauperate and isolated sites can have disproportionate effects on the functional structure of their reef fish assemblages.}, number = {3}, journal = {Ecography}, author = {Bender, Mariana G. and Leprieur, Fabien and Mouillot, David and Kulbicki, Michel and Parravicini, Valeriano and Pie, Marcio R. and Barneche, Diego R. and Oliveira-Santos, Luiz Gustavo R. and Floeter, Sergio R.}, year = {2017}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {425--435}, annote = {pubid: uQVPmWFBlwUC}, } @article{Leprieur2016b, title = {Plate tectonics drive tropical reef biodiversity dynamics}, volume = {7}, issn = {20411723}, doi = {10.1038/ncomms11461}, abstract = {The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics.}, journal = {Nature Communications}, author = {Leprieur, Fabien and Descombes, Patrice and Gaboriau, Theo and Cowman, Peter F. and Parravicini, Valeriano and Kulbicki, Michel and Melian, Carlos J. and de Santana, Charles N. and Heine, Christian and Mouillot, David and Bellwood, David R. and Pellissier, Loïc}, year = {2016}, pages = {11461--11468}, annote = {pubid: 9CGX2owmTHMC}, } @article{Mouillot2013b, title = {The challenge of delineating biogeographical regions: {Nestedness} matters for {Indo}-{Pacific} coral reef fishes}, volume = {40}, issn = {03050270}, doi = {10.1111/jbi.12194}, abstract = {Aim The delineation of regions is a critical procedure in biogeography, but there is still no consensus about the best approach. Traditionally, a compositional dissimilarity index and a clustering algorithm are used to partition locations into regions. However, the choice of index and algorithm may have a profound impact on the final result, particularly when locations display different levels of species richness and when they are nested within each other. Our objective was to estimate the influence of species nestedness among locations on the delineation of biogeographical regions. Location As a case study, we used coral reef fishes (families Chaetodontidae, Pomacentridae and Labridae) from the Indo-Pacific, where a large richness gradient extends, often as a series of nested assemblages, from the species-rich Indo-Australian Archipelago (Coral Triangle) to species-poor peripheral locations. Methods We used the turnover and nestedness components of the Sørensen and Jaccard dissimilarity indices to estimate the effect of nestedness on the delineation of biogeographical regions. In addition, we compared the results with those obtained using a parsimony analysis of endemicity (PAE). Results Low Mantel correlation values revealed that the PAE method assembled locations in a very different way than methods based on dissimilarity indices for Indo-Pacific coral reef fishes. We also found that nestedness mattered when delineating biogeographical units because, for both the Sørensen and the Jaccard indices, reef fish assemblages were grouped differently depending on whether we used the turnover component of each index or the complete index, including the nestedness component. The turnover component ignored variation in species richness attributable to differences in habitat area between locations, and permitted a delineation based solely on species replacement. Main conclusions We demonstrate that the choice of the component used to measure dissimilarity between species assemblages is critical, because it may strongly influence regional delineations, at least for Indo-Pacific coral reef fishes. We conclude that the two components of the dissimilarity indices can reveal complementary insights into the role that history may have played in shaping extant patterns of biodiversity.}, number = {12}, journal = {Journal of Biogeography}, author = {Mouillot, David and de Bortoli, Julien and Leprieur, Fabien and Parravicini, Valeriano and Kulbicki, Michel and Bellwood, David R.}, year = {2013}, note = {tex.mendeley-tags: GASPAR}, keywords = {Coral Triangle, Delineation, Dissimilarity, GASPAR, Indo-Australian Archipelago, Nestedness, PAE, Partitioning, Reef fish assemblages, Turnover, β-diversity}, pages = {2228--2237}, annote = {pubid: k8toY4Q4EC}, } @article{Ottimofiore2017, title = {Responses of coral reef fishes to past climate changes are related to life-history traits}, volume = {7}, issn = {20457758}, doi = {10.1002/ece3.2800}, abstract = {Coral reefs and their associated fauna are largely impacted by ongoing climate change. Unravelling species responses to past climatic variations might provide clues on the consequence of ongoing changes. Here, we tested the relationship between changes in sea surface temperature and sea levels during the Quaternary and present-day distributions of coral reef fish species. We investigated whether species-specific responses are associated with life-history traits. We collected a database of coral reef fish distribution together with life-history traits for the Indo-Pacific Ocean. We ran species distribution models (SDMs) on 3,725 tropical reef fish species using contemporary environmental factors together with a variable describing isolation from stable coral reef areas during the Quaternary. We quantified the variance explained independently by isolation from stable areas in the SDMs and related it to a set of species traits including body size and mobility. The variance purely explained by isolation from stable coral reef areas on the distribution of extant coral reef fish species largely varied across species. We observed a triangular relationship between the contribution of isolation from stable areas in the SDMs and body size. Species, whose distribution is more associated with historical changes, occurred predominantly in the Indo-Australian archipelago, where the mean size of fish assemblages is the lowest. Our results suggest that the legacy of habitat changes of the Quaternary is still detectable in the extant distribution of many fish species, especially those with small body size and the most sedentary. Because they were the least able to colonize distant habitats in the past, fish species with smaller body size might have the most pronounced lags in tracking ongoing climate change.}, number = {6}, journal = {Ecology and Evolution}, author = {Ottimofiore, Eduardo and Albouy, Camille and Leprieur, Fabien and Descombes, Patrice and Kulbicki, Michel and Mouillot, David and Parravicini, Valeriano and Pellissier, Loïc}, year = {2017}, keywords = {climate change, dispersal, Indo-Pacific Ocean, species distribution models}, pages = {1996--2005}, annote = {pubid: eLRq4zTgah0C}, } @article{DAgata2014, title = {Human-mediated loss of phylogenetic and functional diversity in coral reef fishes}, volume = {24}, issn = {09609822}, doi = {10.1016/j.cub.2014.01.049}, abstract = {Summary Beyond the loss of species richness [1-3], human activities may also deplete the breadth of evolutionary history (phylogenetic diversity) and the diversity of roles (functional diversity) carried out by species within communities, two overlooked components of biodiversity. Both are, however, essential to sustain ecosystem functioning and the associated provision of ecosystem services, particularly under fluctuating environmental conditions [1-7]. We quantified the effect of human activities on the taxonomic, phylogenetic, and functional diversity of fish communities in coral reefs, while teasing apart the influence of biogeography and habitat along a gradient of human pressure across the Pacific Ocean. We detected nonlinear relationships with significant breaking points in the impact of human population density on phylogenetic and functional diversity of parrotfishes, at 25 and 15 inhabitants/km2, respectively, while parrotfish species richness decreased linearly along the same population gradient. Over the whole range, species richness decreased by 11.7\%, while phylogenetic and functional diversity dropped by 35.8\% and 46.6\%, respectively. Our results call for caution when using species richness as a benchmark for measuring the status of ecosystems since it appears to be less responsive to variation in human population densities than its phylogenetic and functional counterparts, potentially imperiling the functioning of coral reef ecosystems. © 2014 Elsevier Ltd.}, number = {5}, journal = {Current Biology}, author = {D'agata, Stéphanie and Mouillot, David and Kulbicki, Michel and Andréfouët, Serge and Bellwood, David R. and Cinner, Joshua E. and Cowman, Peter F. and Kronen, Mecki and Pinca, Silvia and Vigliola, Laurent}, year = {2014}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {555--560}, annote = {pubid: 6IBXqrN-DEwC}, } @article{Parravicini2015, title = {Niche shift can impair the ability to predict invasion risk in the marine realm: {An} illustration using {Mediterranean} fish invaders}, volume = {18}, issn = {14610248}, doi = {10.1111/ele.12401}, abstract = {Climatic niche conservatism, the tendency of species-climate associations to remain unchanged across space and time, is pivotal for forecasting the spread of invasive species and biodiversity changes. Indeed, it represents one of the key assumptions underlying species distribution models (SDMs), the main tool currently available for predicting range shifts of species. However, to date, no comprehensive assessment of niche conservatism is available for the marine realm. We use the invasion by Indo-Pacific tropical fishes into the Mediterranean Sea, the world's most invaded marine basin, to examine the conservatism of the climatic niche. We show that tropical invaders may spread far beyond their native niches and that SDMs do not predict their new distributions better than null models. Our results suggest that SDMs may underestimate the potential spread of invasive species and call for prudence in employing these models in order to forecast species invasion and their response to environmental change.}, number = {3}, journal = {Ecology Letters}, author = {Parravicini, Valeriano and Azzurro, Ernesto and Kulbicki, Michel and Belmaker, Jonathan}, year = {2015}, note = {tex.mendeley-tags: GASPAR}, keywords = {Biological invasion, GASPAR, Niche conservatism, Niche expansion, Niche shift, Species distribution models}, pages = {246--253}, annote = {pubid: fFgHTpLxhAC}, } @article{Belmaker2013, title = {Ecological traits and environmental affinity explain {Red} {Sea} fish introduction into the {Mediterranean}}, volume = {19}, issn = {13541013}, doi = {10.1111/gcb.12132}, abstract = {Alien species are considered one of the prime threats to biodiversity, driving major changes in ecosystem structure and function. Identifying the traits associated with alien introduction has been largely restricted to comparing indigenous and alien species or comparing alien species that differ in abundance or impact. However, a more complete understanding may emerge when the entire pool of potential alien species is used as a control, information that is rarely available. In the eastern Mediterranean, the marine environment is undergoing an unparalleled species composition transformation, as a flood of aliens have entered from the Red Sea following the opening of the Suez Canal in 1869. In this study, we compile data on species traits, geographical distribution, and environmental affinity of the entire pool of reef-associated fish species in the Red Sea and more generally across the Indo- Pacific. We use this extensive data to identify the prime characteristics separating Red Sea species that have become alien in the Mediterranean from those that have not. We find that alien species occupy a larger range of environments in their native ranges, explaining their ability to colonize the seasonal Mediterranean. Red Sea species that naturally experience high maximum temperatures in their native range have a high probability of becoming alien. Thus, contrary to predictions of an accelerating number of aliens following increased water temperatures, hotter summers in this region may prevent the establishment of many alien species. We further find that ecological trait diversity of alien species is substantially more evenly spaced and more divergent than random samples from the pool of Red Sea species, pointing at additional processes, such as competition, promoting ecological diversity among alien species. We use these results to provide a first quantitative ranking of the potential of Red Sea species to become established in the eastern Mediterranean. [ABSTRACT FROM AUTHOR]}, number = {5}, journal = {Global Change Biology}, author = {Belmaker, Jonathan and Parravicini, Valeriano and Kulbicki, Michel}, year = {2013}, note = {tex.mendeley-tags: GASPAR}, keywords = {Bioinvasion, GASPAR, Introduction, Lessepsian migration, Marine, Reef fish, Tropicalization}, pages = {1373--1382}, annote = {pubid: SgM-ki2adj0C}, } @article{Stier2014a, title = {Larval dispersal drives trophic structure across {Pacific} coral reefs}, volume = {5}, issn = {20411723}, url = {http://dx.doi.org/10.1038/ncomms6575}, doi = {10.1038/ncomms6575}, abstract = {Top predators are a critical part of healthy ecosystems. Yet, these species are often absent from spatially isolated habitats leading to the pervasive view that fragmented ecological communities collapse from the top down. Here we study reef fish from coral reef commu- nities across the Pacific Ocean. Our analysis shows that species richness of reef fish top predators is relatively stable across habitats that vary widely in spatial isolation and total species richness. In contrast, species richness of prey reef fish declines rapidly with increasing isolation. By consequence, species-poor communities from isolated islands have three times as many predator species per prey species as near-shore communities.We develop and test a colonization–extinction model to reveal how larval dispersal patterns shape this ocean-scale gradient in trophic structure.}, journal = {Nature Communications}, author = {Stier, Adrian C. and Hein, Andrew M. and Parravicini, Valeriano and Kulbicki, Michel}, year = {2014}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {5575--5578}, annote = {pubid: tFzHCjejgA0C}, } @article{Parravicini2021, title = {Coral reef fishes reveal strong divergence in the prevalence of traits along the global diversity gradient}, volume = {288}, doi = {10.1098/rspb.2021.1712}, journal = {Proceedings of the Royal Society B: Biological Sciences}, author = {Parravicini, Valeriano and Bender, Mariana G. and Villéger, Sébastien and Leprieur, Fabien and Pellissier, Loïc and Donati, F. G. A. and Floeter, Sergio R. and Rezende, Enrico L. and Mouillot, David and Kulbicki, Michel}, year = {2021}, pages = {20211712}, annote = {pubid: -w1eE4La9EC}, } @article{Jacquet2017, title = {Extensions of {Island} {Biogeography} {Theory} predict the scaling of functional trait composition with habitat area and isolation}, volume = {20}, issn = {14610248}, doi = {10.1111/ele.12716}, abstract = {The Theory of Island Biogeography (TIB) predicts how area and isolation influence species rich-ness equilibrium on insular habitats. However, the TIB remains silent about functional trait com-position and provides no information on the scaling of functional diversity with area, an observation that is now documented in many systems. To fill this gap, we develop a probabilistic approach to predict the distribution of a trait as a function of habitat area and isolation, extend-ing the TIB beyond the traditional species–area relationship. We compare model predictions to the body-size distribution of piscivorous and herbivorous fishes found on tropical reefs worldwide. We find that small and isolated reefs have a higher proportion of large-sized species than large and connected reefs. We also find that knowledge of species body-size and trophic position improves the predictions of fish occupancy on tropical reefs, supporting both the allometric and trophic theory of island biogeography. The integration of functional ecology to island biogeogra-phy is broadly applicable to any functional traits and provides a general probabilistic approach to study the scaling of trait distribution with habitat area and isolation.}, number = {2}, journal = {Ecology Letters}, author = {Jacquet, Claire and Mouillot, David and Kulbicki, Michel and Gravel, Dominique}, year = {2017}, note = {tex.mendeley-tags: GASPAR}, keywords = {Allometric theory, body-size, food web, GASPAR, island biogeography, tropical reefs}, pages = {135--146}, annote = {pubid: JqN3CTdJtl0C}, } @article{Descombes2015, title = {Forecasted coral reef decline in marine biodiversity hotspots under climate change}, volume = {21}, issn = {13652486}, doi = {10.1111/gcb.12868}, abstract = {Coral bleaching events threaten coral reef habitats globally and cause severe declines of local biodiversity and productivity. Related to high sea surface temperatures, bleaching events are expected to increase as a consequence of future global warming. However, response to climate change is still uncertain as future low latitude climatic conditions have no present-day analogue. Sea surface temperatures during the Eocene epoch were warmer than forecasted changes for the coming century, and distributions of corals during the Eocene may help to inform models forecasting the future of coral reefs. We coupled contemporary and Eocene coral occurrences with information on their respective climatic conditions to model the thermal niche of coral reefs and its potential response to projected climate change. We found that under the RCP8.5 climate change scenario, the global suitability for coral reefs may increase up to 16\% by 2100, mostly due to improved suitability of higher latitudes. In contrast, in its current range, coral reef suitability may decrease up to 46\% by 2100. Reduction in thermal suitability will be most severe in biodiversity hotspots, especially in the Indo-Australian Archipelago. Our results suggest that many contemporary hotspots for coral reefs, including those that have been refugia in the past, spatially mismatch with future shifts in coral reef habitat suitability, posing even more challenges to conservation actions under climate change. This article is protected by copyright. All rights reserved.}, number = {7}, journal = {Global Change Biology}, author = {Descombes, Patrice and Wisz, Mary S. and Leprieur, Fabien and Parravicini, Valeriano and Heine, Christian and Olsen, Steffen M. and Swingedouw, Didier and Kulbicki, Michel and Mouillot, David and Pellissier, Loïc}, year = {2015}, note = {tex.mendeley-tags: GASPAR}, keywords = {Fish, Fossil, GASPAR, Sea surface temperature, Specialists, Species distribution model, Species richness}, pages = {2479--2487}, annote = {pubid: 1Aeql8wG3wEC}, } @article{Kulbicki2013, title = {Global biogeography of reef fishes: {A} hierarchical quantitative delineation of regions}, volume = {8}, issn = {19326203}, doi = {10.1371/journal.pone.0081847}, abstract = {Delineating regions is an important first step in understanding the evolution and biogeography of faunas. However, quantitative approaches are often limited at a global scale, particularly in the marine realm. Reef fishes are the most diversified group of marine fishes, and compared to most other phyla, their taxonomy and geographical distributions are relatively well known. Based on 169 checklists spread across all tropical oceans, the present work aims to quantitatively delineate biogeographical entities for reef fishes at a global scale. Four different classifications were used to account for uncertainty related to species identification and the quality of checklists. The four classifications delivered converging results, with biogeographical entities that can be hierarchically delineated into realms, regions and provinces. All classifications indicated that the Indo-Pacific has a weak internal structure, with a high similarity from east to west. In contrast, the Atlantic and the Eastern Tropical Pacific were more strongly structured, which may be related to the higher levels of endemism in these two realms. The "Coral Triangle", an area of the Indo-Pacific which contains the highest species diversity for reef fishes, was not clearly delineated by its species composition. Our results show a global concordance with recent works based upon endemism, environmental factors, expert knowledge, or their combination. Our quantitative delineation of biogeographical entities, however, tests the robustness of the results and yields easily replicated patterns. The similarity between our results and those from other phyla, such as corals, suggests that our approach may be of broad utility in describing and understanding global marine biodiversity patterns.}, number = {12}, journal = {PLoS ONE}, author = {Kulbicki, Michel and Parravicini, Valeriano and Bellwood, David R. and Arias-González, Jesus Ernesto and Chabanet, Pascale and Floeter, Sergio R. and Friedlander, Alan M. and McPherson, Jana and Myers, Robert E. and Vigliola, Laurent and Mouillot, David}, year = {2013}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {e81847}, annote = {pubid: bbjcffOLshcC}, } @article{Mellin2016, title = {Humans and seasonal climate variability threaten large-bodied coral reef fish with small ranges}, volume = {7}, issn = {20411723}, url = {http://dx.doi.org/10.1038/ncomms10491}, doi = {10.1038/ncomms10491}, abstract = {Coral reefs are among the most species-rich and threatened ecosystems on Earth, yet the extent to which human stressors determine species occurrences, compared with biogeography or environmental conditions, remains largely unknown. With ever-increasing human-mediated disturbances on these ecosystems, an important question is not only how many species can inhabit local communities, but also which biological traits determine species that can persist (or not) above particular disturbance thresholds. Here we show that human pressure and seasonal climate variability are disproportionately and negatively associated with the occurrence of large-bodied and geographically small-ranging fishes within local coral reef communities. These species are 67\% less likely to occur where human impact and temperature seasonality exceed critical thresholds, such as in the marine biodiversity hotspot: the Coral Triangle. Our results identify the most sensitive species and critical thresholds of human and climatic stressors, providing opportunity for targeted conservation intervention to prevent local extinctions.}, journal = {Nature Communications}, author = {Mellin, C. and Mouillot, David and Kulbicki, Michel and McClanahan, Tim R. and Vigliola, Laurent and Bradshaw, C. J. A. and Brainard, R. E. and Chabanet, Pascale and Edgar, G. J. and Fordham, D. A. and Friedlander, Alan M. and Parravicini, Valeriano and Sequeira, A. M. M. and Stuart-Smith, R. D. and Wantiez, Laurent and Caley, M. J.}, year = {2016}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {10491--10499}, annote = {pubid: oYwriLWYh5YC}, } @article{Leprieur2016a, title = {Historical and contemporary determinants of global phylogenetic structure in tropical reef fish faunas}, volume = {39}, issn = {16000587}, doi = {10.1111/ecog.01638}, abstract = {Identifying the main determinants of tropical marine biodiversity is essential for devising appropriate conservation measures mitigating the ongoing degradation of coral reef habitats. Based on a gridded distribution database and phylogenetic information, we compared the phylogenetic structure of assemblages for three tropical reef fish families (Labridae: wrasses, Pomacentridae: damselfishes and Chaetodontidae: butterflyfishes) using the Net Relatedness (NRI) and Nearest Taxon (NTI) indices. We then related these indices to contemporary and historical environmental conditions of coral reefs using spatial regression analyses. Higher levels of phylogenetic clustering were found for fish assemblages in the Indo-Australian Archipelago (IAA), and more particularly when considering the NTI index. The phylogenetic structure of the Pomacentridae, and to a lower extent of the Chaeotodontidae and Labridae, was primarily associated with the location of refugia during the Quaternary period. Phylogenetic clustering in the IAA may partly result from vicariance events associated with coral reef fragmentation during the glacial periods of the Quaternary. Variation in the patterns among fish families further suggest that dispersal abilities may have interacted with past habitat availability in shaping the phylogenetic structure of tropical reef fish assemblages.This article is protected by copyright. All rights reserved.}, number = {9}, journal = {Ecography}, author = {Leprieur, Fabien and Colosio, Simona and Descombes, Patrice and Parravicini, Valeriano and Kulbicki, Michel and Cowman, Peter F. and Bellwood, David R. and Mouillot, David and Pellissier, Loïc}, year = {2016}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {825--835}, annote = {pubid: -fu4zM₆qcIC}, } @article{Luiz2013, title = {Adult and larval traits as determinants of geographic range size among tropical reef fishes}, volume = {110}, issn = {0027-8424}, doi = {10.1073/pnas.1304074110}, abstract = {Most marine organisms disperse via ocean currents as larvae, so it is often assumed that larval-stage duration is the primary determinant of geographic range size. However, empirical tests of this relationship have yielded mixed results, and alternative hypotheses have rarely been considered. Here we assess the relative influence of adult and larval-traits on geographic range size using a global dataset encompassing 590 species of tropical reef fishes in 47 families, the largest compilation of such data to date for any marine group. We analyze this database using linear mixed-effect models to control for phylogeny and geographical limits on range size. Our analysis indicates that three adult traits likely to affect the capacity of new colonizers to survive and establish reproductive populations (body size, schooling behavior, and nocturnal activity) are equal or better predictors of geographic range size than pelagic larval duration. We conclude that adult life-history traits that affect the postdispersal persistence of new populations are primary determinants of successful range extension and, consequently, of geographic range size among tropical reef fishes.}, number = {41}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, author = {Luiz, O. J. and Allen, A. P. and Robertson, D. R. and Floeter, Sergio R. and Kulbicki, Michel and Vigliola, Laurent and Becheler, R. and Madin, J. S.}, year = {2013}, note = {ISBN: 1304074110 tex.mendeley-tags: GASPAR}, keywords = {colonization, GASPAR, macroecology, marine dispersal}, pages = {16498--16502}, annote = {pubid: 4tNoA7Af41QC}, } @article{DAgata2016a, title = {Unexpected high vulnerability of functions in wilderness areas: evidence from coral reef fishes}, volume = {283}, issn = {0962-8452}, doi = {10.1098/rspb.2016.0128}, abstract = {High species richness is thought to support the delivery of multiple ecosystem functions and services under changing environments. Yet, some species might perform unique functional roles while others are redundant. Thus, the benefits of high species richness in maintaining ecosystem functioning are uncertain if functions have little redundancy, potentially leading to high vulnerability of functions. We studied the natural propensity of assemblages to be functionally buffered against loss prior to fishing activities, using functional trait combi- nations, in coral reef fish assemblages across unfished wilderness areas of the Indo-Pacific: Chagos Archipelago, New Caledonia and French Polynesia. Fish functional diversity in these wilderness areas is highly vulnerable to fish- ing, explained by species- and abundance-based redundancy packed into a small combination of traits, leaving most other trait combinations (60\%) sensi- tive to fishing, with no redundancy. Functional vulnerability peaks for mobile and sedentary top predators, and large species in general. Functional vulner- ability decreases for certain functional entities in New Caledonia, where overall functional redundancy was higher. Uncovering these baseline patterns of functional vulnerability can offer early warning signals of the damaging effects from fishing, and may serve as baselines to guide precautionary and even proactive conservation actions.}, number = {1844}, journal = {Proceedings of the Royal Society B: Biological Sciences}, author = {D'agata, Stéphanie and Vigliola, Laurent and Graham, Nicholas A. J. and Wantiez, Laurent and Parravicini, Valeriano and Villéger, Sébastien and Mou-Tham, Gerard and Frolla, Philippe and Friedlander, Alan M. and Kulbicki, Michel and Mouillot, David}, year = {2016}, note = {tex.mendeley-tags: GASPAR}, keywords = {baseline functional vulnerability, coral reef fish, GASPAR, redundancy, wilderness areas}, pages = {20160128}, annote = {pubid: cx97FdCJQX8C}, } @article{Parravicini2014, title = {Global mismatch between species richness and vulnerability of reef fish assemblages}, volume = {17}, issn = {14610248}, doi = {10.1111/ele.12316}, abstract = {The impact of anthropogenic activity on ecosystems has highlighted the need to move beyond the biogeographical delineation of species richness patterns to understanding the vulnerability of species assemblages, including the functional components that are linked to the processes they support. We developed a decision theory framework to quantitatively assess the global taxonomic and functional vulnerability of fish assemblages on tropical reefs using a combination of sensitivity to species loss, exposure to threats and extent of protection. Fish assemblages with high taxonomic and functional sensitivity are often exposed to threats but are largely missed by the global network of marine protected areas. We found that areas of high species richness spatially mismatch areas of high taxonomic and functional vulnerability. Nevertheless, there is strong spatial match between taxonomic and functional vulnerabilities suggesting a potential win-win conservation-ecosystem service strategy if more protection is set in these locations.}, number = {9}, journal = {Ecology Letters}, author = {Parravicini, Valeriano and Villéger, Sébastien and McClanahan, Tim R. and Arias-González, Jesus Ernesto and Bellwood, David R. and Belmaker, Jonathan and Chabanet, Pascale and Floeter, Sergio R. and Friedlander, Alan M. and Guilhaumon, François and Vigliola, Laurent and Kulbicki, Michel and Mouillot, David}, year = {2014}, note = {tex.mendeley-tags: GASPAR}, keywords = {Conservation, GASPAR, Macroecology, Risk assessment, Sensitivity, Vulnerability}, pages = {1101--1110}, annote = {pubid: qbqt7gslDFUC}, } @article{Parravicini2013, title = {Global patterns and predictors of tropical reef fish species richness}, volume = {36}, issn = {09067590}, doi = {10.1111/j.1600-0587.2013.00291.x}, abstract = {In the marine realm, the tropics host an extraordinary diversity of taxa but the drivers underlying the global distribution of marine organisms are still under scrutiny and we still lack an accurate global predictive model. Using a spatial database for 6336 tropical reef fishes, we attempted to predict species richness according to geometric, biogeographical and environmental explanatory variables. In particular, we aimed to evaluate and disentangle the predictive performances of temperature, habitat area, connectivity, mid-domain effect and biogeographical region on reef fish species richness. We used boosted regression trees, a flexible machine-learning technique, to build our predictive model and structural equation modeling to test for potential ‘mediation effects' among predictors. Our model proved to be accurate, explaining 80\% of the total deviance in fish richness using a cross-validated procedure. Coral reef area and biogeographical region were the primary predictors of reef fish species richness, followed by coast length, connectivity, mid-domain effect and sea surface temperature, with interactions between the region and other predictors. Important indirect effects of water temperature on reef fish richness, mediated by coral reef area, were also identified. The relationship between environmental predictors and species richness varied markedly among biogeographical regions. Our analysis revealed that a few easily accessible variables can accurately predict reef fish species richness. They also highlight concerns regarding ongoing environmental declines, with region-specific responses to variation in environmental conditions predicting a variable response to anthropogenic impacts.}, number = {12}, journal = {Ecography}, author = {Parravicini, Valeriano and Kulbicki, Michel and Bellwood, David R. and Friedlander, Alan M. and Arias-González, Jesus Ernesto and Chabanet, Pascale and Floeter, Sergio R. and Myers, Robert E. and Vigliola, Laurent and D'agata, Stéphanie and Mouillot, David}, year = {2013}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {1254--1262}, annote = {pubid: e0LTWoPxLYMC}, } @article{Pellissier2014, title = {Quaternary coral reef refugia preserved fish diversity}, volume = {344}, issn = {0036-8075}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1249853}, doi = {10.1126/science.1249853}, abstract = {The most prominent pattern in global marine biogeography is the biodiversity peak in the Indo-Australian Archipelago. Yet the processes that underpin this pattern are still actively debated. By reconstructing global marine paleoenvironments over the past 3 million years on the basis of sediment cores, we assessed the extent to which Quaternary climate fluctuations can explain global variation in current reef fish richness. Comparing global historical coral reef habitat availability with the present-day distribution of 6316 reef fish species, we find that distance from stable coral reef habitats during historical periods of habitat loss explains 62\% of the variation in fish richness, outweighing present-day environmental factors. Our results highlight the importance of habitat persistence during periods of climate change for preserving marine biodiversity.}, number = {6187}, journal = {Science (New York, N.Y.)}, author = {Pellissier, Loïc and Leprieur, Fabien and Parravicini, Valeriano and Cowman, Peter F. and Kulbicki, Michel and Litsios, G. and Olsen, Steffen M. and Wisz, Mary S. and Bellwood, David R. and Mouillot, David}, year = {2014}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {1016--1019}, annote = {pubid: Lo8V22OuN40C}, } @article{Mouillot2016, title = {Global marine protected areas do not secure the evolutionary history of tropical corals and fishes}, volume = {7}, issn = {2041-1723}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26756609%0Ahttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4729959}, doi = {10.1038/ncomms10359}, abstract = {Although coral reefs support the largest concentrations of marine biodiversity worldwide, the extent to which the global system of marine-protected areas (MPAs) represents individual species and the breadth of evolutionary history across the Tree of Life has never been quantified. Here we show that only 5.7\% of scleractinian coral species and 21.7\% of labrid fish species reach the minimum protection target of 10\% of their geographic ranges within MPAs. We also estimate that the current global MPA system secures only 1.7\% of the Tree of Life for corals, and 17.6\% for fishes. Regionally, the Atlantic and Eastern Pacific show the greatest deficit of protection for corals while for fishes this deficit is located primarily in the Western Indian Ocean and in the Central Pacific. Our results call for a global coordinated expansion of current conservation efforts to fully secure the Tree of Life on coral reefs.}, journal = {Nature Communications}, author = {Mouillot, David and Parravicini, Valeriano and Bellwood, David R. and Leprieur, Fabien and Huang, D. and Cowman, Peter F. and Albouy, Camille and Hughes, T. P. and Thuiller, Wilfried and Guilhaumon, François}, year = {2016}, pmid = {26756609}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {10359--10366}, annote = {pubid: PklR0melJeUC}, } @article{Mouillot2013a, title = {Rare species support vulnerable functions in high-diversity ecosystems}, volume = {11}, issn = {15449173}, doi = {10.1371/journal.pbio.1001569}, abstract = {Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63\% and 98\% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32\% and 89\% of such species are locally and regionally rare, respectively. Remarkably, 47\% of fish species and 55\% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across spatial scales. As such, they are likely to insure against future uncertainty arising from climate change and the ever-increasing anthropogenic pressures on ecosystems. Our results call for a more detailed understanding of the role of rarity and functional vulnerability in ecosystem functioning.}, number = {5}, journal = {PLoS Biology}, author = {Mouillot, David and Bellwood, David R. and Baraloto, Christopher and Chave, Jérôme and Galzin, Rene and Harmelin-Vivien, Mireille and Kulbicki, Michel and Lavergne, Sébastien and Lavorel, Sandra and Mouquet, Nicolas and Paine, C. E. Timothy and Renaud, Julien and Thuiller, Wilfried}, year = {2013}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {e1001569}, annote = {pubid: w0odbtu79TwC}, } @article{Barneche2016, title = {Energetic and ecological constraints on population density of reef fishes}, volume = {283}, url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2015.2186}, doi = {10.1098/rspb.2015.2186}, number = {1823}, journal = {Proceedings of the Royal Society B: Biological Sciences}, author = {Barneche, Diego R. and Kulbicki, Michel and Floeter, Sergio R. and Friedlander, Alan M. and Allen, A. P.}, year = {2016}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {20152186}, annote = {pubid: uWy0R8PweswC}, } @article{Mouillot2014a, title = {Functional over-redundancy and high functional vulnerability in global fish faunas on tropical reefs}, volume = {111}, issn = {1091-6490}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25225388%0Ahttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4183327}, doi = {10.1073/pnas.1317625111}, abstract = {When tropical systems lose species, they are often assumed to be buffered against declines in functional diversity by the ability of the species-rich biota to display high functional redundancy: i.e., a high number of species performing similar functions. We tested this hypothesis using a ninefold richness gradient in global fish faunas on tropical reefs encompassing 6,316 species distributed among 646 functional entities (FEs): i.e., unique combinations of functional traits. We found that the highest functional redundancy is located in the Central Indo-Pacific with a mean of 7.9 species per FE. However, this overall level of redundancy is disproportionately packed into few FEs, a pattern termed functional over-redundancy (FOR). For instance, the most speciose FE in the Central Indo-Pacific contains 222 species (out of 3,689) whereas 38\% of FEs (180 out of 468) have no functional insurance with only one species. Surprisingly, the level of FOR is consistent across the six fish faunas, meaning that, whatever the richness, over a third of the species may still be in overrepresented FEs whereas more than one third of the FEs are left without insurance, these levels all being significantly higher than expected by chance. Thus, our study shows that, even in high-diversity systems, such as tropical reefs, functional diversity remains highly vulnerable to species loss. Although further investigations are needed to specifically address the influence of redundant vs. vulnerable FEs on ecosystem functioning, our results suggest that the promised benefits from tropical biodiversity may not be as strong as previously thought.}, number = {38}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, author = {Mouillot, David and Villéger, Sébastien and Parravicini, Valeriano and Kulbicki, Michel and Arias-González, Jesus Ernesto and Bender, Mariana G. and Chabanet, Pascale and Floeter, Sergio R. and Friedlander, Alan M. and Vigliola, Laurent and Bellwood, David R.}, year = {2014}, pmid = {25225388}, note = {tex.mendeley-tags: GASPAR}, keywords = {GASPAR}, pages = {13757--13762}, annote = {pubid: Yw6v6SrDvuUC}, } @article{Bender2013, title = {Biogeographic, historical and environmental influences on the taxonomic and functional structure of {Atlantic} reef fish assemblages}, volume = {22}, issn = {1466822X}, doi = {10.1111/geb.12099}, abstract = {Aim To disentangle how historic, biogeographic and environmental factors have shaped the composition of different reef fish assemblages, we analysed assemblage structure from a taxonomic (proportions of species from different families) and functional perspective (diet and body size). Location Atlantic Ocean. Methods The distributions of 1629 fish species were compiled for 31 locations across the Atlantic Ocean (39°66′ N, 27°50′ S). These locations provide a richness gradient ranging from 54 species in St Paul's Rocks to 474 in Cuba. We used cluster analyses to assess how historical and biogeographic factors have shaped the taxonomic and functional structure (i.e. the distribution of species within families, diet and body size groups) of assemblages. We then employed a constrained analysis of principal coordinates (CAP) to test the relative influence of the distance from the biodiversity centre in the Atlantic, sea surface temperature, isolation, coral species richness and area, and coastal length on the observed patterns of assemblage structure. Results The taxonomic and functional structure of reef fish assemblages across the Atlantic exhibits a biogeographic fingerprint, with a marked discrimination between species-rich biogenic reefs (concentrated primarily in the Caribbean and composed of small species feeding on invertebrates) and poorer peripheral regions dominated by larger species with more diverse diets. The first CAP axis explains 87\% of body size distribution in assemblages, showing that the effects of sea surface temperature and coral richness and those of isolation are antagonistic and can be embedded into a single dimension. Environmental factors, such as temperature and habitat complexity, explain the disproportionate number of small species in the Caribbean, whereas in the remaining regions the predominance of large-bodied fish increases with isolation due to high dispersal ability. Main conclusions We found that historical events, which have shaped the biogeography of reef fishes, and environmental characteristics (coral reefs versus periphery) have both played a role in structuring the taxonomic and functional components of Atlantic fish assemblages.}, number = {11}, journal = {Global Ecology and Biogeography}, author = {Bender, Mariana G. and Pie, Marcio R. and Rezende, Enrico L. and Mouillot, David and Floeter, Sergio R.}, year = {2013}, note = {tex.mendeley-tags: GASPAR}, keywords = {Assemblage structuring, Atlantic Ocean, Body size, Functional group, GASPAR, Reef fish, Taxonomic structure}, pages = {1173--1182}, annote = {pubid: ZqLB7dQ1iF4C}, } @article{Feng2022, title = {A review of the heterogeneous landscape of biodiversity databases: {Opportunities} and challenges for a synthesized biodiversity knowledge base}, volume = {31}, issn = {1466-8238}, url = {https://onlinelibrary.wiley.com/doi/full/10.1111/geb.13497%0Ahttps://onlinelibrary.wiley.com/doi/abs/10.1111/geb.13497%0Ahttps://onlinelibrary.wiley.com/doi/10.1111/geb.13497}, doi = {10.1111/GEB.13497}, abstract = {Aim Addressing global environmental challenges requires access to biodiversity data across wide spatial, temporal and taxonomic scales. Availability of such data has increased exponentially recently with the proliferation of biodiversity databases. However, heterogeneous coverage, protocols, and standards have hampered integration among these databases. To stimulate the next stage of data integration, here we present a synthesis of major databases, and investigate (a) how the coverage of databases varies across taxonomy, space, and record type; (b) what degree of integration is present among databases; (c) how integration of databases can increase biodiversity knowledge; and (d) the barriers to database integration. Location Global. Time period Contemporary. Major taxa studied Plants and vertebrates. Methods We reviewed 12 established biodiversity databases that mainly focus on geographic distributions and functional traits at global scale. We synthesized information from these databases to assess the status of their integration and major knowledge gaps and barriers to full integration. We estimated how improved integration can increase the data coverage for terrestrial plants and vertebrates. Results Every database reviewed had a unique focus of data coverage. Exchanges of biodiversity information were common among databases, although not always clearly documented. Functional trait databases were more isolated than those pertaining to species distributions. Variation and potential incompatibility of taxonomic systems used by different databases posed a major barrier to data integration. We found that integration of distribution databases could lead to increased taxonomic coverage that corresponds to 23 years' advancement in data accumulation, and improvement in taxonomic coverage could be as high as 22.4\% for trait databases. Main conclusions Rapid increases in biodiversity knowledge can be achieved through the integration of databases, providing the data necessary to address critical environmental challenges. Full integration across databases will require tackling the major impediments to data integration: taxonomic incompatibility, lags in data exchange, barriers to effective data synchronization, and isolation of individual initiatives.}, journal = {Global Ecology and Biogeography}, author = {Feng, Xiao and Enquist, Brian J. and Park, Daniel S. and Boyle, Brad and Breshears, David D. and Gallagher, Rachael V. and Lien, Aaron and Newman, Erica A. and Burger, Joseph R. and Maitner, Brian S. and Merow, Cory and Li, Yaoqi and Huynh, Kimberly M. and Ernst, Kacey and Baldwin, Elizabeth and Foden, Wendy and Hannah, Lee and Jorgensen, Peter M. and Kraft, Nathan J. B. and Lovett, Jon C. and Marquet, Pablo A. and McGill, Brian J. and Morueta‐Holme, Naia and Neves, Danilo M. and Núñez‐Regueiro, Mauricio M. and Oliveira‐Filho, Ary T. and Peet, Robert K. and Pillet, Michiel and Roehrdanz, Patrick R. and Sandel, Brody and Serra‐Diaz, Josep M. and Símová, Irena and Svenning, Jens‐Christian and Violle, Cyrille and Weitemier, Trang D. and Wiser, Susan and López‐Hoffman, Laura}, year = {2022}, keywords = {big data, biodiversity informatics, biogeography, database integration, functional trait, taxonomic system}, pages = {1242--1260}, annote = {pubid: 1YatL4jblGcC}, } @article{Guo2022, title = {High exposure of global tree diversity to human pressure}, volume = {119}, doi = {10.1073/pnas.2026733119}, abstract = {Safeguarding Earth's tree diversity is a conservation priority due to the importance of trees for biodiversity and ecosystem functions and services such as carbon sequestration. Here, we improve the foundation for effective conservation of global tree diversity by analyzing a recently developed database of tree species covering 46,752 species. We quantify range protection and anthropogenic pressures for each species and develop conservation priorities across taxonomic, phylogenetic, and functional diversity dimensions. We also assess the effectiveness of several influential proposed conservation prioritization frameworks to protect the top 17\% and top 50\% of tree priority areas. We find that an average of 50.2\% of a tree species' range occurs in 110-km grid cells without any protected areas (PAs), with 6,377 small-range tree species fully unprotected, and that 83\% of tree species experience nonnegligible human pressure across their range on average. Protecting high-priority areas for the top 17\% and 50\% priority thresholds would increase the average protected proportion of each tree species' range to 65.5\% and 82.6\%, respectively, leaving many fewer species (2,151 and 2,010) completely unprotected. The priority areas identified for trees match well to the Global 200 Ecoregions framework, revealing that priority areas for trees would in large part also optimize protection for terrestrial biodiversity overall. Based on range estimates for ¿46,000 tree species, our findings show that a large proportion of tree species receive limited protection by current PAs and are under substantial human pressure. Improved protection of biodiversity overall would also strongly benefit global tree diversity.}, number = {25}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, author = {Guo, Wen-Yong and Serra-Diaz, Josep M. and Schrodt, Franziska and Eiserhardt, Wolf L. and Maitner, Brian S. and Merow, Cory and Violle, Cyrille and Anand, Madhur and Belluau, Michaël and Bruun, Hans Henrik and Byun, Chaeho and Catford, Jane A. and Cerabolini, Bruno E. L. and Chacón-Madrigal, Eduardo and Ciccarelli, Daniela and Cornelissen, J. Hans C. and Dang-Le, Anh Tuan and de Frutos, Angel and Dias, Arildo S. and Giroldo, Aelton B. and Guo, Kun and Gutiérrez, Alvaro G. and Hattingh, Wesley and He, Tianhua and Hietz, Peter and Hough-Snee, Nate and Jansen, Steven and Kattge, Jens and Klein, Tamir and Komac, Benjamin and Kraft, Nathan J. B. and Kramer, Koen and Lavorel, Sandra and Lusk, Christopher H. and Martin, Adam R. and Mencuccini, Maurizio and Michaletz, Sean T. and Minden, Vanessa and Mori, Akira S. and Niinemets, Ülo and Onoda, Yusuke and Peñuelas, Josep and Pillar, Valério D. and Pisek, Jan and Robroek, Bjorn J. M. and Schamp, Brandon and Slot, Martijn and Sosinski, Ênio Egon and Soudzilovskaia, Nadejda A. and Thiffault, Nelson and van Bodegom, Peter and van der Plas, Fons and Wright, Ian J. and Xu, Wu-Bing and Zheng, Jingming and Enquist, Brian J. and Svenning, Jens-Christian}, year = {2022}, pages = {e2026733119}, } @article{Grenie2017, title = {funrar: {An} {R} package to characterize functional rarity}, volume = {23}, issn = {14724642}, doi = {10.1111/ddi.12629}, abstract = {Emphasis has been put in recent ecological research on investigating phylogenetic, functional and taxonomic facets of biological diversity. While a flourishing number of indices have been proposed for assessing functional diversity, surprisingly few options are available to characterize functional rarity. Functional rarity can play a key role in community and ecosystem dynamics. We introduce here the funrar R package to quantify functional rarity based on species trait differences and species frequencies at local and regional scales. Because of the increasing availability of big datasets in mac-roecology and biogeography, we optimized funrar to work with large datasets of thousands of species and sites. We illustrate the use of the package to investigate the functional rarity of North and Central American mammals.}, number = {12}, journal = {Diversity and Distributions}, author = {Grenié, Matthias and Denelle, Pierre and Tucker, Caroline M. and Munoz, François and Violle, Cyrille}, year = {2017}, keywords = {biodiversity, biodiversity indices, functional biogeography, functional trait, R package, rarity}, pages = {1365--1371}, annote = {pubid: dMpQl7XwOw4C}, } @article{Mahaut2020, title = {Weeds: {Against} the rules?}, volume = {25}, doi = {10.1016/j.tplants.2020.05.013}, abstract = {Establishing laws of plant and ecosystems functioning has been an overarching objective of functional and evolutionary ecology. However, most theories neglect the role of human activities in creating novel ecosystems characterized by species assemblages and environmental factors that are not observed in natural systems. We argue that agricultural weeds, as an emblematic case of such an ?ecological novelty?, constitute an original and underutilized model for challenging current concepts in ecology and evolution. We highlight key aspects of weed ecology and evolutionary biology that can help to test and recast ecological and evolutionary laws in a changing world. We invite ecologists to seize upon weeds as a model system to improve our understanding of the short-term and long-term dynamics of ecological systems in the Anthropocene. AB - Establishing laws of plant and ecosystems functioning has been an overarching objective of functional and evolutionary ecology. However, most theories neglect the role of human activities in creating novel ecosystems characterized by species assemblages and environmental factors that are not observed in natural systems. We argue that agricultural weeds, as an emblematic case of such an ?ecological novelty?, constitute an original and underutilized model for challenging current concepts in ecology and evolution. We highlight key aspects of weed ecology and evolutionary biology that can help to test and recast ecological and evolutionary laws in a changing world. We invite ecologists to seize upon weeds as a model system to improve our understanding of the short-term and long-term dynamics of ecological systems in the Anthropocene.}, number = {11}, journal = {Trends in Plant Science}, author = {Mahaut, Lucie and Cheptou, Pierre-Olivier and Fried, Guillaume and Munoz, François and Storkey, Jonathan and Vasseur, François and Violle, Cyrille and Bretagnolle, Vincent}, year = {2020}, keywords = {Anthropocene, community assembly, eco-evolutionary dynamics, functional trait}, pages = {1107--1116}, annote = {pubid: 5bfplxN71z4C}, } @article{Mahaut2020a, title = {Multiple facets of diversity effects on plant productivity: {Species} richness, functional diversity, species identity and intraspecific competition}, volume = {34}, issn = {13652435}, doi = {10.1111/1365-2435.13473}, abstract = {Deciphering the mechanisms that drive variation in biomass production across plant communities of contrasting species composition and diversity is a main challenge of biodiversity–ecosystem functioning research. Niche complementarity and selection effect have been widely investigated to address biodiversity–productivity relationships. However, the overlooking of the specific role played by key species has limited so far our capacity to comprehensively assess the relative importance of other potential drivers of biodiversity effects. Here, we conducted a grassland diversity–productivity experiment to test how four potential facets of biodiversity effects, namely species richness, functional diversity, species identity and the relaxation of intraspecific competition, account for variations in above and root biomass production. We grew six plant species in monoculture, as well as in every combination of two, three and six species. Plant density was kept constant across the richness gradient but we additionally grew each species in half-density monoculture to estimate the strength of intraspecific competition for each studied species. We characterized eight functional traits, including root traits, related to nutrient and light acquisition and computed both the functional dissimilarity and the community-weighted mean (CWM) of each trait. We further partitioned above-ground biodiversity effect into complementarity and selection effects. We observed strong positive biodiversity effects on both above-ground and root biomass as well as strong positive complementarity effect. These arose largely from the presence of a particular species (Plantago lanceolata) and from CWM trait values more than from a higher functional dissimilarity in plant mixtures. P. lanceolata displayed the highest intraspecific competition, which was strongly relaxed in species mixtures. By contrast, the presence of Sanguisorba minor negatively affected the productivity of plant mixtures, this species suffering more from interspecific than intraspecific competition. This study provides strong evidences that the search for key species is critical to understand the role of species diversity on ecosystem functioning and demonstrates the major role that the balance between intraspecific and interspecific competition plays in biodiversity–ecosystem functioning relationships. Developing more integrative approaches in community and ecosystem ecology can offer opportunities to better understand the role that species diversity plays on ecosystem functioning. A free Plain Language Summary can be found within the Supporting Information of this article.}, number = {1}, journal = {Functional Ecology}, author = {Mahaut, Lucie and Fort, Florian and Violle, Cyrille and Freschet, Grégoire T.}, year = {2020}, keywords = {biodiversity–ecosystem functioning, complementarity effect, functional distinctiveness, functional trait, niche difference, roots, selection effect, species coexistence}, pages = {287--298}, annote = {pubid: t9Ks5LMjN0QC}, } @article{Violle2017a, title = {Functional rarity: {The} ecology of outliers}, volume = {32}, issn = {01695347}, url = {http://www.sciencedirect.com/science/article/pii/S0169534717300381}, doi = {10.1016/j.tree.2017.02.002}, abstract = {Rarity has been a central topic for conservation and evolutionary biologists aiming to determine the species characteristics that cause extinction risk. More recently, beyond the rarity of species, the rarity of functions or functional traits, called functional rarity, has gained momentum in helping to understand the impact of biodiversity decline on ecosystem functioning. However, a conceptual framework for defining and quantifying functional rarity is still lacking. We introduce 12 different forms of functional rarity along gradients of species scarcity and trait distinctiveness. We then highlight the potential key role of functional rarity in the long-term and large-scale maintenance of ecosystem processes, as well as the necessary linkage between functional and evolutionary rarity.}, number = {5}, journal = {Trends in Ecology \& Evolution}, author = {Violle, Cyrille and Thuiller, Wilfried and Mouquet, Nicolas and Munoz, François and Kraft, Nathan J. B. and Cadotte, Marc W. and Livingstone, Stuart W. and Mouillot, David}, year = {2017}, pages = {356--367}, annote = {pubid: oXKBmVzQOggC}, } @article{Mouillot2021, title = {The dimensionality and structure of species trait spaces}, volume = {24}, doi = {10.1111/ele.13778}, abstract = {Trait- based ecology aims to understand the processes that generate the overarch- ing diversity of organismal traits and their influence on ecosystem functioning. Achieving this goal requires simplifying this complexity in synthetic axes defining a trait space and to cluster species based on their traits while identifying those with unique combinations of traits. However, so far, we know little about the dimen- sionality, the robustness to trait omission and the structure of these trait spaces. Here, we propose a unified framework and a synthesis across 30 trait datasets rep- resenting a broad variety of taxa, ecosystems and spatial scales to show that a common trade- off between trait space quality and operationality appears between three and six dimensions. The robustness to trait omission is generally low but highly variable among datasets. We also highlight invariant scaling relationships, whatever organismal complexity, between the number of clusters, the number of species in the dominant cluster and the number of unique species with total species richness. When species richness increases, the number of unique species saturates, whereas species tend to disproportionately pack in the richest cluster. Based on these results, we propose some rules of thumb to build species trait spaces and estimate subsequent functional diversity indices.}, number = {9}, journal = {Ecology Letters}, author = {Mouillot, David and Loiseau, Nicolas and Grenié, Matthias and Algar, Adam C. and Allegra, Michele and Cadotte, Marc W. and Casajus, Nicolas and Denelle, Pierre and Guéguen, Maya and Maire, Anthony and Maitner, Brian and McGill, Brian J. and McLean, Matthew and Mouquet, Nicolas and Munoz, François and Thuiller, Wilfried and Villéger, Sébastien and Violle, Cyrille and Auber, Arnaud}, year = {2021}, keywords = {complexity, functional ecology, hypervolume, species clustering, species uniqueness}, pages = {1988--2009}, annote = {pubid: UY3hNwcQ290C}, } @article{Laroche2020, title = {Analyzing snapshot diversity patterns with the {Neutral} {Theory} can show functional groups' effects on community assembly}, volume = {101}, issn = {00129658}, doi = {10.1002/ecy.2977}, abstract = {A central question of community ecology is to understand how the interplay between processes of the Neutral Theory (e.g., immigration and ecological drift) and niche-based processes (e.g., environmental filtering, intra- and interspecific density dependence) shape species diversity in competitive communities. The articulation between these two categories of mechanisms can be studied through the lens of the intermediate organizational level of “functional groups” (FGs), defined as clusters of species with similar traits. Indeed, FGs stress ecological differences among species and are thus likely to unravel non-neutral interactions within communities. Here we presented a novel approach to explore how FGs affect species coexistence by comparing species and functional diversity patterns. Our framework considers the Neutral Theory as a mechanistic null hypothesis. It assesses how much the functional diversity deviates from species diversity in communities, and compares this deviation, called the “average functional deviation,” to a neutral baseline. We showed that the average functional deviation can indicate reduced negative density dependence or environmental filtering among FGs. We validated our framework using simulations illustrating the two situations. We further analyzed tropical tree communities in Western Ghats, India. Our analysis of the average functional deviation revealed environmental filtering between deciduous and evergreen FGs along a broad rainfall gradient. By contrast, we did not find clear evidence for reduced density dependence among FGs. We predict that applying our approach to new case studies where environmental gradients are milder and FGs are more clearly associated to resource partitioning should reveal the missing pattern of reduced density dependence among FGs.}, number = {4}, journal = {Ecology}, author = {Laroche, Fabien and Violle, Cyrille and Taudière, Adrien and Munoz, François}, year = {2020}, pmid = {31944275}, keywords = {beta-diversity index, community ecology, functional groups, neutral theory, Simpson diversity, spatially implicit, species coexistence, tropical forest}, pages = {e02977}, annote = {pubid: NKlx0PmyA3cC}, } @article{Delalandre2022, title = {Functionally distinct tree species support long-term productivity in extreme environments}, volume = {289}, doi = {10.1098/rspb.2021.1694}, abstract = {Despite evidence of a positive effect of functional diversity on ecosystem productivity, the importance of functionally distinct species (i.e. species that display an original combination of traits) is poorly understood. To investigate how distinct species affect ecosystem productivity, we used a forest-gap model to simulate realistic temperate forest successions along an environmental gradient and measured ecosystem productivity at the end of the successional trajectories. We performed 10 560 simulations with different sets and numbers of species, bearing either distinct or indistinct functional traits, and compared them to random assemblages, to mimic the consequences of a regional loss of species. Long-term ecosystem productivity dropped when distinct species were lost first from the regional pool of species, under the harshest environmental conditions. On the contrary, productivity was more dependent on ordinary species in milder environments. Our findings show that species functional distinctiveness, integrating multiple trait dimensions, can capture species-specific effects on ecosystem productivity. In a context of an environmentally changing world, they highlight the need to investigate the role of distinct species in sustaining ecosystem processes, particularly in extreme environmental conditions.}, journal = {Proceedings of the Royal Society B: Biological Sciences}, author = {Delalandre, Léo and Gaüzère, Pierre and Thuiller, Wilfried and Cadotte, Marc W. and Mouquet, Nicolas and Mouillot, David and Munoz, François and Denelle, Pierre and Loiseau, Nicolas and Morin, Xavier and Violle, Cyrille}, year = {2022}, keywords = {Biodiversity and ecosystem functioning, Forest-gap model, Functional distinctiveness, Functional rarity, Productivity, Virtual ecology}, pages = {20211694}, annote = {pubid: S0CDQJw8Yr4C}, } @article{Grenie2018, title = {Functional rarity of coral reef fishes at the global scale: {Hotspots} and challenges for conservation}, volume = {226}, issn = {00063207}, doi = {10.1016/j.biocon.2018.08.011}, abstract = {Characterizing functional diversity has become central in ecological research and for biodiversity assessment. Understanding the role of species with rare traits, i.e. functionally rare species, in community assembly, ecosystem dynamics and functioning has recently gained momentum. However, functional rarity is still ignored in conservation strategies. Here, we quantified global functional and evolutionary rarity for 2073 species of coral reef fishes and compared the rarity values to IUCN Red List status. Most species were functionally common but geographically rare. However, we found very weak correlation between functional rarity and evolutionary rarity. Functional rarity was highest for species classified as not evaluated or threatened by the IUCN Red List. The location of functional rarity hotspots (Tropical Eastern Pacific) did not match hotspots of species richness and evolutionary distinctiveness (Indo-Australian Archipelago), nor the currently protected areas. We argue that functional rarity should be acknowledged for both species and site prioritization in conservation strategies.}, number = {August}, journal = {Biological Conservation}, author = {Grenié, Matthias and Mouillot, David and Villéger, Sébastien and Denelle, Pierre and Tucker, Caroline M. and Munoz, François and Violle, Cyrille}, year = {2018}, keywords = {Biodiversity facet, Coral triangle, Evolutionary distinctiveness, Functional distinctiveness, Funrar}, pages = {288--299}, annote = {pubid: gkldIfsazJcC}, } @article{Gross2021, title = {Unveiling ecological assembly rules from commonalities in trait distributions}, volume = {24}, doi = {10.1111/ele.13789}, abstract = {Deciphering the effect of neutral and deterministic processes on community as- sembly is critical to understand and predict diversity patterns. The information held in community trait distributions is commonly assumed as a signature of these processes, but empirical and modelling attempts have most often failed to untangle their confounding, sometimes opposing, impacts. Here, we simulated the assembly of trait distributions through stochastic (dispersal limitation) and/or deterministic scenarios (environmental filtering and niche differentiation). We characterized the shape of trait distributions using the skewness– kurtosis relationship. We identi- fied commonalities in the co- variation between the skewness and the kurtosis of trait distributions with a unique signature for each simulated assembly scenario. Our findings were robust to variation in the composition of regional species pools, dispersal limitation and environmental conditions. While ecological communities can exhibit a high degree of idiosyncrasy, identification of commonalities across multiple communities can help to unveil ecological assembly rules in real- world ecosystems.}, number = {8}, journal = {Ecology Letters}, author = {Gross, Nicolas and Le Bagousse-Pinguet, Yoann and Liancourt, Pierre and Saiz, Hugo and Violle, Cyrille and Munoz, François}, year = {2021}, pages = {1668--1680}, annote = {pubid: 0urtJCGzaFQC}, } @article{Violle2017b, title = {A common toolbox to understand, monitor or manage rarity? {A} response to {Carmona} et al.}, volume = {32}, issn = {01695347}, url = {http://dx.doi.org/10.1016/j.tree.2017.10.001}, doi = {10.1016/j.tree.2017.10.001}, number = {12}, journal = {Trends in Ecology \& Evolution}, author = {Violle, Cyrille and Thuiller, Wilfried and Mouquet, Nicolas and Munoz, François and Kraft, Nathan J. B. and Cadotte, Marc W. and Livingstone, Stuart W. and Grenié, Matthias and Mouillot, David}, year = {2017}, pages = {891--893}, annote = {pubid: 6pF0wJmtdfAC}, } @article{Brun2022, title = {Plant community impact on productivity: {Trait} diversity or key (stone) species effects?}, volume = {25}, doi = {10.1111/ele.13968}, abstract = {Outside controlled experimental plots, the impact of community attributes on primary productivity has rarely been compared to that of individual species. Here, we identified plant species of high importance for productivity (key species) in ¿29,000 diverse grassland communities in the European Alps, and compared their effects with those of community-level measures of functional composition (weighted means, variances, skewness and kurtosis). After accounting for the environment, the five most important key species jointly explained more deviance of productivity than any measure of functional composition alone. Key species were generally tall with high specific leaf areas. By dividing the observations according to distinct habitats, the explanatory power of key species and functional composition increased and key species plant types and functional composition- productivity relationships varied systematically, presumably because of changing interactions and trade-offs between traits. Our results advocate for a careful consideration of species' individual effects on ecosystem functioning in complement to community-level measures.}, journal = {Ecology Letters}, author = {Brun, Philipp and Violle, Cyrille and Mouillot, David and Mouquet, Nicolas and Enquist, Brian J. and Munoz, François and Münkemüller, Tamara and Ostling, Annette and Zimmermann, Niklaus E. and Thuiller, Wilfried}, year = {2022}, keywords = {Community-weighted moments, European Alps, Grassland, Keystone species, Trait driver theory}, pages = {913--925}, annote = {pubid: QI7uKX5mnFEC}, } @article{McLean2019, title = {Trait structure and redundancy determine sensitivity to disturbance in marine fish communities}, volume = {25}, issn = {1354-1013}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14662}, doi = {10.1111/gcb.14662}, abstract = {'Functional' diversity is believed to influence ecosystem dynamics through links between organismal traits and ecosystem processes. Theory predicts that key traits and high trait redundancy-large species richness and abundance supporting the same traits-can buffer communities against environmental disturbances. While experiments and data from simple ecological systems lend support, large-scale evidence from diverse, natural systems under major disturbance is lacking. Here, using long-term data from both temperate (English Channel) and tropical (Seychelles Islands) fishes, we show that sensitivity to disturbance depends on communities' initial trait structure and initial trait redundancy. In both ecosystems, we found that increasing dominance by climatically-vulnerable traits rendered fish communities more sensitive to environmental change, while communities with higher trait redundancy were more resistant. To our knowledge, this is the first study demonstrating the influence of trait structure and redundancy on community sensitivity over large temporal and spatial scales in natural systems. Our results exemplify a consistent link between biological structure and community sensitivity that may be transferable across ecosystems and taxa and could help anticipate future disturbance impacts on biodiversity and ecosystem functioning.}, number = {10}, journal = {Global Change Biology}, author = {McLean, Matthew and Auber, Arnaud and Graham, Nicholas A. J. and Houk, Peter and Villéger, Sébastien and Violle, Cyrille and Thuiller, Wilfried and Wilson, Shaun K. and Mouillot, David}, year = {2019}, keywords = {cnrs, france, ifremer, ird, lancaster, lancaster environment centre, marbec, montpellier cedex, université de montpellier}, pages = {3424--3437}, annote = {pubid: ZYsTHYU9jrMC}, } @article{Sabatini2022, title = {Global patterns of vascular plant alpha diversity}, volume = {13}, issn = {20411723}, doi = {10.1038/s41467-022-32063-z}, abstract = {Global patterns of regional (gamma) plant diversity are relatively well known, but whether these patterns hold for local communities, and the dependence on spatial grain, remain controversial. Using data on 170,272 georeferenced local plant assemblages, we created global maps of alpha diversity (local species richness) for vascular plants at three different spatial grains, for forests and non-forests. We show that alpha diversity is consistently high across grains in some regions (for example, Andean-Amazonian foothills), but regional ‘scaling anomalies' (deviations from the positive correlation) exist elsewhere, particularly in Eurasian temperate forests with disproportionally higher fine-grained richness and many African tropical forests with disproportionally higher coarse-grained richness. The influence of different climatic, topographic and biogeographical variables on alpha diversity also varies across grains. Our multi-grain maps return a nuanced understanding of vascular plant biodiversity patterns that complements classic maps of biodiversity hotspots and will improve predictions of global change effects on biodiversity.}, number = {1}, journal = {Nature Communications}, author = {Sabatini, Francesco Maria and Jiménez-Alfaro, Borja and Jandt, Ute and Chytry, Milan and Field, Richard and Kessler, Michael and Lenoir, Jonathan and Schrodt, Franziska and Wiser, Susan K. and Arfin Khan, Mohammed A. S. and Attorre, Fabio and Cayuela, Luis and De Sanctis, Michele and Dengler, Jürgen and Haider, Sylvia and Hatim, Mohamed Z. and Indreica, Adrian and Jansen, Florian and Pauchard, Aníbal and Peet, Robert K. and Petrik, Petr and Pillar, Valério D. and Sandel, Brody and Schmidt, Marco and Tang, Zhiyao and van Bodegom, Peter and Vassilev, Kiril and Violle, Cyrille and Alvarez-Davila, Esteban and Davidar, Priya and Dolezal, Jiri and Hérault, Bruno and Galán-de-Mera, Antonio and Jiménez, Jorge and Kambach, Stephan and Kepfer-Rojas, Sebastian and Kreft, Holger and Lezama, Felipe and Linares-Palomino, Reynaldo and Monteagudo Mendoza, Abel and N'Dja, Justin K. and Phillips, Oliver L. and Rivas-Torres, Gonzalo and Sklenár, Petr and Speziale, Karina and Strohbach, Ben J. and Vásquez Martínez, Rodolfo and Wang, Hua-Feng and Wesche, Karsten and Bruelheide, Helge}, year = {2022}, pmid = {36050293}, note = {ISBN: 4146702232}, pages = {4683}, } @article{Blonder2018, title = {New approaches for delineating n-dimensional hypervolumes}, volume = {9}, issn = {2041210X}, doi = {10.1111/2041-210X.12865}, abstract = {Introduction: D-dimer assay, generally evaluated according to cutoff points calibrated for VTE exclusion, is used to estimate the individual risk of recurrence after a first idiopathic event of venous thromboembolism (VTE). Methods: Commercial D-dimer assays, evaluated according to predetermined cutoff levels for each assay, specific for age (lower in subjects ¡70 years) and gender (lower in males), were used in the recent DULCIS study. The present analysis compared the results obtained in the DULCIS with those that might have been had using the following different cutoff criteria: traditional cutoff for VTE exclusion, higher levels in subjects aged ≥60 years, or age multiplied by 10. Results: In young subjects, the DULCIS low cutoff levels resulted in half the recurrent events that would have occurred using the other criteria. In elderly patients, the DULCIS results were similar to those calculated for the two age-adjusted criteria. The adoption of traditional VTE exclusion criteria would have led to positive results in the large majority of elderly subjects, without a significant reduction in the rate of recurrent event. Conclusion: The results confirm the usefulness of the cutoff levels used in DULCIS.}, number = {2}, journal = {Methods in Ecology and Evolution}, author = {Blonder, Benjamin and Morrow, Cecina Babich and Maitner, Brian S. and Harris, David J. and Lamanna, Christine and Violle, Cyrille and Enquist, Brian J. and Kerkhoff, Andrew J.}, year = {2017}, keywords = {functional diversity, functional space, hypervolume, kernel density estimation, niche, niche modelling, support vector machine}, pages = {305--319}, annote = {pubid: RVqaWcrwK10C}, } @article{Echeverria-Londono2018, title = {Plant functional diversity and the biogeography of biomes in {North} and {South} {America}}, volume = {6}, issn = {2296-701X}, url = {https://www.frontiersin.org/article/10.3389/fevo.2018.00219/full}, doi = {10.3389/fevo.2018.00219}, abstract = {The concept of the biome has a long history dating back to Carl Ludwig Willdenow and Alexander von Humboldt. However, while the association between climate and the structure and diversity of vegetation has a long history, scientists have only recently begun to develop a more synthetic understanding of biomes based on the evolution of plant diversity, function, and community assembly. At the broadest scales, climate filters species based on their functional attributes, and the resulting functional differences in dominant vegetation among biomes are important to modeling the global carbon cycle and the functioning of the Earth system. Nevertheless, across biomes, plant species have been shown to occupy a common set of global functional ‘spectra,' reflecting variation in overall plant size, leaf economics, and hydraulics. Still, comprehensive measures of functional diversity and assessments of functional similarity have not been compared across biomes at continental to global scales. Here, we examine distributions of functional diversity of plant species across the biomes of North and South America, based on distributional information for ¿80,000 vascular plant species and functional trait data for ca. 8,000 of those species. First, we show that despite progress in data integration and synthesis, significant knowledge shortfalls persist that limit our ability to quantify the functional biodiversity of biomes. Second, our analyses of the available data show that all the biomes in North and South America share a common pattern - most geographically common, widespread species in any biome tend to be functionally similar while the most functionally distinctive species are restricted in their distribution. Third, when only the widespread and functionally similar species in each biome are considered, biomes can be more readily distinguished functionally, and patterns of dissimilarity between biomes appear to reflect a correspondence between climate and functional niche space. Taken together, our results suggest that while the study of the functional diversity of biomes is still in its formative stages, further development of the field will yield insights linking evolution, biogeography, community assembly, and ecosystem function.}, number = {December}, journal = {Frontiers in Ecology and Evolution}, author = {Echeverría-Londoño, Susy and Enquist, Brian J. and Neves, Danilo M. and Violle, Cyrille and Boyle, Brad and Kraft, Nathan J. B. and Maitner, Brian S. and McGill, Brian J. and Peet, Robert K. and Sandel, Brody and Smith, Stephen A. and Svenning, Jens-Christian and Wiser, Susan K. and Kerkhoff, Andrew J.}, year = {2018}, pages = {219}, annote = {pubid: qSd0DAb9jMoC}, } @article{Sala2021, title = {Protecting the global ocean for biodiversity, food and climate}, volume = {592}, issn = {1476-4687}, url = {http://dx.doi.org/10.1038/s41586-021-03371-z}, doi = {10.1038/s41586-021-03371-z}, journal = {Nature}, author = {Sala, Enric and Mayorga, Juan and Bradley, Darcy and Cabral, Reniel B. and Atwood, Trisha B. and Auber, Arnaud and Cheung, William and Costello, Christopher and Ferretti, Francesco and Friedlander, Alan M. and Gaines, Steven D. and Garilao, Cristina and Goodell, Whitney and Halpern, Benjamin S. and Hinson, Audra and Kaschner, Kristin and Kesner-Reyes, Kathleen and Leprieur, Fabien and McGowan, Jennifer and Morgan, Lance E. and Mouillot, David and Palacios-Abrantes, Juliano and Possingham, Hugh P. and Rechberger, Kristin D. and Worm, Boris and Lubchenco, Jane}, year = {2021}, pages = {397--402}, annote = {pubid: SEKBqlyTJecC}, } @article{Denelle2020, title = {Generalist plants are more competitive and more functionally similar to each other than specialist plants: insights from network analyses}, volume = {47}, issn = {13652699}, doi = {10.1111/jbi.13848}, abstract = {Aim: Ecological specialization is defined by the variety of environments species occupy. Identifying the mechanisms that influence specialization is critical to understand patterns of species coexistence and biodiversity. However, the functional attributes that result in specialization are still unknown. Similarly, there is contrasting evidence between the degree of specialization and the local abundance of species. We investigated whether specialist and generalist plant species (a) are associated with distinct functional profiles, using core plant functional traits and strategies, (b) show similar functional variation and (c) perform at the local scale. Location: France. Taxon: Herbaceous plants. Methods: We analysed the structure of a bipartite network that includes the occurrences of ∼2,900 plant species at ∼90,000 sites to identify ecologically consistent sets of species and sites (i.e. ‘modules'). This innovative approach then enabled us to define a metric of specialization, by quantifying occurrences of species at sites that belong to one or several modules. We used functional traits related to resource acquisition, competition for light and dispersal ability, as well as indices of competitive, stress tolerance and ruderal strategies. Results: We identified five major modules in the bipartite network related to different environments and composed of species with differing functional attributes. Specialist species were less competitive and shorter, and had higher stress tolerance and stronger resource conservation, while generalist species were taller. Generalists were also more similar to each other than specialists. In addition, specialists had higher local abundances and occurred in communities with plants of similar height. Main conclusions: We found distinctive functional signatures of specialist and generalist species in grassland communities across diverse environments at regional and community scales. By testing classic macro-ecological hypotheses, network metrics can benefit community ecology by identifying distinct ecological units at a large scale and quantifying the links developed by species.}, number = {9}, journal = {Journal of Biogeography}, author = {Denelle, Pierre and Violle, Cyrille and Munoz, François}, year = {2020}, keywords = {bipartite network, generalist species, grassland, plant functional trait, specialist species, specialization}, pages = {1922--1933}, annote = {pubid: RmcNAhKkducC}, } @article{Enquist2019, title = {The commonness of rarity: {Global} and future distribution of rarity across land plants}, volume = {5}, doi = {10.1126/sciadv.aaz0414}, abstract = {A key feature of life's diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant species observation data in order to quantify the fraction of Earth's extant land plant biodiversity that is common versus rare. Tests of different hypotheses for the origin of species commonness and rarity indicates that sampling biases and prominent models such as niche theory and neutral theory cannot account for the observed prevalence of rare species. Instead, the distribution of commonness is best approximated by heavy-tailed distributions like the Pareto or Poisson-lognormal distributions. As a result, a large fraction, ∼36.5\% of an estimated ∼435k total plant species, are exceedingly rare. We also show that rare species tend to cluster in a small number of ‘hotspots' mainly characterized by being in tropical and subtropical mountains and areas that have experienced greater climate stability. Our results indicate that (i) non-neutral processes, likely associated with reduced risk of extinction, have maintained a large fraction of Earth's plant species but that (ii) climate change and human impact appear to now and will disproportionately impact rare species. Together, these results point to a large fraction of Earth's plant species are faced with increased chances of extinction. Our results indicate that global species abundance distributions have important implications for conservation planning in this era of rapid global change.}, number = {11}, journal = {Science Advances}, author = {Enquist, Brian J. and Feng, Xiao and Boyle, Brad and Maitner, Brian S. and Newman, Erica A. and Jorgensen, Peter Møller and Roehrdanz, Patrick R. and Thiers, Barbara M. and Burger, Joseph R. and Corlett, Richard T. and Couvreur, Thomas L. P. and Dauby, Gilles and Donoghue, John C. and Foden, Wendy and Lovett, Jon C. and Marquet, Pablo A. and Merow, Cory and Midgley, Guy and Morueta-Holme, Naia and Neves, Danilo M. and Oliveira-Filho, Ary T. and Kraft, Nathan J. B. and Park, Daniel S. and Peet, Robert K. and Pillet, Michiel and Serra-Diaz, Josep M. and Sandel, Brody and Schildhauer, Mark P. and Símová, Irena and Violle, Cyrille and Wieringa, Jan J. and Wiser, Susan K. and Hannah, Lee and Svenning, Jens-Christian and McGill, Brian J.}, year = {2019}, pages = {eaaz0414}, annote = {pubid: 43B52WW2E64C}, } @article{Auber2022, title = {A functional vulnerability framework for biodiversity conservation}, volume = {13}, issn = {20411723}, doi = {10.1038/s41467-022-32331-y}, abstract = {Setting appropriate conservation strategies in a multi-threat world is a challenging goal, especially because of natural complexity and budget limitations that prevent effective management of all ecosystems. Safeguarding the most threatened ecosystems requires accurate and integrative quantification of their vulnerability and their functioning, particularly the potential loss of species trait diversity which imperils their functioning. However, the magnitude of threats and associated biological responses both have high uncertainties. Additionally, a major difficulty is the recurrent lack of reference conditions for a fair and operational measurement of vulnerability. Here, we present a functional vulnerability framework that incorporates uncertainty and reference conditions into a generalizable tool. Through in silico simulations of disturbances, our framework allows us to quantify the vulnerability of communities to a wide range of threats. We demonstrate the relevance and operationality of our framework, and its global, scalable and quantitative comparability, through three case studies on marine fishes and mammals. We show that functional vulnerability has marked geographic and temporal patterns. We underline contrasting contributions of species richness and functional redundancy to the level of vulnerability among case studies, indicating that our integrative assessment can also identify the drivers of vulnerability in a world where uncertainty is omnipresent.}, number = {1}, journal = {Nature Communications}, author = {Auber, Arnaud and Waldock, Conor and Maire, Anthony and Goberville, Eric and Albouy, Camille and Algar, Adam C. and McLean, Matthew and Brind'Amour, Anik and Green, Alison L. and Tupper, Mark and Vigliola, Laurent and Kaschner, Kristin and Kesner-Reyes, Kathleen and Beger, Maria and Tjiputra, Jerry and Toussaint, Aurèle and Violle, Cyrille and Mouquet, Nicolas and Thuiller, Wilfried and Mouillot, David}, year = {2022}, pmid = {36050297}, note = {ISBN: 4146702232 Publisher: Springer US}, pages = {4774}, } @article{Denelle2019, title = {Distinguishing the signatures of local environmental filtering and regional trait range limits in the study of trait–environment relationships}, volume = {128}, issn = {16000706}, doi = {10.1111/oik.05851}, abstract = {Understanding the imprint of environmental filtering on community assembly along environmental gradients is a key objective of trait-gradient analyses. Depending on local constraints, this filtering generally entails that species departing from an optimum trait value have lower abundances in the community. The Community-Weighted Mean (CWM) and Variance (CWV) of trait values are then expected to depict the optimum and intensity of filtering, respectively. However, the trait distribution within the regional species pool and its limits can also affect local CWM and CWV values apart from the effect of environmental filtering. The regional trait range limits are more likely to be reached in communities at the extremes of environmental gradients. Analogous to the mid-domain effect in biogeography, decreasing CWV values in extreme environments can then represent the influence of regional trait range limits rather than stronger filtering in the local environment. We name this effect the ?Trait-Gradient Boundary Effect? (TGBE). First, we use a community assembly framework to build simulated communities along a gradient from a species pool and environmental filtering with either constant or varying intensity while accounting for immigration processes. We demonstrate the significant influence of TGBE, in parallel to environmental filtering, on CWM and CWV at the extremes of the environmental gradient. We provide a statistical tool based on Approximate Bayesian Computation to decipher the respective influence of local environmental filtering and regional trait range limits. Second, as a case study, we reanalyze the functional composition of alpine plant communities distributed along a gradient of snow cover duration. We show that leaf trait convergence found in communities at the extremes of the gradient reflect an influence of trait range limits rather than stronger environmental filtering. These findings challenge correlative trait-environment relationships and call for more explicitly identifying the mechanisms responsible of trait convergence/divergence along environmental gradients. This article is protected by copyright. All rights reserved.}, number = {7}, journal = {Oikos (Copenhagen, Denmark)}, author = {Denelle, Pierre and Violle, Cyrille and Munoz, François}, year = {2019}, keywords = {community assembly, environmental filtering, functional biogeography}, pages = {960--971}, annote = {pubid: wlzmIqt2EaEC}, } @article{Murgier2021, title = {Rebound in functional distinctiveness following warming and reduced fishing in the {North} {Sea}}, volume = {288}, doi = {10.1098/rspb.2020.1600}, abstract = {Functionally distinct species (i.e. species with unique trait combinations in the community) can support important ecological roles and contribute dispropor- tionately to ecosystem functioning. Yet, how functionally distinct species have responded to recent climate change and human exploitation has been widely overlooked. Here, using ecological traits and long-term fish data in the North Sea, we identified functionally distinct and functionally common species, andevaluatedtheir spatial andtemporaldynamics in relation to environmental variables and fishing pressure. Functionally distinct specieswere characterized by late sexualmaturity, few, large offspring, andhighparental care, many being sharks and skates that play critical roles in structuring food webs. Both func- tionally distinct and functionally common species increased in abundance as ocean temperatures warmed and fishing pressure decreased over the last three decades; however, functionally distinct species increased throughout the North Sea, but primarily in southern North Sea where fishing was histori- cally most intense, indicating a rebound following fleet decommissioning and reduced harvesting. Yet, some of the most functionally distinct species are cur- rently listed as threatened by the IUCN and considered highly vulnerable to fishing pressure. Alarmingly these species have not rebounded. This work highlights the relevance and potential of integrating functional distinctiveness into ecosystem management and conservation prioritization.}, journal = {Proceedings of the Royal Society B: Biological Sciences}, author = {Murgier, Juliette and McLean, Matthew and Maire, Anthony and Mouillot, David and Loiseau, Nicolas and Munoz, François and Violle, Cyrille and Auber, Arnaud}, year = {2021}, keywords = {conservation, ecological trait, ecosystem functioning, fisheries, functional diversity, global change}, pages = {20201600}, annote = {pubid: 0paDrhnEFY0C}, } @article{Loiseau2020, title = {Global distribution and conservation status of ecologically rare mammal and bird species}, volume = {11}, issn = {2041-1723}, url = {http://dx.doi.org/10.1038/s41467-020-18779-w}, doi = {10.1038/s41467-020-18779-w}, abstract = {Identifying species that are both geographically restricted and functionally distinct, i.e. supporting rare traits and functions, is of prime importance given their risk of extinction and their potential contribution to ecosystem functioning. We use global species distributions and functional traits for birds and mammals to identify the ecologically rare species, understand their characteristics, and identify hotspots. We find that ecologically rare species are disproportionately represented in IUCN threatened categories, insufficiently covered by protected areas, and for some of them sensitive to current and future threats. While they are more abundant overall in countries with a low human development index, some countries with high human development index are also hotspots of ecological rarity, suggesting transboundary responsibility for their conservation. Altogether, these results state that more conservation emphasis should be given to ecological rarity given future environmental conditions and the need to sustain multiple ecosystem processes in the long-term.}, journal = {Nature Communications}, author = {Loiseau, Nicolas and Mouquet, Nicolas and Casajus, Nicolas and Grenié, Matthias and Guéguen, Maya and Maitner, Brian and Mouillot, David and Ostling, Annette and Renaud, Julien and Tucker, Caroline and Velez, Laure and Thuiller, Wilfried and Violle, Cyrille}, year = {2020}, note = {ISBN: 4146702018779}, pages = {5071}, annote = {pubid: 5p9vMBpPSXYC}, }