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Functional diversity (FD), the diversity of organism attributes that relates to their interactions with the abiotic and biotic environment, has been increasingly used for the last two decades in ecology, biogeography and conservation. Yet, FD has many facets and their estimations are not standardized nor embedded in a single tool. mFD (multifaceted functional diversity) is an R package that uses matrices of species assemblages and species trait values as building blocks to compute most FD indices. mFD is firstly based on two functions allowing the user to summarize trait and assemblage data. Then it calculates trait‐based distances between species pairs, informs the user whether species have to be clustered into functional entities and finally computes multidimensional functional space. To let the user choose the most appropriate functional space for computing multidimensional functional diversity indices, two mFD functions allow assessing and illustrating the quality of each functional space. Next, mFD provides 6 core functions to calculate 16 existing FD indices based on trait‐based distances, functional entities or species position in a functional space. The mFD package also provides graphical functions based on the ggplot library to illustrate FD values through customizable and high‐resolution plots of species distribution among functional entities or in a multidimensional space. All functions include internal validation processes to check for errors in data formatting which return detailed error messages. To facilitate the use of mFD framework, we built an associated website hosting five tutorials illustrating the use of all the functions step by step. [ABSTRACT FROM AUTHOR]

Species' traits, rather than taxonomic identities, determine community assembly and ecosystem functioning, yet biogeographic patterns have been far less studied for traits. While both environmental conditions and evolutionary history shape trait biogeography, their relative contributions are largely unknown for most organisms. Here, we explore the global biogeography of reef fish traits for 2,786 species from 89 ecoregions spanning eight marine realms with contrasting environmental conditions and evolutionary histories. Across realms, we found a common structure in the distribution of species traits despite a 10-fold gradient in species richness, with a defined "backbone" of 21 trait combinations shared by all realms globally, both temperate and tropical. Across ecoregions, assemblages under similar environmental conditions had similar trait compositions despite hosting drastically different species pools from separate evolutionary lineages. Thus, despite being separated by thousands of kilometers and millions of years of evolution, similar environments host similar trait compositions in reef fish assemblages worldwide. Our findings suggest that similar trait-based management strategies can be applied among regions with distinct species pools, potentially improving conservation outcomes across diverse jurisdictions. [ABSTRACT FROM AUTHOR]

Aim: To determine which morphological characteristics make a fish species a good candidate for introduction and establishment, we tested whether (a) introduced species differ in morphology from non‐introduced species (species only existing in native areas and not introduced to new areas) in each donor assemblage (biogeographic realm fauna); (b) within the introduced species, the morphology of established species (self‐sustaining introduced species) differs from that of the non‐established species; (c) within the established species, those exported out of their native realm have more extreme morphological traits than those translocated within their native realm. Major taxa studied: Freshwater fish. Location: Global. Time period: 1960s–2010s. Methods: We used a global database of freshwater fishes from the six realms. Ten morphological traits were measured on 9,150 species. Principal component analysis was conducted to combine the 10 traits into a multidimensional morphospace. We used permutational multivariate analysis of variance (PERMANOVA) and permutational analysis for the multivariate homogeneity of dispersions (PERMDISP2) to compare the distribution of species groups in the morphospace and Kolmogorov–Smirnov tests to compare their distributions on principal component (PC) axes. Results: The morphology of introduced species differed from that of non‐introduced species in all the six biogeographic realms. Among introduced species, established species had more extreme morphological traits than non‐established species in most realms. Among established species, exported species had more extreme morphological traits than translocated species. Main conclusions: Morphological differences between introduced and non‐introduced species was driven by an anthropogenic trait selection for fisheries and angling, leading to the preference for the introduction of predators with large and laterally compressed bodies. Established species represent a small subset of introduced species morphologies, with established species having more extreme morphological traits than their non‐established counterparts. Established fish have morphologies more adapted to lentic waters, and this trend was more marked for species exported to other realms than for species translocated within their native realm. [ABSTRACT FROM AUTHOR]

The role of speciation processes in shaping current biodiversity patterns represents a major scientific question for ecologists and biogeographers. Hence, numerous methods have been developed to determine the geography of speciation based on co‐occurrence between sister‐species. Most of these methods rely on the correlation between divergence time and several metrics based on the geographic ranges of sister‐taxa (i.e. overlap, asymmetry). The relationship between divergence time and these metrics has scarcely been examined in a spatial context beyond regression curves. Mapping this relationship across spatial grids, however, may unravel how speciation processes have shaped current biodiversity patterns through space and time. This can be particularly relevant for coral reef fishes of the Indo‐Pacific since the origin of the exceptional concentration of biodiversity in the Indo‐Australian Archipelago (IAA) has been actively debated, with several alternative hypotheses involving species diversification and dispersal. We reconstructed the phylogenetic relationships between three species‐rich families of coral reef fish (Chaetodontidae, Labridae, Pomacentridae) and calculated co‐occurrence metrics between closely related lineages of those families. We demonstrated that repeated biogeographic processes can be identified in present‐day species distribution by projecting co‐occurrence metrics between related lineages in a geographical context. Our study also evidence that sister‐species do not co‐occur randomly across the Indo‐Pacific, but tend to overlap their range within the IAA. We identified the imprint of two important biogeographic processes that caused this pattern in 48% of the sister‐taxa considered: speciation events within the IAA and repeated divergence between the Indian and Pacific Ocean, with subsequent secondary contact in the IAA. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Aim In this paper, we applied the concept of 'hierarchical filters' in community ecology to model marine species distribution at nested spatial scales. Location Global, Mediterranean Sea and the Gulf of Gabes ( Tunisia). Methods We combined the predictions of bioclimatic envelope models ( BEMs) and habitat models to assess the current distribution of 20 exploited marine species in the Gulf of Gabes. BEMs were first built at a global extent to account for the full range of climatic conditions encountered by a given species. Habitat models were then built using fine-grained habitat variables at the scale of the Gulf of Gabes. We also used this hierarchical filtering approach to project the future distribution of these species under both climate change (the A2 scenario implemented with the Mediterranean climatic model NEMOMED8) and habitat loss (the loss of Posidonia oceanica meadows) scenarios. Results The hierarchical filtering approach predicted current species geographical ranges to be on average 56% smaller than those predicted using the BEMs alone. This pattern was also observed under the climate change scenario. Combining the habitat loss and climate change scenarios indicated that the magnitude of range shifts due to climate change was larger than from the loss of P. oceanica meadows. Main conclusions Our findings emphasize that BEMs may overestimate current and future ranges of marine species if species-habitat relationships are not also considered. A hierarchical filtering approach that accounts for fine-grained habitat variables limits the uncertainty associated with model-based recommendations, thus ensuring their outputs remain applicable within the context of marine resource management. [ABSTRACT FROM AUTHOR]

Bottom trawl survey data are commonly used as a sampling technique to assess the spatial distribution of commercial species. However, this sampling technique does not always correctly detect a species even when it is present, and this can create significant limitations when fitting species distribution models. In this study, we aim to test the relevance of a mixed methodological approach that combines presence-only and presence-absence distribution models. We illustrate this approach using bottom trawl survey data to model the spatial distributions of 27 commercially targeted marine species. We use an environmentally- and geographically-weighted method to simulate pseudo-absence data. The species distributions are modelled using regression kriging, a technique that explicitly incorporates spatial dependence into predictions. Model outputs are then used to identify areas that met the conservation targets for the deployment of artificial anti-trawling reefs. To achieve this, we propose the use of a fuzzy logic framework that accounts for the uncertainty associated with different model predictions. For each species, the predictive accuracy of the model is classified as ‘high’. A better result is observed when a large number of occurrences are used to develop the model. The map resulting from the fuzzy overlay shows that three main areas have a high level of agreement with the conservation criteria. These results align with expert opinion, confirming the relevance of the proposed methodology in this study. [ABSTRACT FROM AUTHOR]

Aim To forecast the potential effects of climate change in the Mediterranean Sea on the species richness and mean body size of coastal fish assemblages. Location The Mediterranean Sea. Methods Using an ensemble forecasting approach, we used species distribution modelling to project the potential distribution of 288 coastal fish species by the middle and end of the 21st century based on the IPCC A2 scenario implemented with the Mediterranean climatic model NEMOMED8. Results A mean rise of 1.4 °C was projected for the Mediterranean Sea by the middle of the 21st century and 2.8 °C by the end of the 21st century. Projections for the end of the century suggest that: (1) 54 species are expected to lose their climatically suitable habitat, (2) species richness was predicted to decrease across 70.4% of the continental shelf area, especially in the western Mediterranean Sea and several parts of the Aegean Sea, and (3) mean fish body size would increase over 74.8% of the continental shelf area. Small-bodied species that are not targeted by either commercial or recreational fleets presented, on average, the highest predicted decrease in geographic range size. Main conclusions Projected climate change in the Mediterranean Sea may have deleterious effects on coastal fish diversity, including a significant loss of climatically suitable habitat for endemic fish species. In addition, climate change may contribute to the loss of small and low trophic-level fishes, which may have ecosystem-wide impacts by reducing food supply to larger and higher trophic-level species. Fishing pressure is already selectively removing large-bodied species from marine ecosystems, and so fishing and climatic change might act in tandem to drive both direct and secondary extinctions. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim To explore global patterns of riverine fish endemism by applying an island biogeography framework to river drainage basins and highlight evolutionary mechanisms producing two kinds of endemism: neo-endemism, arising from within-drainage cladogenetic speciation, and palaeo-endemism, arising from species range contraction or anagenetic speciation. Location World-wide. Methods We use a uniquely comprehensive data set of riverine fish species distributions to map global fish endemism patterns. We then use the relationships between (1) total species richness and proportions of endemic species and (2) total species richness and a measure of in situ (i.e. within-drainage basin) probability of speciation by cladogenesis, to identify the two distinct forms of endemism. After separating drainage basins into two different sets according to dominance of one of these two forms, we apply a model averaging procedure to highlight, for both datasets, the environmental and historical variables that better explain endemism patterns. We finally analyse the effect of biotic components related to dispersal ability on the percentages of both kinds of endemism among lineages. Results Our results indicate that the two types of endemism are distributed differently across space and taxonomic lineages: (1) neo-endemism, positively related to the overall richness of the drainage basin, is essentially linked to in situ cladogenetic speciation and is positively related to drainage basin area, negatively related to climate variability since glacial periods and negatively related to all proxies of dispersal ability; and (2) palaeo-endemism, not directly contributing to drainage basin richness, is a pure process of extinction through range contraction and/or isolation through time and is mostly related to geographic isolation, glacial history and positively related to marine-derived origin of families. Main conclusions The non-random spatial and taxonomic distribution of neo-endemism and palaeo-endemism sharply reflects the role of evolutionary processes and provides a way to identify areas of high conservation interest based on their high present and future diversification potential. [ABSTRACT FROM AUTHOR]

The FishMed database provides traits, phylogeny, current and projected species distribution of Mediterranean fishes, and associated sea surface temperature (SST) from the regional oceanic model NEMOMED8. Data for the current geographical distributions of 635 Mediterranean fish species were compiled from a published expert knowledge atlas of fishes of the northern Atlantic and the Mediterranean (FNAM) edited between 1984 and 1986 and from an updated exotic fish species list. Two future sets of projected species distributions were obtained for the middle and end of the 21st century by using an ensemble forecasting approach for 288 coastal Mediterranean fish species based on SST according to the IPPC/SRES A2 scenario implemented with the Mediterranean climatic model NEMOMED8. The functional part of the database encompasses 12 biological and ecological traits (maximal and common lengths, vertical distribution, habitat, migration type, mode of reproduction, sex shift, semelparity, diet type (larvae and adults), social behavior, species origin, and depth) for the 635 fish species. To build the phylogeny we inferred the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank including 62% ofMediterranean teleost species plus nine outgroups. Maximum likelihood Bayesian phylogenetic and dating analyses were calibrated using 20 fossil species. An additional 124 fish species were grafted onto the chronogram according to their taxonomic affinity to obtain a phylogenetic tree including 498 species. Finally we also present the associated SST data for the observed period (1961-1980) and for themiddle (2040-2059) and the end of the 21st century (2080-2099) obtained fromNEMOMED8 according to the IPCC A2 scenario. The FishMed database might be of interest in the context of global anthropogenic changes as coastal Mediterranean ecosystems are currently recognized as one of the most impacted ecosystems on earth. [ABSTRACT FROM AUTHOR]