2020 |
Albouy, C., et al. "Global vulnerability of marine mammals to global warming." Sci Rep. 10.1 (2020): 548.
Résumé: Although extinctions due to climate change are still uncommon, they might surpass those caused by habitat loss or overexploitation over the next few decades. Among marine megafauna, mammals fulfill key and irreplaceable ecological roles in the ocean, and the collapse of their populations may therefore have irreversible consequences for ecosystem functioning and services. Using a trait-based approach, we assessed the vulnerability of all marine mammals to global warming under high and low greenhouse gas emission scenarios for the middle and the end of the 21st century. We showed that the North Pacific Ocean, the Greenland Sea and the Barents Sea host the species that are most vulnerable to global warming. Future conservation plans should therefore focus on these regions, where there are long histories of overexploitation and there are high levels of current threats to marine mammals. Among the most vulnerable marine mammals were several threatened species, such as the North Pacific right whale (Eubalaena japonica) and the dugong (Dugong dugon), that displayed unique combinations of functional traits. Beyond species loss, we showed that the potential extinctions of the marine mammals that were most vulnerable to global warming might induce a disproportionate loss of functional diversity, which may have profound impacts on the future functioning of marine ecosystems worldwide.
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Arneth, A., et al. "Post-2020 biodiversity targets need to embrace climate change." Pnas. 117.49 (2020): 30882–30891.
Résumé: Recent assessment reports by the Intergovernmental Panel on Climate Change (IPCC) and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) have highlighted the risks to humanity arising from the unsustainable use of natural resources. Thus far, land, freshwater, and ocean exploitation have been the chief causes of biodiversity loss. Climate change is projected to be a rapidly increasing additional driver for biodiversity loss. Since climate change and biodiversity loss impact human societies everywhere, bold solutions are required that integrate environmental and societal objectives. As yet, most existing international biodiversity targets have overlooked climate change impacts. At the same time, climate change mitigation measures themselves may harm biodiversity directly. The Convention on Biological Diversity’s post-2020 framework offers the important opportunity to address the interactions between climate change and biodiversity and revise biodiversity targets accordingly by better aligning these with the United Nations Framework Convention on Climate Change Paris Agreement and the Sustainable Development Goals. We identify the considerable number of existing and proposed post-2020 biodiversity targets that risk being severely compromised due to climate change, even if other barriers to their achievement were removed. Our analysis suggests that the next set of biodiversity targets explicitly addresses climate change-related risks since many aspirational goals will not be feasible under even lower-end projections of future warming. Adopting more flexible and dynamic approaches to conservation, rather than static goals, would allow us to respond flexibly to changes in habitats, genetic resources, species composition, and ecosystem functioning and leverage biodiversity’s capacity to contribute to climate change mitigation and adaptation.
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Brandt, M., et al. "An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities." Front. Mar. Sci.. 7 (2020): 234.
Résumé: The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removing short DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from similar to 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (>= 10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNA for logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (>= 10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.
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Chiarello, M., et al. "Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes." Proc. R. Soc. B-Biol. Sci.. 287.1927 (2020): 20200642.
Résumé: Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However, the diversity of such microbiomes is mostly described in a few coral species and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the total microbial diversity of coral reefs could be important, yet potentially vulnerable to the loss of animal species. Analysis of the surface microbiome from 74 taxa, including teleost fishes, hard and soft corals, crustaceans, echinoderms, bivalves and sponges, revealed that more than 90% of their prokaryotic phylogenetic richness was specific and not recovered in surrounding plankton. Estimate of the total richness associated with coral reef animal surface microbiomes reached up to 2.5% of current estimates of Earth prokaryotic diversity. Therefore, coral reef animal surfaces should be recognized as a hotspot of marine microbial diversity. Loss of the most vulnerable reef animals expected under present-day scenarios of reef degradation would induce an erosion of 28% of the prokaryotic richness, with unknown consequences on coral reef ecosystem functioning.
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Clavareau, L., et al. "Elasmobranch bycatch distributions and mortality: Insights from the European tropical tuna purse-seine fishery." Global Ecology and Conservation. 24 (2020): e01211.
Résumé: Despite bycatch of elasmobranch (sharks and rays) being a major concern in most fisheries worldwide, there is a lack of knowledge on their spatio-temporal species distribution, biology (life stage and sex-ratios), as well as their at-haulback mortality rate. Observer data from the French and Spanish tropical purse-seine tuna fisheries operating in the eastern Atlantic and western Indian Oceans between 2005 and 2017 were analysed to investigate elasmobranch bycatch. Data included 24 elasmobranchs species and distribution patterns of catch per unit of effort (CPUE) by species and sex-ratio were found to vary with life stages, areas, seasons and fishing modes. In general, higher catches were found in FAD-associated sets (>40%) than free tuna school sets (<17%) although this can vary depending on the species. For the large majority of species, a high proportion of juveniles were caught (30.7–100%), apparent at-haulback mortality rates was high (24.3–63.9%) and finally sex ratios was unbalanced (13.3–66.7% of females). Areas and seasons identified from these different components should be of interest for the monitoring and management of elasmobranch bycatches.
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Du, X., et al. "Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process." Mol. Ecol. (2020).
Résumé: Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0-20 cm, Middle: 20-40 cm, and Substratum: 40-100 cm) in a typical grassland by examining both distance-decay (DDRs) and species-area relationships (SARs), taxonomically and phylogenetically, as well as community assembly processes. Each layer exhibited significant biogeographic patterns in both DDR and SAR (p < .05), with taxonomic turnover rates higher than phylogenetic ones. Specifically, the spatial turnover rates, beta and z values, respectively, ranged from 0.016 +/- 0.005 to 0.023 +/- 0.005 and 0.065 +/- 0.002 to 0.077 +/- 0.004 across soil strata, and both increased with depth. Moreover, the prokaryotic community in grassland soils assembled mainly according to deterministic rather than stochastic mechanisms. By using normalized stochasticity ratio (NST) based on null model, the relative importance of deterministic ratios increased from 48.0 to 63.3% from Upper to Substratum, meanwhile a phylogenetic based method revealed average beta NTI also increased with depth, from -5.29 to 19.5. Using variation partitioning and distance approaches, both geographic distance and soil properties were found to strongly affect biodiversity structure, the proportions increasing with depth, but spatial distance was always the main underlying factor. These indicated increasingly deterministic proportions in accelerating turnover rates for spatial assembly of prokaryotic biodiversity. Our study provided new insights on biogeography in different strata, revealing importance of assembly patterns and mechanisms of prokaryote communities in below-surface soils.
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Hill, S. L., et al. "Reference points for predators will progress ecosystem-based management of fisheries." Fish and Fisheries. 21.2 (2020): 368–378.
Résumé: Ecosystem-based management of fisheries aims to allow sustainable use of fished stocks while keeping impacts upon ecosystems within safe ecological limits. Both the FAO Code of Conduct for Responsible Fisheries and the Aichi Biodiversity Targets promote these aims. We evaluate implementation of ecosystem-based management in six case-study fisheries in which potential indirect impacts upon bird or mammal predators of fished stocks are well publicized and well studied. In particular, we consider the components needed to enable management strategies to respond to information from predator monitoring. Although such information is available in all case-studies, only one has a reference point defining safe ecological limits for predators and none has a method to adjust fishing activities in response to estimates of the state of the predator population. Reference points for predators have been developed outside the fisheries management context, but adoption by fisheries managers is hindered a lack of clarity about management objectives and uncertainty about how fishing affects predator dynamics. This also hinders the development of adjustment methods because these generally require information on the state of ecosystem variables relative to reference points. Nonetheless, most of the case-studies include precautionary measures to limit impacts on predators. These measures are not used tactically and therefore risk excessive restrictions on sustainable use. Adoption of predator reference points to inform tactical adjustment of precautionary measures would be an appropriate next step towards ecosystem-based management.
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Jeliazkov, A., et al. "A global database for metacommunity ecology, integrating species, traits, environment and space." Sci. Data. 7.1 (2020): 6.
Résumé: The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.
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Lacoste, E., C. W. McKindsey, and P. Archambault. "Biodiversity–Ecosystem Functioning (BEF) approach to further understanding aquaculture–environment interactions with application to bivalve culture and benthic ecosystems." Reviews in Aquaculture (2020).
Résumé: Coastal benthic ecosystems may be impacted by numerous human activities, including aquaculture, which continues to expand rapidly. Indeed, today aquaculture worldwide provides more biomass for human consumption than do wild fisheries. This rapid development raises questions about the interactions the practice has with the surrounding environment. In order to design strategies of sustainable ecosystem exploitation and marine spatial planning, a better understanding of coastal ecosystem functioning is needed so that tools to quantify impacts of human activities, including aquaculture, may be developed. To achieve this goal, some possible directions proposed are integrated studies leading to new concepts, model development based on these concepts and comparisons of various ecosystems on a global scale. This review draws on existing literature to (i) briefly summarize the major ecological interactions between off-bottom shellfish aquaculture and the environment, (ii) introduce research on the influence of benthic diversity on ecosystem functioning (BEF relationships) and (iii) propose a holistic approach to conduct aquaculture–environment studies using a BEF approach, highlighting the need for integrated studies that could offer insights and perspectives to guide future research efforts and improve the environmental management of aquaculture.
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Leclerc, C., et al. "Global changes threaten functional and taxonomic diversity of insular species worldwide." Divers. Distrib.. 26.4 (2020): 402–414.
Résumé: Aim The assessment of biodiversity patterns under global changes is currently biased towards taxonomic diversity, thus overlooking the ecological and functional aspects of species. Here, we characterized both taxonomic and functional diversity of insular biodiversity threatened by multiple threats. Location Worldwide islands (n = 4,348). Methods We analysed the relative importance of eleven major threats, including biological invasions or climate change, on 2,756 insular endemic mammals and birds. Species were functionally described using five ecological traits related to diet, habitat and body mass. We computed complementary taxonomic and functional diversity indices (richness, specialization, originality and vulnerability) of species pools affected by each threatening process to investigate relationships between diversity dimensions and threats. We also determined whether species-specific traits are associated with specific threats. Results On average, 8% of insular endemic species at risk of extinction are impacted by threats, while 20% of their functional richness is affected. However, a marked disparity in functional richness values associated with each threat can be highlighted. In particular, cultivation and wildlife exploitation are the greatest threats to insular endemic species. Moreover, each threat may contribute to the loss of at least 10% of functional diversity, because it affects threatened species that support unique and extreme functions. Finally, we found complex patterns of species-specific traits associated with particular threats that is not explain by the threatening processes (directly affecting survival or modifying habitat). For instance, cultivation threatens very large mammals, while urbanization threatens very small mammals. Main conclusions These findings reinforce the importance of exploring the vulnerability of biodiversity facets in the face of multiple threats. Anthropogenic pressures may result in a loss of unique functions within insular ecosystems, which provides important insights into the understanding of threatening processes at a global scale.
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Legras, G., et al. "Assessing functional diversity: the influence of the number of the functional traits." Theor. Ecol.. 13.1 (2020): 117–126.
Résumé: The impact of the variation of the number of functional traits on functional diversity assessment is still poorly known. Although the covariation between these two parameters may be desirable in some situations (e.g. if adding functional traits provides relevant new functional information), it may also result from mathematical artefacts and lead to misinterpretation of the results obtained. Here, we have tested the behaviour of a set of nine indices widely used for assessing the three main components of functional diversity (i.e. functional richness, evenness and divergence), according to the variation in the number of functional traits. We found that the number of functional traits may strongly impact the values of most of the indices considered, whatever the functional information they contain. The FRic, TOP and n-hypervolume indices that have been developed to characterize the functional richness component appeared to be highly sensitive to the variation in the number of traits considered. Regarding functional divergence, most of the indices considered (i.e. Q, FDis and FSpe) also showed a high degree of sensitivity to the number of traits considered. In contrast, we found that indices used to compute functional evenness (FEve and Ru), as well as one of the indices related to functional divergence (FDiv), are weakly influenced by the variation in the number of traits. All these results suggest that interpretation of most of the functional diversity indices considered cannot only be based on their values as they are, but requires taking into account the way in which they have been computed.
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Loiseau, N., et al. "Global distribution and conservation status of ecologically rare mammal and bird species." Nat. Commun.. 11.1 (2020): 5071.
Résumé: 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. There are many available ways to rank species for conservation prioritization. Here the authors identify species of mammals and birds that are both spatially restricted and functionally distinct, finding that such species are currently insufficiently protected and disproportionately sensitive to current and future threats.
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Marques, V., et al. "Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences." Ecography (2020).
Résumé: Human activities impact all ecosystems on Earth, which urges scientists to better understand biodiversity changes across temporal and spatial scales. Environmental DNA (eDNA) metabarcoding is a promising non-invasive method to assess species composition in a wide range of ecosystems. Yet, this method requires the completeness of a reference database, i.e. a list of DNA sequences attached to each species of the regional pool, which is rarely met. As an alternative, molecular operational taxonomic units (MOTUs) can be extracted as clusters of sequences. However, the extent to which the diversity of MOTUs can predict the diversity of species across spatial scales is unknown. Here, we used 196 samples along the Rhone river (France) for which the reference database is complete to assess whether a blind eDNA approach can reliably predict the ground-truth number of species at different spatial scales. Using the 12S rDNA teleo primer, we curated and clustered 60 million sequences into MOTUs using a new assembled bioinformatic pipeline. We show that stringent quality filters were necessary to remove artefact noise, notably MOTUs present in a single PCR replicate, which represented 55% of MOTUs (103). Post-clustering cleaning also removed 19 additional erroneous MOTUs and only discarded one truly present species. We then show that the diversity of retained fish MOTUs accurately predicted the local (alpha, r = 0.98) and regional (gamma) ground-truth species diversity (67 MOTUs versus 63 species), but also the species dissimilarity between samples (beta-diversity, r = 0.98). This work paves the way towards extending the use of eDNA metabarcoding in community ecology and biogeography despite major gaps in genetic reference databases.
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Marsac, F., et al. "Seamounts, plateaus and governance issues in the southwestern Indian Ocean, with emphasis on fisheries management and marine conservation, using the Walters Shoal as a case study for implementing a protection framework." Deep Sea Research Part II: Topical Studies in Oceanography. 176 (2020): 104715.
Résumé: There is a growing interest in the management of seamounts of the Southwestern Indian Ocean (SWIO) both in waters under national jurisdictions and in the Areas Beyond National Jurisdiction (ABNJ). New scientific knowledge has been gathered through various oceanographic cruises during the past decade, and new agreements are under consideration globally to promote conservation and sustainable use of the biodiversity in the ABNJ, where the deep sea ecosystems associated with seamounts are a growing matter of concern. SWIO seamounts have attracted the interests of fishers since the 1960s, and contracts for mining exploration have been granted recently. Seamounts are known to shelter rich, fragile and poorly resilient ecosystems whose important ecological functions are threatened by various anthropogenic pressures. Whereas many seamounts and shoals are located in national waters, many others fall in the ABNJ, with no current legal status per se. To ensure conservation of their habitats and biodiversity, it is essential that protection measures are instigated under an internationally recognized legal and institutional framework. In this paper, we review the current state of such a framework relevant to seamounts, with emphasis on fisheries and conservation in the SWIO. An emblematic seamount, the Walters Shoal, is selected as a case study to discuss how it could become a fully-protected space in the ABNJ. As a large part of the SWIO is under the mandate of the Nairobi Convention (as a Regional Sea under the auspices of UNEP), guidelines are proposed to encourage dedicated seamount governance within the framework of this Convention.
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Mouton, T. L., et al. "Increasing climate-driven taxonomic homogenization but functional differentiation among river macroinvertebrate assemblages." Glob. Change Biol. (2020).
Résumé: Global change is increasing biotic homogenization globally, which modifies the functioning of ecosystems. While tendencies towards taxonomic homogenization in biological communities have been extensively studied, functional homogenization remains an understudied facet of biodiversity. Here, we tested four hypotheses related to long-term changes (1991-2016) in the taxonomic and functional arrangement of freshwater macroinvertebrate assemblages across space and possible drivers of these changes. Using data collected annually at 64 river sites in mainland New Zealand, we related temporal changes in taxonomic and functional spatial beta-diversity, and the contribution of individual sites to beta-diversity, to a set of global, regional, catchment and reach-scale environmental descriptors. We observed long-term, mostly climate-induced, temporal trends towards taxonomic homogenization but functional differentiation among macroinvertebrate assemblages. These changes were mainly driven by replacements of species and functional traits among assemblages, rather than nested species loss. In addition, there was no difference between the mean rate of change in the taxonomic and functional facets of beta-diversity. Climatic processes governed overall population and community changes in these freshwater ecosystems, but were amplified by multiple anthropogenic, topographic and biotic drivers of environmental change, acting widely across the landscape. The functional diversification of communities could potentially provide communities with greater stability, resistance and resilience capacity to environmental change, despite ongoing taxonomic homogenization. Therefore, our study highlights a need to further understand temporal trajectories in both taxonomic and functional components of species communities, which could enable a clearer picture of how biodiversity and ecosystems will respond to future global changes.
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Puerta, P., et al. "Influence of Water Masses on the Biodiversity and Biogeography of Deep-Sea Benthic Ecosystems in the North Atlantic." Front. Mar. Sci.. 7 (2020): 239.
Résumé: Circulation patterns in the North Atlantic Ocean have changed and re-organized multiple times over millions of years, influencing the biodiversity, distribution, and connectivity patterns of deep-sea species and ecosystems. In this study, we review the effects of the water mass properties (temperature, salinity, food supply, carbonate chemistry, and oxygen) on deep-sea benthic megafauna (from species to community level) and discussed in future scenarios of climate change. We focus on the key oceanic controls on deep-sea megafauna biodiversity and biogeography patterns. We place particular attention on cold-water corals and sponges, as these are ecosystem-engineering organisms that constitute vulnerable marine ecosystems (VME) with high associated biodiversity. Besides documenting the current state of the knowledge on this topic, a future scenario for water mass properties in the deep North Atlantic basin was predicted. The pace and severity of climate change in the deep-sea will vary across regions. However, predicted water mass properties showed that all regions in the North Atlantic will be exposed to multiple stressors by 2100, experiencing at least one critical change in water temperature (+2 degrees C), organic carbon fluxes (reduced up to 50%), ocean acidification (pH reduced up to 0.3), aragonite saturation horizon (shoaling above 1000 m) and/or reduction in dissolved oxygen (> 5%). The northernmost regions of the North Atlantic will suffer the greatest impacts. Warmer and more acidic oceans will drastically reduce the suitable habitat for ecosystem-engineers, with severe consequences such as declines in population densities, even compromising their long-term survival, loss of biodiversity and reduced biogeographic distribution that might compromise connectivity at large scales. These effects can be aggravated by reductions in carbon fluxes, particularly in areas where food availability is already limited. Declines in benthic biomass and biodiversity will diminish ecosystem services such as habitat provision, nutrient cycling, etc. This study shows that the deep-sea VME affected by contemporary anthropogenic impacts and with the ongoing climate change impacts are unlikely to withstand additional pressures from more intrusive human activities. This study serves also as a warning to protect these ecosystems through regulations and by tempering the ongoing socio-political drivers for increasing exploitation of marine resources.
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Soares, A., et al. "Feeding habits and population aspects of the spotted goatfish, Pseudupeneus maculatus (Perciformes: Mullidae), on the continental shelf of northeast Brazil." Sci. Mar.. 84.2 (2020): 119–131.
Résumé: This study provides information about the feeding habits, population aspects and spatial distribution of the spotted goatfish, Pseudupeneus maculatus, along the coast of the tropical Brazilian continental shelf. Distribution patterns are described using length frequencies and catch rates. Stable isotope ratios of carbon (delta C-13) and nitrogen (delta N-15), along with stomach contents, were analysed to determine the diet of the spotted goatfish. Multivariate analysis and numerical indicators of the diet, such as numerical frequency. frequency of occurrence and weight percentage, were computed to evaluate the diet composition. The mean trophic position was defined using both stable isotope ratios and stomach content analysis. The length at first maturity for the species was determined as 13.7 cm. A slight pattern in size distribution was observed, with mean size increasing with depth along the shelf. The diet was mainly composed of crustaceans, teleosts and Polychaeta. No clear dietary difference was found between habitat types, water depth or latitude. Both trophic positions estimated by stable isotopes and stomach contents analysis ranged between levels 3 and 4. P. maculatus was found to be feeding on many rare and infrequent prey items, classifying it as a generalist zoobenthivorous predator, probably due to its efficient search strategy.
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Villon, S., et al. "A new method to control error rates in automated species identification with deep learning algorithms." Sci Rep. 10.1 (2020): 10972.
Résumé: Processing data from surveys using photos or videos remains a major bottleneck in ecology. Deep Learning Algorithms (DLAs) have been increasingly used to automatically identify organisms on images. However, despite recent advances, it remains difficult to control the error rate of such methods. Here, we proposed a new framework to control the error rate of DLAs. More precisely, for each species, a confidence threshold was automatically computed using a training dataset independent from the one used to train the DLAs. These species-specific thresholds were then used to post-process the outputs of the DLAs, assigning classification scores to each class for a given image including a new class called “unsure”. We applied this framework to a study case identifying 20 fish species from 13,232 underwater images on coral reefs. The overall rate of species misclassification decreased from 22% with the raw DLAs to 2.98% after post-processing using the thresholds defined to minimize the risk of misclassification. This new framework has the potential to unclog the bottleneck of information extraction from massive digital data while ensuring a high level of accuracy in biodiversity assessment.
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2019 |
Alves-Júnior, F. D. A., et al. "Taxonomy of deep-sea shrimps of the Superfamily Oplophoroidea Dana 1852 (Decapoda: Caridea) from Southwestern Atlantic." Zootaxa. 4613.3 (2019): 401–442.
Résumé: In this paper, we provide some available information about the occurrence and some taxonomic aspects of 19 species from the Superfamily Oplophoroidea in the southwestern Atlantic (Brazilian waters), with the update to 22 species of Oplophoroidea occurring in Brazilian waters. Samples were collected during two sets of surveys. The first was performed in 2009 and 2011 in the Potiguar Basin in northeast of Brazil (03–05°S; 38–35°W; between the States of Ceará and Rio Grande do Norte) under the framework of the project “Avaliação da biota bentônica e planctônica da Bacia Potiguar e Ceará (Bpot)”, with samples collected from bottom trawls in the continental slope at depth ranging from 150–2068 m. Second, under the in the framework of the ABRACOS (Acoustic along the Brazilian coast), performed in 2015 and 2017 on seamounts and offshore areas in Northeast Brazil (Ceará Chain, Rio Grande do Norte and Rocas Atoll, Fernando de Noronha Archipelago and Pernambuco State), with samples with pelagic micronekton and mesopelagic nets, in depths ranging from 50–1260 m. We highlight the occurrence of 14 species of the family Acanthephyridae and 5 species of the family Oplophoridae, including the first occurrences of five species to Brazilian deep waters: Acanthephyra kingsleyi Spence Bate, 1888, Ephyrina ombango Crosnier & Forest, 1973, Meningodora compsa (Chace, 1940), M. longisulca Kikuchi, 1985 and Systellapsis curvispina Crosnier, 1987. These records increase the knowledge on deep-sea shrimps occurring in Southwestern Atlantic.
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Barneche, D. R., et al. "Body size, reef area and temperature predict global reef-fish species richness across spatial scales." Glob. Ecol. Biogeogr.. 28.3 (2019): 315–327.
Résumé: Aim To investigate biotic and abiotic correlates of reef-fish species richness across multiple spatial scales. Location Tropical reefs around the globe, including 485 sites in 109 sub-provinces spread across 14 biogeographic provinces. Time period Present. Major taxa studied 2,523 species of reef fish. Methods We compiled a database encompassing 13,050 visual transects. We used hierarchical linear Bayesian models to investigate whether fish body size, reef area, isolation, temperature, and anthropogenic impacts correlate with reef-fish species richness at each spatial scale (i.e., sites, sub-provinces, provinces). Richness was estimated using coverage-based rarefaction. We also tested whether species packing (i.e., transect-level species richness/m(2)) is correlated with province-level richness. Results Body size had the strongest effect on species richness across all three spatial scales. Reef area and temperature were both positively correlated with richness at all spatial scales. At the site scale only, richness decreased with reef isolation. Species richness was not correlated with proxies of human impacts. Species packing was correlated with species richness at the province level following a sub-linear power function. Province-level differences in species richness were also mirrored by patterns of body size distribution at the site scale. Species-rich provinces exhibited heterogeneous assemblages of small-bodied species with small range sizes, whereas species-poor provinces encompassed homogeneous assemblages composed by larger species with greater dispersal capacity. Main conclusions Our findings suggest that body size distribution, reef area and temperature are major predictors of species richness and accumulation across scales, consistent with recent theories linking home range to species-area relationships as well as metabolic effects on speciation rates. Based on our results, we hypothesize that in less diverse areas, species are larger and likely more dispersive, leading to larger range sizes and less turnover between sites. Our results indicate that changes in province-level (i.e., regional) richness should leave a tractable fingerprint in local assemblages, and that detailed studies on local-scale assemblage composition may be informative of responses occurring at larger scales.
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Benedetti, F., et al. "Climate change may have minor impact on zooplankton functional diversity in the Mediterranean Sea." Divers. Distrib.. 25.4 (2019): 568–581.
Résumé: Aim To assess the impact of climate change on the functional diversity of marine zooplankton communities. Location The Mediterranean Sea. Methods We used the functional traits and geographic distributions of 106 copepod species to estimate the zooplankton functional diversity of Mediterranean surface assemblages for the 1965-1994 and 2069-2098 periods. Multiple environmental niche models were trained at the global scale to project the species habitat suitability in the Mediterranean Sea and assess their sensitivity to climate change predicted by several scenarios. Simultaneously, the species traits were used to compute a functional dendrogram from which we identified seven functional groups and estimated functional diversity through Faith's index. We compared the measured functional diversity to the one originated from null models to test if changes in functional diversity were solely driven by changes in species richness. Results All but three of the 106 species presented range contractions of varying intensity. A relatively low decrease of species richness (-7.42 on average) is predicted for 97% of the basin, with higher losses in the eastern regions. Relative sensitivity to climate change is not clustered in functional space and does not significantly vary across the seven copepod functional groups defined. Changes in functional diversity follow the same pattern and are not different from those that can be expected from changes in richness alone. Main conclusions Climate change is not expected to alter copepod functional traits distribution in the Mediterranean Sea, as the most and the least sensitive species are functionally redundant. Such redundancy should buffer the loss of ecosystem functions in Mediterranean zooplankton assemblages induced by climate change. Because the most negatively impacted species are affiliated to temperate regimes and share Atlantic biogeographic origins, our results are in line with the hypothesis of increasingly more tropical Mediterranean communities.
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Boavida, J., et al. "Out of the Mediterranean? Post-glacial colonization pathways varied among cold-water coral species." J. Biogeogr.. 46.5 (2019): 915–931.
Résumé: Aim: To infer cold-water corals' (CWC) post-glacial phylogeography and assess the role of Mediterranean Sea glacial refugia as origins for the recolonization of the northeastern Atlantic Ocean. Location: Northeastern Atlantic Ocean and Mediterranean Sea. Taxon: Lophelia pertusa, Madrepora oculata. Methods: We sampled CWC using remotely operated vehicles and one sediment core for coral and sediment dating. We characterized spatial genetic patterns (microsatellites and a nuclear gene fragment) using networks, clustering and measures of genetic differentiation. Results: Inferences from microsatellite and sequence data were congruent, and showed a contrast between the two CWC species. Populations of L. pertusa present a dominant pioneer haplotype, local haplotype radiations and a majority of endemic variation in lower latitudes. Madrepora oculata populations are differentiated across the northeastern Atlantic and genetic lineages are poorly admixed even among neighbouring sites. Conclusions: Our study shows contrasting post-glacial colonization pathways for two key habitat-forming species in the deep sea. The CWC L. pertusa has likely undertaken a long-range (post-glacial) recolonization of the northeastern Atlantic directly from refugia located along southern Europe (Mediterranean Sea or Gulf of Cadiz). In contrast, the stronger genetic differentiation of M. oculata populations mirrors the effects of long-term isolation in multiple refugia. We suggest that the distinct and genetically divergent, refugial populations initiated the post-glacial recolonization of the northeastern Atlantic margins, leading to a secondary contact in the northern range and reaching higher latitudes much later, in the late Holocene. This study highlights the need to disentangle the influences of present-day dispersal and evolutionary processes on the distribution of genetic polymorphisms, to unravel the influence of past and future environmental changes on the connectivity of cosmopolitan deep-sea ecosystems associated with CWC.
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Chao, A., et al. "An attribute-diversity approach to functional diversity, functional beta diversity, and related (dis)similarity measures." Ecol. Monogr.. 89.2 (2019): Unsp-e01343.
Résumé: Based on the framework of attribute diversity (a generalization of Hill numbers of order q), we develop a class of functional diversity measures sensitive not only to species abundances but also to trait-based species-pairwise functional distances. The new method refines and improves on the conventional species-equivalent approach in three areas: (1) the conventional method often gives similar values (close to unity) to assemblages with contrasting levels of functional diversity; (2) when a distance metric is unbounded, the conventional functional diversity depends on the presence/absence of other assemblages in the study; (3) in partitioning functional gamma diversity into alpha and beta components, the conventional gamma is sometimes less than alpha. To resolve these issues, we add to the attribute-diversity framework a novel concept: tau, the threshold of functional distinctiveness between any two species; here, tau can be chosen to be any positive value. Any two species with functional distance >= tau are treated as functionally equally distinct. Our functional diversity quantifies the effective number of functionally equally distinct species (or “virtual functional groups”) with all pairwise distances at least tau for different species pairs. We advocate the use of two complementary diversity profiles (tau profile and q profile), which depict functional diversity with varying levels of tau and q, respectively. Both the conventional species-equivalent method (i.e., tau is the maximum of species-pairwise distances) and classic taxonomic diversity (i.e., tau is the minimum of non-zero species-pairwise distances) are incorporated into our proposed tau profile for an assemblage. For any type of species-pairwise distance matrices, our attribute-diversity approach allows proper diversity partitioning, with the desired property gamma >= alpha and thus avoids all the restrictions that apply to the conventional diversity decomposition. Our functional alpha and gamma are interpreted as the effective numbers of functionally equally distinct species, respectively, in an assemblage and in the pooled assemblage, while beta is the effective number of equally large assemblages with no shared species and all species in the assemblages being equally distinct. The resulting beta diversity can be transformed to obtain abundance-sensitive Sorensen- and Jaccard-type functional (dis)similarity profiles. Hypothetical and real examples are used to illustrate the framework. Online software and R codes are available to facilitate computations.
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Donati, G. F. A., et al. "A process-based model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages." Ecography (2019).
Résumé: Habitat dynamics interacting with species dispersal abilities could generate gradients in species diversity and prevalence of species traits when the latter are associated with species dispersal potential. Using a process-based model of diversification constrained by a dispersal parameter, we simulated the interplay between reef habitat dynamics during the past 140 million years and dispersal, shaping lineage diversification history and assemblage composition globally. The emerging patterns from the simulations were compared to current prevalence of species traits related to dispersal for 6315 tropical reef fish species. We found a significant spatial congruence between the prevalence of simulated low dispersal values and areas with a large proportion of species characterized by small adult body size, narrow home range mobility behaviour, pelagic larval duration shorter than 21 days and diurnal activity. Species characterized by such traits were found predominantly in the Indo-Australian Archipelago and the Caribbean Sea. Furthermore, the frequency distribution of the dispersal parameter was found to match empirical distributions for body size, PLD and home range mobility behaviour. Also, the dispersal parameter in the simulations was associated to diversification rates and resulted in trait frequency matching empirical distributions. Overall, our findings suggest that past habitat dynamics, in conjunction with dispersal processes, influenced diversification in tropical reef fishes, which may explain the present-day geography of species traits.
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Durant, J. M., et al. "Contrasting effects of rising temperatures on trophic interactions in marine ecosystems." Sci Rep. 9 (2019): 15213.
Résumé: In high-latitude marine environments, primary producers and their consumers show seasonal peaks of abundance in response to annual light cycle, water column stability and nutrient availability. Predatory species have adapted to this pattern by synchronising life-history events such as reproduction with prey availability. However, changing temperatures may pose unprecedented challenges by decoupling the predator-prey interactions. Here we build a predator-prey model accounting for the full life-cycle of fish and zooplankton including their phenology. The model assumes that fish production is bottom-up controlled by zooplankton prey abundance and match or mismatch between predator and prey phenology, and is parameterised based on empirical findings of how climate influences phenology and prey abundance. With this model, we project possible climate-warming effects on match-mismatch dynamics in Arcto-boreal and temperate biomes. We find a strong dependence on synchrony with zooplankton prey in the Arcto-boreal fish population, pointing towards a possible pronounced population decline with warming because of frequent desynchronization with its zooplankton prey. In contrast, the temperate fish population appears better able to track changes in prey timing and hence avoid strong population decline. These results underline that climate change may enhance the risks of predator-prey seasonal asynchrony and fish population declines at higher latitudes.
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Escalas, A., et al. "Microbial functional diversity: From concepts to applications." Ecol. Evol.. 9.20 (2019): 12000–12016.
Résumé: Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.
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Fernandez-Arcaya, U., et al. "Large-scale distribution of a deep-sea megafauna community along Mediterranean trawlable grounds." Sci. Mar.. 83 (2019): 175–187.
Résumé: The large-scale distribution pattern of megafauna communities along the Mediterranean middle slope was explored. The study was conducted between 500 and 800 m depth where deep-water fishery occurs. Although community studies carried out deeper than 500 m are partly available for some geographic areas, few large-scale comparative studies have been carried out. Within the framework of the MEDITS survey programme, we compared the megafauna community structure in ten geographical sub-areas (GSAs) along the Mediterranean coasts. Additionally, the spatial distribution of fishing was analysed using vessel monitoring by satellite information. Overall, the community showed a significant difference between sub-areas, with a decreasing eastward pattern in abundance and biomass. Longitude was the main factor explaining variation among sub-areas (by generalized additive models). However, we found a region which did not follow the general pattern. GSA 6 (northern Spain) showed significantly lower abundance and a different composition structure to the adjacent areas. The decrease in community descriptors (i.e. abundance and biomass) in this area is probably a symptom of population changes induced by intense fishery exploitation. Overall, a combination of environmental variables and human-induced impacts appears to influence the bentho-pelagic communities along the slope areas of the Mediterranean.
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Gaboriau, T., et al. "Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes." Proc. R. Soc. B-Biol. Sci.. 286.1911 (2019): 20191506.
Résumé: We develop a spatially explicit model of diversification based on palaeohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the 'time-area', 'tropical niche conservatism', 'ecological limits' and 'evolutionary speed' livpotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are nonmutually exclusive and that their relative influence depends on the time scale considered. Simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating biodiversity patterns.
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Kermagoret, C., et al. "Dataset on marine ecosystem services supplied by coral reefs, sandy beaches and coastal lagoons in different eutrophication states." Data Brief. 25 (2019): 104078.
Résumé: This data article provides indicators of Ecosystem Service (ES) supply for coral reefs, sandy beaches and coastal lagoons in different ecological states regarding eutrophication. 14 ES are considered: food through fisheries; material; molecules; coastal protection; nutrient regulation; pathogen regulation; climate regulation; support of recreational and leisure activities; contribution to a pleasant landscape; contribution to culture and territorial identity; emblematic biodiversity; habitat; trophic networks; recruitment. For each ecosystem 3 to 4 eutrophication states are described. Indicators of ES supply are filled on the basis of a literature review supplemented with expert-knowledge. A semi-quantification of the indicator value is finally provided. Tendencies and trade-offs between ES are analyzed in How does eutrophication impact bundles of ecosystem services in multiple coastal habitats using state-and-transition models [1]. (c) 2019 The Authors. Published by Elsevier Inc.
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Letessier, T. B., et al. "Remote reefs and seamounts are the last refuges for marine predators across the Indo-Pacific." PLoS. Biol.. 17.8 (2019): e3000366.
Résumé: Since the 1950s, industrial fisheries have expanded globally, as fishing vessels are required to travel further afield for fishing opportunities. Technological advancements and fishery subsidies have granted ever-increasing access to populations of sharks, tunas, billfishes, and other predators. Wilderness refuges, defined here as areas beyond the detectable range of human influence, are therefore increasingly rare. In order to achieve marine resources sustainability, large no-take marine protected areas (MPAs) with pelagic components are being implemented. However, such conservation efforts require knowledge of the critical habitats for predators, both across shallow reefs and the deeper ocean. Here, we fill this gap in knowledge across the Indo-Pacific by using 1,041 midwater baited videos to survey sharks and other pelagic predators such as rainbow runner (Elagatis bipinnulata), mahimahi (Coryphaena hippurus), and black marlin (Istiompax indica). We modeled three key predator community attributes: vertebrate species richness, mean maximum body size, and shark abundance as a function of geomorphology, environmental conditions, and human pressures. All attributes were primarily driven by geomorphology (35%-62% variance explained) and environmental conditions (14%-49%). While human pressures had no influence on species richness, both body size and shark abundance responded strongly to distance to human markets (12%-20%). Refuges were identified at more than 1,250 km from human markets for body size and for shark abundance. These refuges were identified as remote and shallow seabed features, such as seamounts, submerged banks, and reefs. Worryingly, hotpots of large individuals and of shark abundance are presently under-represented within no-take MPAs that aim to effectively protect marine predators, such as the British Indian Ocean Territory. Population recovery of predators is unlikely to occur without strategic placement and effective enforcement of large no-take MPAs in both coastal and remote locations.
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McLean, M., et al. "Trait structure and redundancy determine sensitivity to disturbance in marine fish communities." Glob. Change Biol.. 25.10 (2019): 3424–3437.
Résumé: Trait 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 (e.g., small, fast-growing pelagics/corallivores) 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.
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McLean, M., et al. "Fish communities diverge in species but converge in traits over three decades of warming." Glob. Change Biol.. 25.11 (2019): 3972–3984.
Résumé: Describing the spatial and temporal dynamics of communities is essential for understanding the impacts of global environmental change on biodiversity and ecosystem functioning. Trait-based approaches can provide better insight than species-based (i.e. taxonomic) approaches into community assembly and ecosystem functioning, but comparing species and trait dynamics may reveal important patterns for understanding community responses to environmental change. Here, we used a 33-year database of fish monitoring to compare the spatio-temporal dynamics of taxonomic and trait structure in North Sea fish communities. We found that the majority of variation in both taxonomic and trait structure was explained by a pronounced spatial gradient, with distinct communities in the southern and northern North Sea related to depth, sea surface temperature, salinity and bed shear stress. Both taxonomic and trait structure changed significantly over time; however taxonomically, communities in the south and north diverged towards different species, becoming more dissimilar over time, yet they converged towards the same traits regardless of species differences. In particular, communities shifted towards smaller, faster growing species with higher thermal preferences and pelagic water column position. Although taxonomic structure changed over time, its spatial distribution remained relatively stable, whereas in trait structure, the southern zone of the North Sea shifted northward and expanded, leading to homogenization. Our findings suggest that global environmental change, notably climate warming, will lead to convergence towards traits more adapted for novel environments regardless of species composition.
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Moullec, F., et al. "An End-to-End Model Reveals Losers and Winners in a Warming Mediterranean Sea." Front. Mar. Sci.. 6 (2019).
Résumé: The Mediterranean Sea is now recognized as a hotspot of global change, ranking among the fastest warming ocean regions. In order to project future plausible scenarios of marine biodiversity at the scale of the whole Mediterranean basin, the current challenge is to develop an explicit representation of the multispecies spatial dynamics under the combined influence of fishing pressure and climate change. Notwithstanding the advanced state-of-the-art modelling of food webs in the region, no previous studies have projected the consequences of climate change on marine ecosystems in an integrated way, considering changes in ocean dynamics, in phyto- and zoo-plankton productions, shifts in Mediterranean species distributions and their trophic interactions at the whole basin scale. We used an integrated modelling chain including a high-resolution regional climate model, a regional biogeochemistry model and a food web model OSMOSE to project the potential effects of climate change on biomass and catches for a wide array of species in the Mediterranean Sea. We showed that projected climate change would have large consequences for marine biodiversity by the end of the 21st century under a business-as-usual scenario (RCP8.5 with current fishing mortality). The total biomass of high trophic level species (fish and macroinvertebrates) is projected to increase by 5% and 22% while total catch is projected to increase by 0.3% and 7% by 2021-2050 and 2071-2100, respectively. However, these global increases masked strong spatial and inter-species contrasts. The bulk of increase in catch and biomass would be located in the southeastern part of the basin while total catch could decrease by up to 23% in the western part. Winner species would mainly belong to the pelagic group, are thermophilic and/or exotic, of smaller size and of low trophic level while loser species are generally large-sized, some of them of great commercial interest, and could suffer from a spatial mismatch with potential prey subsequent to a contraction or shift of their geographic range. Given the already poor conditions of exploited resources, our results suggest the need for fisheries management to adapt to future changes and to incorporate climate change impacts in future management strategy evaluation.
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Oberdorff, T., et al. "Unexpected fish diversity gradients in the Amazon basin." Sci. Adv.. 5.9 (2019): eaav8681.
Résumé: Using the most comprehensive fish occurrence database, we evaluated the importance of ecological and historical drivers in diversity patterns of subdrainage basins across the Amazon system. Linear models reveal the influence of climatic conditions, habitat size and sub-basin isolation on species diversity. Unexpectedly, the species richness model also highlighted a negative upriver-downriver gradient, contrary to predictions of increasing richness at more downriver locations along fluvial gradients. This reverse gradient may be linked to the history of the Amazon drainage network, which, after isolation as western and eastern basins throughout the Miocene, only began flowing eastward 1-9 million years (Ma) ago. Our results suggest that the main center of fish diversity was located westward, with fish dispersal progressing eastward after the basins were united and the Amazon River assumed its modern course toward the Atlantic. This dispersal process seems not yet achieved, suggesting a recent formation of the current Amazon system.
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Saeedi, H., et al. "Global marine biodiversity in the context of achieving the Aichi Targets: ways forward and addressing data gaps." PeerJ. 7 (2019): e7221.
Résumé: In 2010, the Conference of the Parties of the Convention on Biological Diversity agreed on the Strategic Plan for Biodiversity 2011-2020 in Aichi Prefecture, Japan. As this plan approaches its end, we discussed whether marine biodiversity and prediction studies were nearing the Aichi Targets during the 4th World Conference on Marine Biodiversity held in Montreal, Canada in June 2018. This article summarises the outcome of a five-day group discussion on how global marine biodiversity studies should be focused further to better understand the patterns of biodiversity. We discussed and reviewed seven fundamental biodiversity priorities related to nine Aichi Targets focusing on global biodiversity discovery and predictions to improve and enhance biodiversity data standards (quantity and quality), tools and techniques, spatial and temporal scale framing, and stewardship and dissemination. We discuss how identifying biodiversity knowledge gaps and promoting efforts have and will reduce such gaps, including via the use of new databases, tools and technology, and how these resources could be improved in the future. The group recognised significant progress toward Target 19 in relation to scientific knowledge, but negligible progress with regard to Targets 6 to 13 which aimed to safeguard and reduce human impacts on biodiversity.
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Tribot, A. - S., et al. "Species diversity and composition drive the aesthetic value of coral reef fish assemblages." Biol. Lett.. 15.11 (2019): 20190703.
Résumé: Cultural and recreational values of biodiversity are considered as important dimensions of nature's contribution to people. Among these values, the aesthetics can be of major importance as the appreciation of beauty is one of the simplest forms of human emotional response. Using an online survey, we disentangled the effects of different facets of biodiversity on aesthetic preferences of coral reef fish assemblages that are among the most emblematic assemblages on Earth. While we found a positive saturating effect of species' richness on human preference, we found a net negative effect of species abundance, no effect of species functional diversity and contrasting effects of species composition depending on species' attractiveness. Our results suggest that the biodiversity-human interest relationship is more complex than has been previously stated. By integrating several scales of organization, our study is a step forward in better evaluating the aesthetic value of biodiversity.
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Benedetti, F., et al. "Investigating uncertainties in zooplankton composition shifts under climate change scenarios in the Mediterranean Sea." Ecography. 41.2 (2018): 345–360.
Résumé: Ensemble niche modelling has become a common framework to predict changes in assemblages composition under climate change scenarios. The amount of uncertainty generated by the different components of this framework has rarely been assessed. In the marine realm forecasts have usually focused on taxa representing the top of the marine food-web, thus overlooking their basal component: the plankton. Calibrating environmental niche models at the global scale, we modelled the habitat suitability of 106 copepod species and estimated the dissimilarity between present and future zooplanktonic assemblages in the surface Mediterranean Sea. We identified the patterns (species replacement versus nestedness) driving the predicted dissimilarity, and quantified the relative contributions of different uncertainty sources: environmental niche models, greenhouse gas emission scenarios, circulation model configurations and species prevalence. Our results confirm that the choice of the niche modelling method is the greatest source of uncertainty in habitat suitability projections. Presence-only and presence-absence methods provided different visions of the niches, which subsequently lead to different future scenarios of biodiversity changes. Nestedness with decline in species richness is the pattern driving dissimilarity between present and future copepod assemblages. Our projections contrast with those reported for higher trophic levels, suggesting that different components of the pelagic food-web may respond discordantly to future climatic changes.
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Colin, N., et al. "Functional diversity measures revealed impacts of non-native species and habitat degradation on species-poor freshwater fish assemblages." Sci. Total Environ.. 625 (2018): 861–871.
Résumé: Trail-based ecology has been developed for decades lo infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive clataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N 389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have <= 3 species (specialization, FSpe; onginaliy, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive clatasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is essential to develop better management strategies. (C) 2013 Elsevier B.V. All rights reserved.
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Descombes, P., et al. "Linking species diversification to palaeo-environmental changes: A process-based modelling approach." Glob. Ecol. Biogeogr.. 27.2 (2018): 233–244.
Résumé: Aim: The importance of quantifying the contribution of historical processes in shaping current biodiversity patterns is now recognized, but quantitative approaches that explicitly link speciation, extinction and dispersal processes to palaeo-environmental changes are currently lacking. Here, we propose a spatial diversification model of lineages through time (SPLIT) based on the reconstruction of palaeo-environments. We illustrate our approach using mangroves as a case study and evaluate whether habitat changes caused by plate tectonics explain the current biodiversity patterns of this group. Innovations: The SPLIT model allows one to simulate the evolutionary dynamics of species ranges by spatially linking speciation, extinction and dispersal processes to habitat changes over geological time periods. The SPLIT model provides a mechanistic expectation of speciation and extinction assuming that species are ecologically identical and not interacting. The likelihood of speciation and extinction is equivalent across species and depends on two dispersal parameters interacting with habitat dynamics (d a maximum dispersal distance and ds a distance threshold beyond which gene flow is absent). Beyond classical correlative approaches, this model tracks biodiversity dynamics under palaeo-environmental changes and provides multiple expectations (i.e., alpha-, beta-diversity, phylogenies) that can be compared to empirical patterns. Main conclusions: The SPLIT model allows a better understanding of the origin of biodiversity by explicitly accounting for habitat changes over geological times. The simulations applied to the mangrove case study reproduced the observed longitudinal gradient in species richness, the empirical pattern of beta-diversity and also provided inference on diversification rates. Future developments may include niche evolution and species interactions to evaluate the importance of non-neutral mechanisms. The method is fully implemented in the InsideDNA platform for bioinformatics analyses, and all modelling results can be accessed via interactive web links.
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Gaboriau, T., et al. "Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo-Pacific." Ecography. 41.8 (2018): 1295–1306.
Résumé: 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.
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Galiana, N., et al. "The spatial scaling of species interaction networks." Nat. Ecol. Evol.. 2.5 (2018): 782–790.
Résumé: Species-area relationships (SARs) are pivotal to understand the distribution of biodiversity across spatial scales. We know little, however, about how the network of biotic interactions in which biodiversity is embedded changes with spatial extent. Here we develop a new theoretical framework that enables us to explore how different assembly mechanisms and theoretical models affect multiple properties of ecological networks across space. We present a number of testable predictions on network-area relationships (NARs) for multi-trophic communities. Network structure changes as area increases because of the existence of different SARs across trophic levels, the preferential selection of generalist species at small spatial extents and the effect of dispersal limitation promoting beta-diversity. Developing an understanding of NARs will complement the growing body of knowledge on SARs with potential applications in conservation ecology. Specifically, combined with further empirical evidence, NARs can generate predictions of potential effects on ecological communities of habitat loss and fragmentation in a changing world.
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Grenie, M., et al. "Functional rarity of coral reef fishes at the global scale: Hotspots and challenges for conservation." Biol. Conserv.. 226 (2018): 288–299.
Résumé: 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.
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Jaspers, C., et al. "Ocean current connectivity propelling the secondary spread of a marine invasive comb jelly across western Eurasia." Glob. Ecol. Biogeogr.. 27.7 (2018): 814–827.
Résumé: Aim: Invasive species are of increasing global concern. Nevertheless, the mechanisms driving further distribution after the initial establishment of non-native species remain largely unresolved, especially in marine systems. Ocean currents can be a major driver governing range occupancy, but this has not been accounted for in most invasion ecology studies so far. We investigate how well initial establishment areas are interconnected to later occupancy regions to test for the potential role of ocean currents driving secondary spread dynamics in order to infer invasion corridors and the source-sink dynamics of a non-native holoplanktonic biological probe species on a continental scale. Location: Western Eurasia. Time period: 1980s-2016. Major taxa studied: 'Comb jelly' Mnemiopsis leidyi. Methods: Based on 12,400 geo-referenced occurrence data, we reconstruct the invasion history of M. leidyi in western Eurasia. We model ocean currents and calculate their stability to match the temporal and spatial spread dynamics with large-scale connectivity patterns via ocean currents. Additionally, genetic markers are used to test the predicted connectivity between subpopulations. Results: Ocean currents can explain secondary spread dynamics, matching observed range expansions and the timing of first occurrence of our holoplanktonic non-native biological probe species, leading to invasion corridors in western Eurasia. In northern Europe, regional extinctions after cold winters were followed by rapid recolonizations at a speed of up to 2,000 km per season. Source areas hosting year-round populations in highly interconnected regions can re-seed genotypes over large distances after local extinctions. Main conclusions: Although the release of ballast water from container ships may contribute to the dispersal of non-native species, our results highlight the importance of ocean currents driving secondary spread dynamics. Highly interconnected areas hosting invasive species are crucial for secondary spread dynamics on a continental scale. Invasion risk assessments should consider large-scale connectivity patterns and the potential source regions of non-native marine species.
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Legras, G., N. Loiseau, and J. - C. Gaertner. "Functional richness: Overview of indices and underlying concepts." Acta Oecol.-Int. J. Ecol.. 87 (2018): 34–44.
Résumé: Functional richness, currently defined as the amount of niche space occupied by the species within a community, is one of the three major components of functional diversity. Different indices have been developed in order to quantify this component. However, the range of indices available for assessing functional richness, often mathematically complex and based on different rationales, can cause confusion for field ecologists and lead to misinterpretation of the results obtained. In this context, we have provided the first study exclusively focused on the comparison of the definitions, advantages and drawbacks of a large set of functional richness indices. The first part of this work is focused on four indices (FDP&G, FRic, TOP and N-hypervolumes indices) that are currently the most commonly used for assessing functional richness. We have completed our study by including recently developed indices that enable us to take into account the intraspecific trait variability (i.e. FRim index and TDP framework), because there is currently a growing scientific consensus regarding the necessity of including this aspect in the assessment of the functional diversity of communities. We demonstrate that although authors have argued that their index describes the functional richness, each of them describes only part of it, and this part may strongly differ from one index to another. Rather than advocating the general use of a single index and/or systematically avoiding others, our study highlights the need for selecting indices in close relation with the context, the available data and the aims of each study. Such a strategy is an essential preliminary step for preventing misunderstanding and artefactual controversies. Along these lines, we propose some guidelines to help users in selecting the most appropriate indices according both to the facet of functional richness on which they wish to focus and to the characteristics of the available data.
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Leitao, R. P., et al. "Disentangling the pathways of land use impacts on the functional structure of fish assemblages in Amazon streams." Ecography. 41.1 (2018): 219–232.
Résumé: Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the Amazon to date, examining functional responses of fish assemblages to land use. We sampled fish assemblages from two large human-modified regions, and characterized stream conditions by physical habitat attributes and key landscape-change variables, including density of road crossings (i.e. riverscape fragmentation), deforestation, and agricultural intensification. Fish species were functionally characterized using ecomorphological traits describing feeding, locomotion, and habitat preferences, and these traits were used to derive indices that quantitatively describe the functional structure of the assemblages. Using structural equation modeling, we disentangled multiple drivers operating at different spatial scales, identifying causal pathways that significantly affect stream condition and the structure of the fish assemblages. Deforestation at catchment and riparian network scales altered the channel morphology and the stream bottom structure, changing the functional identity of assemblages. Local deforestation reduced the functional evenness of assemblages (i.e. increased dominance of specific trait combinations) mediated by expansion of aquatic vegetation cover. Riverscape fragmentation reduced functional richness, evenness and divergence, suggesting a trend toward functional homogenization and a reduced range of ecological niches within assemblages following the loss of regional connectivity. These results underscore the often-unrecognized importance of different land use changes, each of which can have marked effects on stream biodiversity. We draw on the relationships observed herein to suggest priorities for the improved management of stream systems in the multiple-use landscapes that predominate in human-modified tropical forests.
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Magris, R. A., et al. "Biologically representative and well-connected marine reserves enhance biodiversity persistence in conservation planning." Conserv. Lett.. 11.4 (2018): Unsp-e12439.
Résumé: Current methods in conservation planning for promoting the persistence of biodiversity typically focus on either representing species geographic distributions or maintaining connectivity between reserves, but rarely both, and take a focal species, rather than a multispecies, approach. Here, we link prioritization methods with population models to explore the impact of integrating both representation and connectivity into conservation planning for species persistence. Using data on 288 Mediterranean fish species with varying conservation requirements, we show that: (1) considering both representation and connectivity objectives provides the best strategy for enhanced biodiversity persistence and (2) connectivity objectives were fundamental to enhancing persistence of small-ranged species, which are most in need of conservation, while the representation objective benefited only wide-ranging species. Our approach provides a more comprehensive appraisal of planning applications than approaches focusing on either representation or connectivity, and will hopefully contribute to build more effective reserve networks for the persistence of biodiversity.
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Maire, E., et al. "Community-wide scan identifies fish species associated with coral reef services across the Indo-Pacific." Proc. R. Soc. B-Biol. Sci.. 285.1883 (2018): 20181167.
Résumé: Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute, beyond the socio-environmental and species richness effects, to the biomass and coral cover on Indo-Pacific reefs. We found that only a limited set of species (51 out of approx. 400, = approx. 13%), belonging to various functional groups and evolutionary lineages, are strongly and positively associated with fish biomass and live coral cover. Many of these species have not previously been identified as functionally important, and thus may be involved in unknown, yet important, biological mechanisms that help sustain healthy and productive coral reefs. CWS has the potential to reveal species that are key to ecosystem functioning and services and to guide management strategies as well as new experiments to decipher underlying causal ecological processes.
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Mazel, F., et al. "Prioritizing phylogenetic diversity captures functional diversity unreliably." Nat. Commun.. 9 (2018): 2888.
Résumé: In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have assumed that maximizing phylogenetic diversity (PD) should indirectly capture FD, a hypothesis that we name the “phylogenetic gambit”. Here, we empirically test this gambit using data on ecologically relevant traits from >15,000 vertebrate species. Specifically, we estimate a measure of surrogacy of PD for FD. We find that maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain obscures the fact that in over one-third of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky conservation strategy.
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Mérillet, L., et al. "Using underwater video to assess megabenthic community vulnerability to trawling in the Grande Vasière (Bay of Biscay)." Environmental Conservation. 45.2 (2018): 163–172.
Résumé: Trawling activities are considered to be one of the main sources of disturbance to the seabed worldwide. We aimed to disentangle the dominance of environmental variations and trawling intensity in order to explain the distribution of diversity patterns over 152 sampling sites in the French trawl fishing-ground, the Grande Vasière. Using a towed underwater video device, we identified 39 taxa to the finest taxonomic level possible, which were clustered according to their vulnerability to trawling disturbance based on functional traits. Using generalized linear models, we investigated whether the density distribution of each vulnerability group was sensitive to trawling intensity and habitat characteristics. Our analyses revealed a structuring effect of depth and substratum on community structure. The distribution of the more vulnerable group was a negative function of trawling intensity, while the distributions of the less vulnerable groups were independent of trawling intensity. Video monitoring coupled with trait-based vulnerability assessment of macro-epibenthic communities might be more relevant than the traditional taxonomic approach to identifying the areas that are most vulnerable to fishing activities in conservation planning.
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Milner-Gulland, E. J., et al. "Translating the terrestrial mitigation hierarchy to marine megafauna by-catch." Fish. Fish.. 19.3 (2018): 547–561.
Résumé: In terrestrial and coastal systems, the mitigation hierarchy is widely and increasingly used to guide actions to ensure that no net loss of biodiversity ensues from development. We develop a conceptual model which applies this approach to the mitigation of marine megafauna by-catch in fisheries, going from defining an overarching goal with an associated quantitative target, through avoidance, minimization, remediation to offsetting. We demonstrate the framework's utility as a tool for structuring thinking and exposing uncertainties. We draw comparisons between debates ongoing in terrestrial situations and in by-catch mitigation, to show how insights from each could inform the other; these are the hierarchical nature of mitigation, out-of-kind offsets, research as an offset, incentivizing implementation of mitigation measures, societal limits and uncertainty. We explore how economic incentives could be used throughout the hierarchy to improve the achievement of by-catch goals. We conclude by highlighting the importance of clear agreed goals, of thinking beyond single species and individual jurisdictions to account for complex interactions and policy leakage, of taking uncertainty explicitly into account and of thinking creatively about approaches to by-catch mitigation in order to improve outcomes for conservation and fishers. We suggest that the framework set out here could be helpful in supporting efforts to improve by-catch mitigation efforts and highlight the need for a full empirical application to substantiate this.
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Miloslavich, P., et al. "Essential ocean variables for global sustained observations of biodiversity and ecosystem changes." Global Change Biology. 24.6 (2018): 2416–2433.
Résumé: Sustained observations of marine biodiversity and ecosystems focused on specific conservation and management problems are needed around the world to effectively mitigate or manage changes resulting from anthropogenic pressures. These observations, while complex and expensive, are required by the international scientific, governance and policy communities to provide baselines against which the effects of human pressures and climate change may be measured and reported, and resources allocated to implement solutions. To identify biological and ecological essential ocean variables (EOVs) for implementation within a global ocean observing system that is relevant for science, informs society, and technologically feasible, we used a driver-pressure-state-impact-response (DPSIR) model. We (1) examined relevant international agreements to identify societal drivers and pressures on marine resources and ecosystems, (2) evaluated the temporal and spatial scales of variables measured by 100+ observing programs, and (3) analysed the impact and scalability of these variables and how they contribute to address societal and scientific issues. EOVs were related to the status of ecosystem components (phytoplankton and zooplankton biomass and diversity, and abundance and distribution of fish, marine turtles, birds and mammals), and to the extent and health of ecosystems (cover and composition of hard coral, seagrass, mangrove and macroalgal canopy). Benthic invertebrate abundance and distribution and microbe diversity and biomass were identified as emerging EOVs to be developed based on emerging requirements and new technologies. The temporal scale at which any shifts in biological systems will be detected will vary across the EOVs, the properties being monitored and the length of the existing time-series. Global implementation to deliver useful products will require collaboration of the scientific and policy sectors and a significant commitment to improve human and infrastructure capacity across the globe, including the development of new, more automated observing technologies, and encouraging the application of international standards and best practices.
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Muller-Karger, F. E., et al. "Advancing Marine Biological Observations and Data Requirements of the Complementary Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs) Frameworks." Front. Mar. Sci.. 5 (2018).
Résumé: Measurements of the status and trends of key indicators for the ocean and marine life are required to inform policy and management in the context of growing human uses of marine resources, coastal development, and climate change. Two synergistic efforts identify specific priority variables for monitoring: Essential Ocean Variables (EOVs) through the Global Ocean Observing System (GOOS), and Essential Biodiversity Variables (EBVs) from the Group on Earth Observations Biodiversity Observation Network (GEO BON). Both systems support reporting against internationally agreed conventions and treaties. GOOS, established under the auspices of the Intergovernmental Oceanographic Commission (IOC), plays a leading role in coordinating global monitoring of the ocean and in the definition of EOVs. GEO BON is a global biodiversity observation network that coordinates observations to enhance management of the world’s biodiversity and promote both the awareness and accounting of ecosystem services. Convergence and agreement between these two efforts are required to streamline existing and new marine observation programs to advance scientific knowledge effectively and to support the sustainable use and management of ocean spaces and resources. In this context, the Marine Biodiversity Observation Network (MBON), a thematic component of GEO BON, is collaborating with GOOS, the Ocean Biogeographic Information System (OBIS), and the Integrated Marine Biosphere Research (IMBeR) project to ensure that EBVs and EOVs are complementary, representing alternative uses of a common set of scientific measurements. This work is informed by the Joint Technical Commission for Oceanography and Marine Meteorology (JCOMM), an intergovernmental body of technical experts that helps international coordination on best practices for observing, data management and services, combined with capacity development expertise. Characterizing biodiversity and understanding its drivers will require incorporation of observations from traditional and molecular taxonomy, animal tagging and tracking efforts, ocean biogeochemistry, and ocean observatory initiatives including the deep ocean and seafloor. The partnership between large-scale ocean observing and product distribution initiatives (MBON, OBIS, JCOMM, and GOOS) is an expedited, effective way to support international policy-level assessments (e.g., the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services or IPBES), along with the implementation of international development goals (e.g., the United Nations Sustainable Development Goals).
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Olivier, D., et al. "Functional-biogeography of the reef fishes of the islands of the Gulf of California: Integrating functional divergence into marine conservation." Glob. Ecol. Conserv.. 16 (2018): e00506.
Résumé: The Gulf of California (GC) is a semi-closed sea in the Tropical Eastern Pacific and is recognised as a highly diverse marine ecosystem. Despite this status, this region is still poorly studied in comparison to other marine hotspots. To start filling this gap, we attempt to provide a global overview of reef-fish diversity around the numerous islands of the region. We evaluated species richness, the abundance and biomass, and the functional diversity of the fish assemblages for the major islands of the GC. We first highlight that the southwestern part of the central GC is the hotspot of reef-fishes diversity within the GC, in terms of species richness, functional diversity, and fish abundance. We then found out an important functional divergence between fish assemblages of northern and southern regions. The fish biomass of each region is dominated by different species, characterised by different ecological traits (the opposite of functional convergence). This functional divergence may be explained by an important oceanographic heterogeneity along the latitudinal axis of the GC. The northern part shows larger climate fluctuations while the southern part is more tropical and climatically stable. Such functional divergence is a biodiversity facet to take into account when determining the sites to focus conservation action. In the GC, this criterion allows the importance of some sites to be highlighted to preserve the legacy of the reef-fishes, despite their lower diversity levels. (C) 2018 The Authors. Published by Elsevier B.V.
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Toussaint, A., et al. "Non-native species led to marked shifts in functional diversity of the world freshwater fish faunas." Ecol. Lett.. 21.11 (2018): 1649–1659.
Résumé: Global spread of non-native species profoundly changed the world biodiversity patterns, but how it translates into functional changes remains unanswered at the world scale. We here show that while in two centuries the number of fish species per river increased on average by 15% in 1569 basins worldwide, the diversity of their functional attributes (i.e. functional richness) increased on average by 150%. The inflation of functional richness was paired with changes in the functional structure of assemblages, with shifts of species position toward the border of the functional space of assemblages (i.e. increased functional divergence). Non-native species moreover caused shifts in functional identity toward higher body sized and less elongated species for most of assemblages throughout the world. Although varying between rivers and biogeographic realms, such changes in the different facets of functional diversity might still increase in the future through increasing species invasion and may further modify ecosystem functioning.
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Tribot, A. - S., J. Deter, and N. Mouquet. "Integrating the aesthetic value of landscapes and biological diversity." Proc. R. Soc. B-Biol. Sci.. 285.1886 (2018): 20180971.
Résumé: As a cultural ecosystem service, the aesthetic value of landscapes contributes to human well-being, but studies linking biodiversity and ecosystem services generally do not account for this particular service. Therefore, congruence between the aesthetic perception of landscapes, ecological value and biodiversity remains poorly understood. Here, we describe the conceptual background, current methodologies and future challenges of assessing landscape aesthetics and its relationship with biodiversity. We highlight the methodological gaps between the assessment of landscape aesthetics, ecological diversity and functioning. We discuss the challenges associated with connecting landscape aesthetics with ecological value, and the scaling issues in the assessment of human aesthetics perception. To better integrate aesthetic value and ecological components of biodiversity, we propose to combine the study of aesthetics and the understanding of ecological function at both the species and landscape levels. Given the urgent need to engage society in conservation efforts, this approach, based on the combination of the aesthetic experience and the recognition of ecological functioning by the general public, will help change our culture of nature and promote ecologically oriented conservation policies.
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Wasof, S., et al. "Dominance of individual plant species is more important than diversity in explaining plant biomass in the forest understorey." J. Veg. Sci.. 29.3 (2018): 521–531.
Résumé: QuestionsHow does plant community diversity influence variation in plant biomass? There are two competing hypotheses: the biomass ratio' hypothesis, where biomass is influenced by the abundance and traits of the most dominant species, and the diversity' hypothesis, where the diversity of organisms influences biomass through mechanisms such as niche complementarity. However, no studies have tested which one of these two hypotheses better explains the variation in plant biomass in the forest understorey. LocationTemperate deciduous forests in northern France. MethodsFor the forest understorey, we assessed species diversity and biomass as well as soil and light conditions in 133 forest plots of 100m(2) each. Using mixed-effect models and after controlling for potential confounding factors, we tested the biomass ratio' hypothesis by relating the relative abundance of the most dominant species across our study sites and the CWM of plant traits (leaf area and plant height) to biomass. The diversity' hypothesis was tested by relating biomass to various measures of taxonomic, functional and phylogenetic diversity. ResultsBiomass of the forest understorey was mainly related to the relative abundance and the trait values of the most dominant species, supporting the biomass ratio' hypothesis. In contrast to the diversity' hypothesis, functional diversity indices had a negative impact on biomass. We found no contribution of taxonomic or phylogenetic diversity indices. ConclusionThe abundance and traits of the most dominant species matter more than taxonomic, functional or phylogenetic diversity of the forest understorey in explaining its biomass. Thus, there is a need for experiments that aim to fully understand keystone species' responses to on-going changing biotic and abiotic conditions and to predict their effects on ecosystem functioning and processes.
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Abgrall, C., et al. "Shifts and linkages of functional diversity between above- and below-ground compartments along a flooding gradient." Funct. Ecol.. 31.2 (2017): 350–360.
Résumé: 1. Trait-based approaches have the potential to reveal general and predictive relationships between organisms and ecosystem functioning. However, the mechanisms underlying the functional structure of communities are still unclear. Within terrestrial ecosystems, several studies have shown that many ecological processes are controlled by the interacting above-and belowground compartments. However, few studies have used traits to reveal the functional relationships between plants and soil fauna. Mostly, research combining plants and soil fauna solely used the traits of one assemblage in predictive studies. 2. Above-ground (plants) and below-ground (Collembola) compartments were sampled over a flooding gradient in northern France along the Seine River. First, we measured the effect of flooding on functional and taxonomic assembly within both communities. We then considered the linkages between plant and Collembolan species richness, community traits and assessed whether traits of both compartments converged at high flooding intensity (abiotic filtering) and diverged when this constraint is released (biotic filtering). 3. Species richness of both taxa followed the same bell-shaped pattern along the gradient, while a similar significant pattern of functional richness was only observed for plants. Further analyses revealed a progressive shift from trait convergence to divergence for plants, but not for Collembola, as constraints intensity decreased. Instead, our results highlighted that Collembola traits were mainly linked to the variations in plant traits. This leads, within Collembola assemblages, to convergence of a subset of perception and habitat-related traits for which the relationship with plant traits was assessed. 4. Synthesis. Using a trait-based approach, our study highlighted that functional relationships occur between above-and below-ground compartments. We underlined that functional composition of plant communities plays a key role in structuring Collembola assemblages in addition to the role of abiotic variables. Our study clearly shows that functional diversity provides a new approach to link the above-and below-ground compartments and might, therefore, be further considered when studying ecological processes at the interface between both compartments.
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Andrello, M., et al. "Global mismatch between fishing dependency and larval supply from marine reserves." Nat. Commun.. 8 (2017): 16039.
Résumé: Marine reserves are viewed as flagship tools to protect exploited species and to contribute to the effective management of coastal fisheries. Yet, the extent to which marine reserves are globally interconnected and able to effectively seed areas, where fisheries are most critical for food and livelihood security is largely unknown. Using a hydrodynamic model of larval dispersal, we predict that most marine reserves are not interconnected by currents and that their potential benefits to fishing areas are presently limited, since countries with high dependency on coastal fisheries receive very little larval supply from marine reserves. This global mismatch could be reversed, however, by placing new marine reserves in areas sufficiently remote to minimize social and economic costs but sufficiently connected through sea currents to seed the most exploited fisheries and endangered ecosystems.
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Bakker, J., et al. "Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact." Sci Rep. 7 (2017): 16886.
Résumé: Sharks are charismatic predators that play a key role in most marine food webs. Their demonstrated vulnerability to exploitation has recently turned them into flagship species in ocean conservation. Yet, the assessment and monitoring of the distribution and abundance of such mobile species in marine environments remain challenging, often invasive and resource-intensive. Here we pilot a novel, rapid and non-invasive environmental DNA (eDNA) metabarcoding approach specifically targeted to infer shark presence, diversity and eDNA read abundance in tropical habitats. We identified at least 21 shark species, from both Caribbean and Pacific Coral Sea water samples, whose geographical patterns of diversity and read abundance coincide with geographical differences in levels of anthropogenic pressure and conservation effort. We demonstrate that eDNA metabarcoding can be effectively employed to study shark diversity. Further developments in this field have the potential to drastically enhance our ability to assess and monitor elusive oceanic predators, and lead to improved conservation strategies.
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Bender, M. G., et al. "Isolation drives taxonomic and functional nestedness in tropical reef fish faunas." Ecography. 40.3 (2017): 425–435.
Résumé: 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 composition of assemblages still remains poorly known. Here, using an extensive database on the functional traits and the distributions 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 combinations 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.
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Calcagno, V., et al. "Diversity spurs diversification in ecological communities." Nat. Commun.. 8 (2017): 15810.
Résumé: Diversity is a fundamental, yet threatened, property of ecological systems. The idea that diversity can itself favour diversification, in an autocatalytic process, is very appealing but remains controversial. Here, we study a generalized model of ecological communities and investigate how the level of initial diversity influences the possibility of evolutionary diversification. We show that even simple models of intra- and inter-specific ecological interactions can predict a positive effect of diversity on diversification: adaptive radiations may require a threshold number of species before kicking-off. We call this phenomenon DDAR (diversity-dependent adaptive radiations) and identify mathematically two distinct pathways connecting diversity to diversification, involving character displacement and the positive diversity-productivity relationship. Our results may explain observed delays in adaptive radiations at the macroscale and diversification patterns reported in experimental microbial communities, and shed new light on the dynamics of ecological diversity, the diversity-dependence of diversification rates, and the consequences of biodiversity loss.
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Coll, M., and J. Steenbeek. "Standardized ecological indicators to assess aquatic food webs: The ECOIND software plug-in for Ecopath with Ecosim models." Environ. Modell. Softw.. 89 (2017): 120–130.
Résumé: Ecological indicators are useful tools to analyse and communicate historical changes in ecosystems and plausible future scenarios while evaluating environmental status. Here we introduce a new plug-in to the Ecopath with Ecosim (EwE) food web modelling approach, which is widely used to quantitatively describe aquatic ecosystems. The plug-in (ECOIND) calculates standardized ecological indicators. We describe the primary functionality of ECOIND and provide an example of its application in both static and temporal-spatial dynamic modelling, while we highlight several related features including a new taxonomy input database (species traits) and the ability to analyse input uncertainty on output results. ECOIND adds new capabilities to the widely used EwE food web modelling approach and enables broadening its applications into biodiversity and conservation-based frameworks to contribute to integrated ecosystem analyses. (C) 2016 Elsevier Ltd. All rights reserved.
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Cormier-Salem, M. - C., et al. "The mangrove's contribution to people: Interdisciplinary pilot study of the Can Gio Mangrove Biosphere Reserve in Viet Nam." Comptes Rendus Geoscience. 349.6 (2017): 341–350.
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Darling, E. S., et al. "Relationships between structural complexity, coral traits, and reef fish assemblages." Coral Reefs. 36.2 (2017): 561–575.
Résumé: With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia's Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals-with different traits and life histories-continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.
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Fournier, B., et al. "An integrative framework of coexistence mechanisms in competitive metacommunities." Ecography. 40.5 (2017): 630–641.
Résumé: Species distribution in a metacommunity varies according to their traits, the distribution of environmental conditions and connectivity among localities. These ingredients contribute to coexistence across spatial scales via species sorting, patch dynamics, mass effects and neutral dynamics. These mechanisms however seldom act in isolation and the impact of landscape configuration on their relative importance remains poorly understood. We present a new model of metacommunity dynamics that simultaneously considers these four possible mechanisms over spatially explicit landscapes and propose a statistical approach to partition their contribution to species distribution. We find that landscape configuration can induce dispersal limitations that have negative consequences for local species richness. This result was more pronounced with neutral dynamics and mass effect than with species sorting or patch dynamics. We also find that the relative importance of the four mechanisms varies not only among landscape configurations, but also among species, with some species being mostly constrained by dispersal and/or drift and others by sorting. Changes in landscape properties might lead to a shift in coexistence mechanisms and, by extension, to a change in community composition. This confirms the importance of considering landscape properties for conservation and management. Our results illustrate the idea that ecological communities are the results of multiple mechanisms acting at the same time and complete our understanding of spatial processes in competitive metacommunities.
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Keller, S., et al. "Demersal cephalopod communities in the Mediterranean: a large-scale analysis." Mar. Ecol.-Prog. Ser.. 584 (2017): 105–118.
Résumé: Cephalopod assemblages at the scale of the entire Mediterranean Sea were analysed using information from 2 decades of standardized scientific bottom trawl surveys. Western and eastern assemblages (6 yr of data) were compared using a combined approach of multivariate ordination techniques and non-linear regressions. These methods enabled us to distinguish assemblages and simultaneously analyse the influence of geographic, bathymetric and environmental (sea surface temperature and chlorophyll a concentration) gradients on observed community patterns. Despite few differences in species composition between sub-basins, the relative contribution of species differed. Bathymetry was the primary structural driver for the cephalopod communities of both basins, and contributed to 3 assemblages (shallow water, upper slope and middle slope). Winter temperature influenced community assemblages more strongly in the western than in the eastern basin, in contrast to a small but consistent winter productivity influence on community assemblages in both basins. Thus, the environmental parameters analysed did not cause an immediate change in cephalopod assemblages, but rather an effect lagged by several months. Differences in the relative importance of environmental drivers show that different processes operate in the 2 basins. These results demonstrate similarities and differences between Mediterranean basins regarding important cephalopod functional groups. This information should help integrative ecosystem management approaches currently used in fisheries and conservation management.
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Loiseau, N., et al. "Multi-component β-diversity approach reveals conservation dilemma between species and functions of coral reef fishes." J. Biogeogr.. 44.3 (2017): 537–547.
Résumé: AimWe applied a multicomponent approach based on the decomposition of taxonomic (both presence-absence and abundance) and functional beta diversity to determine the influence of ecological factors in shaping spatial distribution diversity of coral reef fishes, and the implications for conservation decisions. LocationLagoons of ten atolls characterized by low human pressure but with contrasted geomorphology in the Tuamotu Archipelago, French Polynesia. MethodsWe computed beta diversities and their partitioning components, both at local (inter-transect, from 200m to 10km) and large (among atolls, from 22 to 350km) spatial scales. Null models were applied to test whether the observed beta diversity differed from random expectation. Multiple generalized dissimilarity models were run to test which environmental factors were the best predictors of observed beta diversities. ResultsBeta diversity was indistinguishable from randomness at both spatial scales. Species remained generally interchangeable among transects within an atoll and to some extent among atolls. However, strong deviance explained by models showed that the number of species, the number of individuals and functional traits present in transects and atolls were determined by deterministic factors (i.e. environmental factors). Modelling each beta diversity component separately also revealed partial mismatch among atolls and among species and functional dissimilarities. The influence of environmental variables strongly varied among atolls, species and functional dissimilarities. Main conclusionsBy revealing the spatial scaling of ecological factors and partial congruence among species and functional diversity, assessment of beta diversity provides insight into conservation planning. Our results support the idea that conservation planning applied to protect taxonomic diversity cannot be fully extended to functional diversity. We have addressed the dilemma of which diversity component should be favoured in conservation strategies.
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Silva Junior, C. a. B., et al. "Functional diversity of fish in tropical estuaries: A traits-based approach of communities in Pernambuco, Brazil." Estuar. Coast. Shelf Sci.. 198 (2017): 413–420.
Résumé: Environmental changes and human activities may have strong impacts on biodiversity and ecosystem functioning. While biodiversity is traditionally based on species richness and composition, there is a growing concern to take into account functional diversity to assess and manage species communities. In spite of their economic importance, functional diversity quantified by a traits-based approach is still poorly documented in tropical estuaries. In this study, the functional diversity of fishes was investigated within four estuaries in Pernambuco state, northeast of Brazil. These areas are subject to different levels of human impact (e.g. mangrove deforestation, shrimp farming, fishing etc.) and environmental conditions. Fishes were collected during 34 scientific surveys. A total of 122 species were identified and 12 functional traits were quantified describing two main functions: food acquisition and locomotion. Fish abundance and functional dissimilarities data were combined into a multivariate analysis, the Double Principal Coordinate Analysis, to identify the functional typology of fish assemblages according to the estuary. Results showed that Itapissuma, the largest estuary with a wider mangrove forest area, differs from the other three estuaries, showing higher mean values per samples of species richness S and quadratic entropy Q. Similarly, it presented a different functional typology (the first two axes of the DPCoA account for 68.7% of total inertia, while those of a traditional PCA based solely on species abundances provided only 17.4%). Conversely, Suape, Sirinhaem, and to a lower extent Rio Formoso, showed more similarity in their diversity. This result was attributed to their predominantly marine influenced hydrological features, and similar levels of species abundances and in morphological traits. Overall, this study, combining diversity indices and a recent multivariate analysis to access species contribution to functional typology, allows to deepen diversity assessment by providing additional information regarding the functional pattern of fish assemblages. (C) 2016 Elsevier Ltd. All rights reserved.
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Tedesco, P. A., et al. "A global database on freshwater fish species occurrence in drainage basins." Sci. Data. 4 (2017): 170141.
Résumé: A growing interest is devoted to global-scale approaches in ecology and evolution that examine patterns and determinants of species diversity and the threats resulting from global change. These analyses obviously require global datasets of species distribution. Freshwater systems house a disproportionately high fraction of the global fish diversity considering the small proportion of the earth's surface that they occupy, and are one of the most threatened habitats on Earth. Here we provide complete species lists for 3119 drainage basins covering more than 80% of the Earth surface using 14953 fish species inhabiting permanently or occasionally freshwater systems. The database results from an extensive survey of native and non-native freshwater fish species distribution based on 1436 published papers, books, grey literature and web-based sources. Alone or in combination with further datasets on species biological and ecological characteristics and their evolutionary history, this database represents a highly valuable source of information for further studies on freshwater macroecology, macroevolution, biogeography and conservation.
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Villeger, S., et al. "Functional ecology of fish: current approaches and future challenges." Aquat. Sci.. 79.4 (2017): 783–801.
Résumé: Fish communities face increasing anthropogenic pressures in freshwater and marine ecosystems that modify their biodiversity and threaten the services they supply to human populations. To address these issues, studies have been increasingly focusing on functions of fish that are linked to their main ecological roles in aquatic ecosystems. Fish are indeed known to control other organisms through predation, mediate nutrient fluxes, and can act as ecosystem engineers. Here for each of the key functions played by fish, we present the functional traits that have already been used to assess them. We include traits measurable from observations on living individuals, morphological features measured on preserved organisms or traits categorized using information from the literature, and we discuss their respective advantages and limitations. We then list future research directions to foster a more complete functional approach for fish ecology that needs to incorporate functional traits describing, food provisioning and cultural services while accounting more frequently for intraspecific variability. Finally, we highlight ecological and evolutionary questions that could be addressed using meta-analyses of large trait databases, and how a trait-based framework could provide valuable insights on the mechanistic links between global changes, functional diversity of fish assemblages, and ecosystem services.
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Violle, C., et al. "Functional Rarity: The Ecology of Outliers." Trends Ecol. Evol.. 32.5 (2017): 356–367.
Résumé: 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.
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2016 |
Cazelles, K., et al. "On the integration of biotic interaction and environmental constraints at the biogeographical scale." Ecography. 39.10 (2016): 921–931.
Résumé: Biogeography is primarily concerned with the spatial distribution of biodiversity, including performing scenarios in a changing environment. The efforts deployed to develop species distribution models have resulted in predictive tools, but have mostly remained correlative and have largely ignored biotic interactions. Here we build upon the theory of island biogeography as a first approximation to the assembly dynamics of local communities embedded within a metacommunity context. We include all types of interactions and introduce environmental constraints on colonization and extinction dynamics. We develop a probabilistic framework based on Markov chains and derive probabilities for the realization of species assemblages, rather than single species occurrences. We consider the expected distribution of species richness under different types of ecological interactions. We also illustrate the potential of our framework by studying the interplay between different ecological requirements, interactions and the distribution of biodiversity along an environmental gradient. Our framework supports the idea that the future research in biogeography requires a coherent integration of several ecological concepts into a single theory in order to perform conceptual and methodological innovations, such as the switch from single-species distribution to community distribution.
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Coll, M., et al. "Ecological indicators to capture the effects of fishing on biodiversity and conservation status of marine ecosystems." Ecological Indicators. 60 (2016): 947–962.
Résumé: IndiSeas (“Indicators for the Seas”) is a collaborative international working group that was established in 2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data availability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii) mean maximum life span of surveyed fish species, (iv) proportion of predatory fish in the surveyed community, (v) proportion of under and moderately exploited stocks, (vi) total biomass of surveyed species, and (vii) mean trophic level of the landed catch. In line with the Nagoya Strategic Plan of the Convention on Biological Diversity (2011–2020), we extended this suite to emphasize the broader biodiversity and conservation risks in exploited marine ecosystems. We selected a subset of indicators from a list of empirically based candidate biodiversity indicators initially established based on ecological significance to complement the original IndiSeas indicators. The additional selected indicators were: (viii) mean intrinsic vulnerability index of the fish landed catch, (ix) proportion of non-declining exploited species in the surveyed community, (x) catch-based marine trophic index, and (xi) mean trophic level of the surveyed community. Despite the lack of data in some ecosystems, we also selected (xii) mean trophic level of the modelled community, and (xiii) proportion of discards in the fishery as extra indicators. These additional indicators were examined, along with the initial set of IndiSeas ecological indicators, to evaluate whether adding new biodiversity indicators provided useful additional information to refine our understanding of the status evaluation of 29 exploited marine ecosystems. We used state and trend analyses, and we performed correlation, redundancy and multivariate tests. Existing developments in ecosystem-based fisheries management have largely focused on exploited species. Our study, using mostly fisheries independent survey-based indicators, highlights that biodiversity and conservation-based indicators are complementary to ecological indicators of fishing pressure. Thus, they should be used to provide additional information to evaluate the overall impact of fishing on exploited marine ecosystems.
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D'agata, S., et al. "Marine reserves lag behind wilderness in the conservation of key functional roles." Nat. Commun.. 7 (2016): 12000.
Résumé: 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 h travel time from the main market compared with even the oldest (38 years old), largest (17,500 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.
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Evans, S. M., et al. "Patterns of species range evolution in Indo-Pacific reef assemblages reveal the Coral Triangle as a net source of transoceanic diversity." Biol. Lett.. 12.6 (2016): 20160090.
Résumé: The Coral Triangle in the Indo-Pacific is a region renowned for exceptional marine biodiversity. The area could have acted as a 'centre of origin' where speciation has been prolific or a 'centre of survival' by providing refuge during major environmental shifts such as sea-level changes. The region could also have acted as a 'centre of accumulation' for species with origins outside of the Coral Triangle, owing to it being at a central position between the Indian and Pacific oceans. Here, we investigated support for these hypotheses using population-level DNA sequence-based reconstructions of the range evolution of 45 species (314 populations) of Indo-Pacific reef-associated organisms. Our results show that populations undergoing the most ancient establishment were significantly more likely to be closer to the centre of the Coral Triangle than to peripheral locations. The data are consistent with the Coral Triangle being a net source of coral-reef biodiversity for the Indo-Pacific region, suggesting that the region has acted primarily as a centre of survival, a centre of origin or both. These results provide evidence of how a key location can influence the large-scale distributions of biodiversity over evolutionary timescales.
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Giakoumi, S., et al. "Space invaders; biological invasions in marine conservation planning." Divers. Distrib.. 22.12 (2016): 1220–1231.
Résumé: AimBiological invasions are major contributors to global change and native biodiversity decline. However, they are overlooked in marine conservation plans. Here, we examine for the first time the extent to which marine conservation planning research has addressed (or ignored) biological invasions. Furthermore, we explore the change of spatial priorities in conservation plans when different approaches are used to incorporate the presence and impacts of invasive species. LocationGlobal analysis with a focus on the Mediterranean Sea region. MethodsWe conducted a systematic literature review consisting of three steps: (1) article selection using a search engine, (2) abstract screening and (3) review of pertinent articles, which were identified in the second step. The information extracted included the scale and geographical location of each case study as well as the approach followed regarding invasive species. We also applied the software Marxan to produce and compare conservation plans for the Mediterranean Sea that either protect, or avoid areas impacted by invasives, or ignore the issue. One case study focused on the protection of critical habitats, and the other on endemic fish species. ResultsWe found that of 119 papers on marine spatial plans in specific biogeographic regions, only three (2.5%) explicitly took into account invasive species. When comparing the different conservation plans for each case study, we found that the majority of selected sites for protection (ca. 80%) changed in the critical habitat case study, while this proportion was lower but substantial (27%) in the endemic fish species case study. Main conclusionsBiological invasions are being widely disregarded when planning for conservation in the marine environment across local to global scales. More explicit consideration of biological invasions can significantly alter spatial conservation priorities. Future conservation plans should explicitly account for biological invasions to optimize the selection of marine protected areas.
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Jacquet, C., et al. "No complexity-stability relationship in empirical ecosystems." Nat. Commun.. 7 (2016): 12573.
Résumé: Understanding the mechanisms responsible for stability and persistence of ecosystems is one of the greatest challenges in ecology. Robert May showed that, contrary to intuition, complex randomly built ecosystems are less likely to be stable than simpler ones. Few attempts have been tried to test May's prediction empirically, and we still ignore what is the actual complexity-stability relationship in natural ecosystems. Here we perform a stability analysis of 116 quantitative food webs sampled worldwide. We find that classic descriptors of complexity (species richness, connectance and interaction strength) are not associated with stability in empirical food webs. Further analysis reveals that a correlation between the effects of predators on prey and those of prey on predators, combined with a high frequency of weak interactions, stabilize food web dynamics relative to the random expectation. We conclude that empirical food webs have several non-random properties contributing to the absence of a complexity-stability relationship.
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Jeanbille, M., et al. "Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments." Front. Microbiol.. 7 (2016): Unsp-1303.
Résumé: Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.
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Jousset, A., et al. "High functional diversity stimulates diversification in experimental microbial communities." Sci. Adv.. 2.6 (2016): e1600124.
Résumé: There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available.
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Leprieur, F., et al. "Historical and contemporary determinants of global phylogenetic structure in tropical reef fish faunas." Ecography. 39.9 (2016): 825–835.
Résumé: 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.
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Maire, Eva, et al. "How accessible are coral reefs to people? A global assessment based on travel time." Ecol. Lett.. 19.4 (2016): 351–360.
Résumé: The depletion of natural resources has become a major issue in many parts of the world, with the most accessible resources being most at risk. In the terrestrial realm, resource depletion has classically been related to accessibility through road networks. In contrast, in the marine realm, the impact on living resources is often framed into the Malthusian theory of human density around ecosystems. Here, we develop a new framework to estimate the accessibility of global coral reefs using potential travel time from the nearest human settlement or market. We show that 58% of coral reefs are located <30min from the nearest human settlement. We use a case study from New Caledonia to demonstrate that travel time from the market is a strong predictor of fish biomass on coral reefs. We also highlight a relative deficit of protection on coral reef areas near people, with disproportional protection on reefs far from people. This suggests that conservation efforts are targeting low-conflict reefs or places that may already be receiving de facto protection due to their isolation. Our global assessment of accessibility in the marine realm is a critical step to better understand the interplay between humans and resources.
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Mouillot, D., et al. "Global marine protected areas do not secure the evolutionary history of tropical corals and fishes." Nat. Commun.. 7 (2016): 10359.
Résumé: 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.
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Navarro, J., et al. "Differences in the relative roles of environment, prey availability and human activity in the spatial distribution of two marine mesopredators living in highly exploited ecosystems." J. Biogeogr.. 43.3 (2016): 440–450.
Résumé: Aim Identifying the main factors affecting the spatial distribution of marine predators is essential in order to evaluate their distribution patterns, predict the potential impact of human activities on their populations and design accurate management actions. This information is also valuable from a more general management perspective, as marine predators are often considered indicators of habitat quality. In this context, we aimed to determine the degree to which environmental features, prey availability and human activities interact and influence spatial distribution of two marine mesopredator elasmobranchs, the small-spotted catshark (Scyliorhinus canicula) and the Mediterranean starry ray (Raja asterias), living in a highly human-exploited environment. Location Mediterranean Sea. Methods With information obtained from an extended experimental survey, we investigated the relative importance of environmental variables, prey availability and human activities on the spatial distribution of the abundance, biomass and occurrence rate of these marine mesopredators using deviance partitioning analyses. Results Our results revealed that environmental variables were the most important factors explaining the spatial distribution of Mediterranean starry ray, whereas small-spotted catshark distribution was also influenced by prey availability and human factors. From a management point of view, these findings suggest that Mediterranean starry ray could be a good candidate as an indicator species of demersal environmental quality. On the other hand, the distribution of the small-spotted catshark, which responds in an interactive and complex way to environment, prey availability and particular human activities, may be misleading as an environmental indicator. Main conclusions The spatial distribution of elasmobranchs in highly human-impacted marine areas can reflect the interactive and combined effects of multiple factors. To avoid misunderstandings, attention should be paid to statistical procedures allowing the separation of pure and joint contribution of the factors driving the observed spatial patterns.
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Quétel, C., et al. "Iles Eparses (SW Indian Ocean) as reference ecosystems for environmental research." Acta Oecologica (2016): 1–8.
Résumé: TAAF ensures since 2007 the management of 5 small tropical islands lying in the southwestern Indian Ocean: the Iles Eparses. These islands share an exceptional natural heritage including many marine and terrestrial endemic species. At a regional scale the Iles Eparses are some of the most pristine ecosystems, largely preserved from anthropogenic impacts due to their geographical isolation and a historically very limited human occupation. In this context, TAAF wished that Iles Eparses become unique natural laboratories for earth scientists and environmental process observation – like climate change impacts – but also sustainable biodiversity sanctuaries for which the scientific community should provide baseline ecological data to inform on appropriate conservation tools. An inter-agency research consortium emerged in 2009 to meet this commitment for the Iles Eparses. This program was intended to set a science framework in accordance with France' objectives for Research and Conservation. It enabled between 2009 and 2014 the implementation of 18 cross-disciplinary research projects ranging from geology to ecology and represented by the variety of the proposed articles in this special issue. Altogether research projects have dramatically increased knowledge on the Iles Eparses' ecosystems and have provided the first overview of their diversity, their functions and their dynamics and its determinants. In particular applied research efforts have supplied a significant amount of ecological evidence that is now available to develop optimal conservation strategy to ensure the Iles Eparses' long-term biodiversity value. These findings point out that the continuation of research activity in the Iles Eparses should be considered a priority.
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Seddon, N., et al. "Biodiversity in the Anthropocene: prospects and policy." Proc. R. Soc. B-Biol. Sci.. 283.1844 (2016): 20162094.
Résumé: Meeting the ever-increasing needs of the Earth's human population without excessively reducing biological diversity is one of the greatest challenges facing humanity, suggesting that newapproaches to biodiversity conservation are required. One idea rapidly gaining momentum-as well as opposition-is to incorporate the values of biodiversity into decision-making using economic methods. Here, we develop several lines of argument for how biodiversity might be valued, building on recent developments in natural science, economics and science-policy processes. Then we provide a synoptic guide to the papers in this special feature, summarizing recent research advances relevant to biodiversity valuation and management. Current evidence suggests that more biodiverse systems have greater stability and resilience, and that by maximizing key components of biodiversity we maximize an ecosystem's long-term value. Moreover, many services and values arising from biodiversity are interdependent, and often poorly captured by standard economic models. We conclude that economic valuation approaches to biodiversity conservation should (i) account for interdependency and (ii) complement rather than replace traditional approaches. To identify possible solutions, we present a framework for understanding the foundational role of hard-to-quantify ` biodiversity services' in sustaining the value of ecosystems to humanity, and then use this framework to highlight new directions for pure and applied research. In most cases, clarifying the links between biodiversity and ecosystem services, and developing effective policy and practice for managing biodiversity, will require a genuinely interdisciplinary approach.
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Sheehan, E. V., et al. "An experimental comparison of three towed underwater video systems using species metrics, benthic impact and performance." Methods Ecol. Evol.. 7.7 (2016): 843–852.
Résumé: Managing ecological systems, which operate over large spatial scales, is inherently difficult and often requires sourcing data from different countries and organizations. The assumption might be made that data collected using similar methodologies are comparable, but this is rarely tested. Here, benthic video data recorded using different towed underwater video systems (TUVSs) were experimentally compared. Three technically different TUVSs were compared on different seabed types (rocky, mixed ground and sandy) in Kingmere Marine Conservation Zone, off the south coast of England. For each TUVS, species metrics (forward facing camera), seabed impact (backward facing camera) and operational performance (strengths and limitations of equipment and video footage) were compared with the aim of providing recommendations on their future use and comparability of data between different systems. Statistically significant differences between species richness, density, cover and assemblage composition were detected amongst devices and were believed to be mostly due to their optical specifications. As a result of their high image definition and large field of vision both the benthic contacting heavy and benthic tending TUVS provided good quality footage and ecological measurements. However, the heaviest TUVS proved difficult to operate on irregular ground and was found to cause the most impact to the seabed. The lightest TUVS (benthic contacting light) struggled to maintain contact with the seabed. The benthic tending TUVS was able to fly over variable seabed relief and was comparably the least destructive. Results from this study highlight that particular care should be given to sled and optic specifications when developing a medium- or long-term marine protected area monitoring programme. Furthermore, when using data gathered from multiple sources to test ecological questions, different equipment specifications may confound observed ecological differences. A benthic tending TUVS is recommended for benthic surveys over variable habitat types, particularly in sensitive areas, such as marine protected areas.
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Toussaint, A., et al. "Global functional diversity of freshwater fish is concentrated in the Neotropics while functional vulnerability is widespread." Sci Rep. 6 (2016): 22125.
Résumé: Worldwide biodiversity assessments have mainly focused on species richness but little is known about the diversity of species roles, i.e. functional diversity, while this is a key facet to understanding the consequences of global changes on the ecosystem services to human societies. Here, we report the world pattern of functional diversity of freshwater fish using a database encompassing morphological characteristics of more than 9,000 species. The Neotropical realm hosts more than 75% of global functional diversity while other realms each host less than 25%. This discrepancy is mediated by high functional uniqueness in some diversified Neotropical fish orders. Surprisingly, functional diversity patterns were weakly related to functional vulnerability. In the Neotropics the loss of threatened species will cause a limited loss of functional diversity (<10%) whereas in the Nearctic and Palearctic realms, decline of the functional diversity will reach 43% and 33%, respectively, conferring a high functional vulnerability to these realms. Conservation of the Neotropical fish diversity is a key target to maintain world fish functional diversity, but this should not hide the pressing need to conserve the vulnerable fish faunas of the rest of the world, in which functional diversity is to a large extent supported by threatened species.
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Tribot, A. - S., et al. "Taxonomic and functional diversity increase the aesthetic value of coralligenous reefs." Sci Rep. 6 (2016): 34229.
Résumé: The aesthetic value of landscapes contributes to human well-being. However, studies which have investigated the link between biodiversity and ecosystem services have not taken aesthetic value into account. In this study we evaluated how the aesthetics of coralligenous reefs, a key marine ecosystem in the Mediterranean, is perceived by the general public and how aesthetic preferences are related to biodiversity facets (taxonomic, phylogenetic and functional diversities). We performed both biodiversity measures and online-surveys of aesthetic perception on photographic quadrats sampled along the French Mediterranean coast. Our results show that species richness and functional richness have a significant positive effect on aesthetic value. Most of the ecological literature, exploring the relationship between biodiversity and ecosystem functioning and service has focused so far on 'economical' aspects of biodiversity (provision or regulation). Our results illustrate that cultural facets, such as 'beauty', should also be central in our motivations to preserve ecological diversity.
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2015 |
Coll, M., et al. "'Low-hanging fruit' for conservation of marine vertebrate species at risk in the Mediterranean Sea." Frontiers in Microbiology. 24.2 (2015): 226–239.
Résumé: AimConservation priorities need to take the feasibility of protection measures into account. In times of economic pressure it is essential to identify the low-hanging fruit' for conservation: areas where human impacts are lower and biological diversity is still high, and thus conservation is more feasible. LocationWe used the Mediterranean large marine ecosystem (LME) as a case study to identify the overlapping areas of low threats and high diversity of vertebrate species at risk. MethodsThis LME is the first in the world to have a complete regional IUCN Red List assessment of the native marine fish. We augmented these data with distributions of marine mammals, marine turtles and seabirds at risk, and we calculated the spatial distributions of species at risk (IUCN densities). Using cumulative threats we identified priority areas for conservation of species at risk' (PACS), where IUCN diversities are high and threats are low. We assessed whether IUCN diversities and PACS were spatially congruent among taxa and we quantified whether PACS corresponded to current and proposed protected areas. ResultsIUCN densities and PACS were not highly correlated spatially among taxa. Continental shelves and deep-sea slopes of the Alboran Sea, western Mediterranean and Tunisian Plateau/Gulf of Sidra are identified as relevant for fish species at risk. The eastern side of the western Mediterranean and the Adriatic Sea are identified as most relevant for endemic fish, and shelf and open sea areas distributed through the LME are most important for marine mammals and turtles at risk, while specific locations of the western Mediterranean Sea and the Aegean and Levantine seas are highlighted for seabirds. Main conclusionsLarge parts of the areas of PACS fell outside current or proposed frameworks to be prioritized for conservation. PACS may be suitable candidates for contributing to the 10% protection target for the Mediterranean Sea by 2020.
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Cucherousset, J., and S. Villeger. "Quantifying the multiple facets of isotopic diversity: New metrics for stable isotope ecology." Ecological Indicators. 56 (2015): 152–160.
Résumé: Abstract
Stable isotope analyses have emerged as an insightful tool for ecologists, with quantitative methods being developed to analyse data at the population, community and food web levels. In parallel, functional ecologists have developed metrics to quantify the multiple facets of functional diversity in a n-dimensional space based on functional traits. Here, we transferred and adapted metrics developed by functional ecologists into a set of four isotopic diversity metrics (isotopic divergence, dispersion, evenness and uniqueness) complementary to the existing metrics. Specifically, these new metrics are mathematically independent of the number of organisms analysed and account for the abundance of organisms. They can also be calculated with more than two stable isotopes. In addition, we also provide a procedure for calculating the levels of isotopic overlap (similarity and turnover) between two groups of organisms. These metrics have been implemented into new functions in R made freely available to users and we illustrated their application using stable isotope values from a freshwater fish community. Transferring the framework developed initially for measuring functional diversity to stable isotope ecology will allow more efficient assessments of changes in the multiple facets of isotopic diversity following anthropogenic disturbances.
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Mazel, F., et al. "Mammalian phylogenetic diversity-area relationships at a continental scale." Ecology. 96.10 (2015): 2814–2822.
Résumé: In analogy to the species-area relationship (SAR), one of the few laws in ecology, the phylogenetic diversity-area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increase with area. Although investigating PDAR has the potential to unravel the underlying processes shaping assemblages across spatial scales and to predict PD loss through habitat reduction, it has been little investigated so far. Focusing on PD has noticeable advantages compared to species richness (SR), since PD also gives insights on processes such as speciation/extinction, assembly rules and ecosystem functioning. Here we investigate the universality and pervasiveness of the PDAR at continental scale using terrestrial mammals as study case. We define the relative robustness of PD (compared to SR) to habitat loss as the area between the standardized PDAR and standardized SAR (i.e., standardized by the diversity of the largest spatial window) divided by the area under the standardized SAR only. This metric quantifies the relative increase of PD robustness compared to SR robustness. We show that PD robustness is higher than SR robustness but that it varies among continents. We further use a null model approach to disentangle the relative effect of phylogenetic tree shape and nonrandom spatial distribution of evolutionary history on the PDAR. We find that, for most spatial scales and for all continents except Eurasia, PDARs are not different from expected by a model using only the observed SAR and the shape of the phylogenetic tree at continental scale. Interestingly, we detect a strong phylogenetic structure of the Eurasian PDAR that can be predicted by a model that specifically account for a finer biogeographical delineation of this continent. In conclusion, the relative robustness of PD to habitat loss compared to species richness is determined by the phylogenetic tree shape but also depends on the spatial structure of PD.
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Mostajir, B., et al. "Microbial Food Webs in Aquatic and Terrestrial Ecosystems." Eds. J. - C. Bertrand, et al. Environmental Microbiology: Fundamentals and Applications. Springer Netherlands, 2015. 485–509.
Résumé: In microbial food webs, different types of interactions occur between microorganisms themselves and with meio- and macroorganisms. After an historical and general introduction, the biological components of the microbial food webs in the pelagic and benthic marine and lake ecosystems, as well as in the terrestrial ecosystems, are presented. The functioning of the microbial food webs in different ecosystems is illustrated and explained, including the trophic pathways and transfer of matter from microbial food webs toward meio- and macroorganisms of the superior trophic levels, the nutrient recycling in the aquatic environments, and the decomposition of organic matter in soils. Finally, the factors regulating microbial food webs, primarily “top-down” and “bottom-up” controls, are described with a special focus on the role of viruses in the aquatic microbial food webs.
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2014 |
Cheng, L., et al. "Temporal changes in the taxonomic and functional diversity of fish communities in shallow Chinese lakes: the effects of river–lake connections and aquaculture." Aquatic Conservation: Marine and Freshwater Ecosystems. 24.1 (2014): 23–34.
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D'Agata, S., et al. "Human-Mediated Loss of Phylogenetic and Functional Diversity in Coral Reef Fishes." Current Biology. 24.5 (2014): 555–560.
Résumé: 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 parrot-fishes, at 25 and 15 inhabitants/km(2), respectively, while parrot-fish 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.
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Jeanmougin, M., et al. "Fine-scale urbanization affects Odonata species diversity in ponds of a megacity (Paris, France)." Acta Oecologica-International Journal of Ecology. 59 (2014): 26–34.
Résumé: Current developments in urban ecology include very few studies focused on pond ecosystems, though ponds are recognized as biodiversity hotspots. Using Odonata as an indicator model, we explored changes in species composition in ponds localized along an urban gradient of a megacity (Paris, France). We then assessed the relative importance of local- and landscape-scale variables in shaping Odonata alpha-diversity patterns using a model-averaging approach. Analyses were performed for adult (A) and adult plus exuviae (AE) census data. At 26 ponds, we recorded 657 adults and 815 exuviae belonging to 17 Odonata species. The results showed that the Odonata species assemblage composition was not determined by pond localization along the urban gradient. Similarly, pond characteristics were found to be similar among urban, suburban and periurban ponds. The analyses of AE census data revealed that fine-scale urbanization (i.e., increased density of buildings surrounding ponds) negatively affects Odonata alpha-diversity. In contrast, pond localization along the urban gradient weakly explained the alpha-diversity patterns. Several local-scale variables, such as the coverage of submerged macrophytes, were found to be significant drivers of Odonata alpha-diversity. Together, these results show that the degree of urbanization around ponds must be considered instead of pond localization along the urban gradient when assessing the potential impacts of urbanization on Odonata species diversity This work also indicates the importance of exuviae sampling in understanding the response of Odonata to urbanization. (C) 2014 Elsevier Masson SAS. All rights reserved.
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Katsanevakis, S., et al. "Invading the Mediterranean Sea: biodiversity patterns shaped by human activities." Front. Mar. Sci. 1 (2014).
Résumé: Human activities, such as shipping, aquaculture, and the opening of the Suez Canal, have led to the introduction of nearly 1000 alien species into the Mediterranean Sea. We investigated how human activities, by providing pathways for the introduction of alien species, may shape the biodiversity patterns in the Mediterranean Sea. Richness of Red Sea species introduced through the Suez Canal (Lessepsian species) is very high along the eastern Mediterranean coastline, reaching a maximum of 129 species per 100 km2, and declines toward the north and west. The distribution of species introduced by shipping is strikingly different, with several hotspot areas occurring throughout the Mediterranean basin. Two main hotspots for aquaculture-introduced species are observed (the Thau and Venice lagoons). Certain taxonomic groups were mostly introduced through specific pathways—fish through the Suez Canal, macrophytes by aquaculture, and invertebrates through the Suez Canal and by shipping. Hence, the local taxonomic identity of the alien species was greatly dependent on the dominant maritime activities/interventions and the related pathways of introduction. The composition of alien species differs among Mediterranean ecoregions; such differences are greater for Lessepsian and aquaculture-introduced species. The spatial pattern of native species biodiversity differs from that of alien species: the overall richness of native species declines from the north-western to the south-eastern regions, while the opposite trend is observed for alien species. The biodiversity of the Mediterranean Sea is changing, and further research is needed to better understand how the new biodiversity patterns shaped by human activities will affect the Mediterranean food webs, ecosystem functioning, and the provision of ecosystem services.
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Mazel, F., et al. "Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity." Global Ecology and Biogeography. 23.8 (2014): 836–847.
Résumé: Aim To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them with 'classical' hotspots based on species richness (SR) alone. Location Global. Methods SR, PD and FD were computed for 782 terrestrial ecoregions using the distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework incorporating the relative species coverage in each ecoregion. We built large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each facet of diversity. Finally we defined hotspots as the top-ranked ecoregions. Results While ignoring relative species coverage led to a fairly good congruence between biome-scale top ranked SR, PD and FD hotspots, ecoregions harbouring a rich and abundantly represented evolutionary history and FD did not match with the top-ranked ecoregions defined by SR. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than SR as a function of area. Main conclusions The fact that PD/FD reach their maximum value faster than SR could suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it has been quantified at a global scale and should have important consequences for conservation. Incorporating relative species coverage into the delineation of multifaceted hotspots of diversity led to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail to preserve those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at a global scale.
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Oikonomou, A., F. Leprieur, and I. D. Leonardos. "Biogeography of freshwater fishes of the Balkan Peninsula." Hydrobiologia. 738.1 (2014): 205–220.
Résumé: Delineating biogeographical regions is a critical step towards the establishment and evaluation of conservation priorities. In the present study, we analysed the distribution patterns of the freshwater fish of an understudied European biodiversity hotspot, the Balkan Peninsula. Based on the most extensive available database of native freshwater fish species distributions, we performed a hierarchical clustering analysis to identify the major biogeographical regions of the Balkan Peninsula. We also highlighted the 'hottest hotspots' of freshwater fish diversity across the delimited biogeographical regions by describing the patterns of species richness, endemic and vulnerable species; indicator species were also determined. The bioregionalisation scheme consisted of eight groups of drainage basins that correspond to distinct regions of the Balkan Peninsula. Overall, the delineated biogeographical regions varied in terms of species richness, endemism, vulnerability (i.e. extinction threats) and indicator species composition. From a conservation perspective, this study emphasises the prioritisation of areas characterised by high levels of irreplaceability (endemism) and vulnerability (i.e. the Attikobeotia region, Ionian Sea and Prespa Lakes) and stresses the necessity of implementing a network of protected freshwater areas across the Balkan Peninsula.
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Parravicini, V., et al. "Global mismatch between species richness and vulnerability of reef fish assemblages." Ecology Letters. 17.9 (2014): 1101–1110.
Résumé: 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.
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Pellissier, L., et al. "Quaternary coral reef refugia preserved fish diversity." Science. 344.6187 (2014): 1016–1019.
Résumé: 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.
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Potier, M., et al. "Influence of mesoscale features on micronekton and large pelagic fish communities in the Mozambique Channel." Deep-Sea Research Part II.Topical Studies in Oceanography. 100.No spécial (2014): 184–199.
Résumé: We investigated the diversity and distribution of two communities, micronekton organisms and large predatory fishes, sampled in mesoscale features of the Mozambique Channel from 2003 to 2009, by combining mid-water trawls, stomach contents of fish predators and instrumented longline fishing surveys. The highest species richness for assemblages was found in divergences and fronts rather than in the core of eddies. Despite an unbalanced scheme, diversity indices did not differ significantly between cyclonic and anticyclonic eddies, divergences and fronts. We found that eddies and associated physical cues did not substantially affect the distribution of micronektonic species which are mainly driven by the diel vertical migration pattern. Top predators exhibited a more complex response. Swordfish (Xiphias gladius) associated better with mesoscale features than tunas, with a clear preference for divergences which is consistent with the diel vertical migrations and occurrence of its main prey, the flying squids Sthenoteuthis oualaniensis (Ommastrephidae). On the other hand, the probability of presence of yellowfin tuna was not tied to any specific eddy structure. However, the highest values of positive yellowfin CPUEs were associated with low horizontal gradients of sea-level anomalies. We also showed a non-linear response of positive yellowfin CPUEs with respect to the depth of the minimal oxygen content. The larger the distance between the hooks and the minimal oxygen layer, towards the surface or at greater depths, the higher the CPUE, highlighting that yellowfin congregated in well-oxygenated waters. Micronekton sampled by mid-water trawls and stomach contents exhibited different species composition. The highly mobile organisms were not caught by trawling whereas they remain accessible to predators. The combination of stomach contents and mid-water trawls undoubtedly improved our understanding of the micronekton assemblage distribution. Our results provide some evidence that mesoscale features in the Mozambique Channel do not strongly affect the distribution of the mid-trophic level organisms such as micronekton and most of the large predatory fishes, and hypotheses are proposed to support this result.
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Zupan, L., et al. "Spatial mismatch of phylogenetic diversity across three vertebrate groups and protected areas in Europe." Diversity and Distributions. 20.6 (2014): 674–685.
Résumé: Aim We investigate patterns of phylogenetic diversity in relation to species diversity for European birds, mammals and amphibians to evaluate their congruence and highlight areas of particular evolutionary history. We estimate the extent to which the European network of protected areas (PAs) network retains interesting evolutionary history areas for the three groups separately and simultaneously. Location Europe Methods Phylogenetic (QE(PD)) and species diversity (SD) were estimated using the Rao's quadratic entropy at 10 ' resolution. We determined the regional relationship between QE(PD) and SD for each taxa with a spatial regression model and used the tails of the residuals (QE(RES)) distribution to identify areas of higher and lower QE(PD) than predicted. Spatial congruence of biodiversity between groups was assessed with Pearson correlation coefficient. A simple classification scheme allowed building a convergence map where a convergent pixel equalled to a QE(RES) value of the same sign for the three groups. This convergence map was overlaid to the current PAs network to estimate the level of protection in convergent pixels and compared it to a null expectation built on 1000 randomization of PAs over the landscape. Results QE(RES) patterns across vertebrates show a strong spatial mismatch highlighting different evolutionary histories. Convergent areas represent only 2.7% of the Western Palearctic, with only 8.4% of these areas being covered by the current PAs network while a random distribution would retain 10.4% of them. QE(RES) are unequally represented within PAs: areas with higher QE(PD) than predicted are better covered than expected, while low QE(PD) areas are undersampled. Main conclusions Patterns of diversity strongly diverge between groups of vertebrates in Europe. Although Europe has the world's most extensive PAs network, evolutionary history of terrestrial vertebrates is unequally protected. The challenge is now to reconcile effective conservation planning with a contemporary view of biodiversity integrating multiple facets.
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Buisson, L., et al. "Toward a loss of functional diversity in stream fish assemblages under climate change." Glob. Change Biol.. 19.2 (2013): 387–400.
Résumé: The assessment of climate change impacts on biodiversity has so far been biased toward the taxonomic identification of the species likely either to benefit from climate modifications or to experience overall declines. There have still been few studies intended to correlate the characteristics of species to their sensitivity to climate change, even though it is now recognized that functional trait-based approaches are promising tools for addressing challenges related to global changes. In this study, two functional indices (originality and uniqueness) were first measured for 35 fish species occurring in French streams. They were then combined to projections of range shifts in response to climate change derived from species distribution models. We set out to investigate: (1) the relationship between the degrees of originality and uniqueness of fish species, and their projected response to future climate change; and (2) the consequences of individual responses of species for the functional diversity of fish assemblages. After accounting for phylogenetic relatedness among species, we have demonstrated that the two indices used measure two complementary facets of the position of fish species in a functional space. We have also rejected the hypothesis that the most original and/or less redundant species would necessarily experience the greatest declines in habitat suitability as a result of climate change. However, individual species range shifts could lead simultaneously both to a severe decline in the functional diversity of fish assemblages, and to an increase in the functional similarity among assemblages, supporting the hypothesis that disturbance favors communities with combination of common traits and biotic homogenization as well. Our findings therefore emphasize the importance of going beyond the simple taxonomic description of diversity to provide a better assessment of the likely future effects of environmental changes on biodiversity, thus helping to design more effective conservation and management measures.
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Dobrovolski, R., et al. "Global agricultural expansion and carnivore conservation biogeography." Biol. Conserv.. 165 (2013): 162–170.
Résumé: Global conservation prioritization must address conflicting land uses. We tested for spatial congruence between agricultural expansion in the 21st century and priority areas for carnivore conservation worldwide. We evaluated how including agricultural expansion data in conservation planning reduces such congruence and estimated the consequences of such an approach for the performance of resulting priority area networks. We investigated the correlation between projections of agricultural expansion and the solutions of global spatial prioritizations for carnivore conservation through the implementation of different goals: (1) purely maximizing species representation and (2) representing species while avoiding sites under high pressure for agriculture expansion. We also evaluated the performance of conservation solutions based on species' representation and their spatial congruence with established global prioritization schemes. Priority areas for carnivore conservation were spatially correlated with future agricultural distribution and were more similar to global conservation schemes with high vulnerability. Incorporating future agricultural expansion in the site selection process substantially reduced spatial correlation with agriculture, resulting in a spatial solution more similar to global conservation schemes with low vulnerability. Accounting for agricultural expansion resulted in a lower representation of species, as the average proportion of the range represented reduced from 58% to 32%. We propose that priorities for carnivore conservation could be integrated into a strategy that concentrates different conservation actions towards areas where they are likely to be more effective regarding agricultural expansion. (C) 2013 Elsevier Ltd. All rights reserved.
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Escalas, A., et al. "A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales." Environmental microbiology. 15.10 (2013): 2642–2657.
Résumé: Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (alpha), regional (gamma) and the overall difference between local communities (beta). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the beta component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically explicit relationship among the alpha, beta and gamma components. We propose a unified quantitative framework based on the Rao quadratic entropy, to obtain an additive decomposition of diversity (gamma = alpha + beta), so the three components can be compared, and that integrate the relationship (phylogenetic or functional) among Microbial Diversity Units that compose a microbial community. We show how this framework is adapted to all types of molecular data, and we highlight crucial issues in microbial ecology that would benefit from this framework and propose ready-to-use R-functions to easily set up our approach.
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Gravel, D., et al. "Inferring food web structure from predator-prey body size relationships." Methods in Ecology and Evolution. 4.11 (2013): 1083–1090.
Résumé: 1. Current global changes make it important to be able to predict which interactions will occur in the emerging ecosystems. Most of the current methods to infer the existence of interactions between two species require a good knowledge of their behaviour or a direct observation of interactions. In this paper, we overcome these limitations by developing a method, inspired from the niche model of food web structure, using the statistical relationship between predator and prey body size to infer the matrix of potential interactions among a pool of species. 2. The novelty of our approach is to infer, for any species of a given species pool, the three species-specific parameters of the niche model. The method applies to both local and metaweb scales. It allows one to evaluate the feeding interactions of a new species entering the community. 3. We find that this method gives robust predictions of the structure of food webs and that its efficiency is increased when the strength of the body-size relationship between predators and preys increases. 4. We finally illustrate the potential of the method to infer the metaweb structure of pelagic fishes of the Mediterranean sea under different global change scenarios.
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Maury, O., and J. - C. Poggiale. "From individuals to populations to communities: A dynamic energy budget model of marine ecosystem size-spectrum including life history diversity." Journal of Theoretical Biology. 324 (2013): 52–71.
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Mouillot, D., et al. "The challenge of delineating biogeographical regions: nestedness matters for Indo-Pacific coral reef fishes." Journal of Biogeography. 40.12 (2013): 2228–2237.
Résumé: AimThe 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. LocationAs 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. MethodsWe used the turnover and nestedness components of the SOrensen 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). ResultsLow 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 SOrensen 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 conclusionsWe 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.
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