Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Recent theoretical and field studies conducted in both terrestrial and marine ecosystems have suggested that diversity could be a more complex and multi-component concept than previously thought. However, it is still poorly understood to what extent the information provided by the various indices is complementary with regard to diversity, and to what extent this complementarity is reproducible in different situations or at different scales of observation. In the present work, we have analysed the reproducibility of the empirical relationships between 11 diversity indices related to four major aspects (components) of species diversity (species richness, rarity, evenness and species taxonomy) in order to determine whether there is a general pattern of redundancy or complementarity in diversity measures that holds across years, areas and spatial scales. We have applied this approach to groundfish diversity through the analysis of 2404 trawl hauls collected during the first large-scale annual surveys carried out using a single sampling design throughout the northern Mediterranean Sea (ranging from 36.3 to 45.7 degrees N, and 5.3 degrees W to 28 degrees E). Whatever the years, areas and scales studied, we found a strong reproducibility in the number and the nature of the main complementary components of diversity. The whole set of diversity indices considered may be roughly split into 6 complementary groups of descriptors. This result highlights that, in contrast to what is still the usual practice, monitoring diversity should not be based on only one or two of the most widely used components, even at large scale. Finally, in a context where developing tools for monitoring diversity is considered as a high priority worldwide, the strong reproducibility of the relationships between diversity indices we observed offers a basis for discussion of the feasibility and relevance of proposing a general shortlist of indices for monitoring diversity at different management scales.
Ecography (0906-7590) (Wiley-blackwell Publishing, Inc), 2010-12 , Vol. 33 , N. 6 , P. 1123-1135

Droits : 2010 The Authors / Ecography
http://archimer.ifremer.fr/doc/00029/14064/11382.pdf
DOI:10.1111/j.1600-0587.2009.06259.x
http://archimer.ifremer.fr/doc/00029/14064/

Éditeur(s) : Inter-Research
Résumé : The species richness pattern of groundfish species in the entire northern Mediterranean Sea was examined at 3 spatial scales: region, large biogeographical zone and basin. We analysed 1914 trawl hauls collected using a single sampling design in the trawlable areas of the continental shelves between the Strait of Gibraltar and the Strait of Dardanelles (from 36.3 to 45.7 degrees N and 5.3 degrees W to 28 E). Spatial pattern in species diversity was assessed using complementary methods (Chao2 estimates of total species richness, mean species richness and beta diversity). No matter which scale was used, the expected longitudinally decreasing trend in species richness, which has been widely described in previous studies, did not appear when comparing estimates of total species richness per unit of area. Only the mean species richness pattern showed a moderate eastwards decrease at the largest spatial scale, but the trend progressively disappeared as the scale of analysis was reduced. In contrast to what is usually expected, our results suggest that Atlantic inflow does not play a key role in the present spatial pattern of fish species richness within the northern Mediterranean Sea. Furthermore, we show that the Aegean Sea can no longer be considered the least species-diverse zone in the northern Mediterranean Sea. Our results provide the first description of a quantitative 'reference state', with which the temporal changes in species richness patterns throughout the entire northern Mediterranean Sea can be compared in the future.
Marine Ecology Progress Series (0171-8630) (Inter-Research), 2007-07 , Vol. 341 , P. 191-203

Droits : 2007 Inter-Research
http://archimer.ifremer.fr/doc/2007/publication-3569.pdf
DOI:10.3354/meps341191
http://archimer.ifremer.fr/doc/00000/3569/

Éditeur(s) : HAL CCSD Wiley
Résumé : A standardized rapid inventory method providing information on both tree species diversity and aboveground carbon stocks in tropical forests will be an important tool for evaluating efforts to conserve biodiversity and to estimate the carbon emissions that result from deforestation and degradation (REDD). Herein, we contrast five common plot methods differing in shape, size, and effort requirements to estimate tree diversity and aboveground tree biomass (AGB). We simulated the methods across six Neotropical forest sites that represent a broad gradient in forest structure, tree species richness, and floristic composition, and we assessed the relative performance of methods by evaluating the bias and precision of their estimates of AGB and tree diversity. For a given sample of forest area, a several small' (<1ha) sampling strategy led to a smaller coefficient of variation (CV) in the estimate of AGB than a few large' one. The effort (person-days) required to achieve an accurate AGB estimate (<10% CV), however, was greater for the smallest plots (0.1ha) than for a compromise approach using 0.5ha modified Gentry plots, which proved to be the most efficient method to estimate AGB across all forest types. Gentry plots were also the most efficient at providing accurate estimates of tree diversity (<10% CV of Hill number). We recommend the use of the 0.5ha modified Gentry plot method in future rapid inventories, and we discuss a set of criteria that should inform any choice of inventory method.
ISSN: 0006-3606

hal-01032408
https://hal.archives-ouvertes.fr/hal-01032408
DOI : 10.1111/btp.12006

Éditeur(s) : Elsevier
Résumé : The multi-component aspect of species diversity of groundfish assemblages was examined on the basis of a set of experimental trawl surveys conducted on the east coast of Corsica. We analysed and compared the structuration of diversity within three different bathymetric strata: the continental shelf (60-120 m depth), the upper slope (250-400 m) and the lower slope (450-570 m). For each of these three bathymetric strata, we simultaneously analysed 12 indices that are theoretically complementary and relate to 4 diversity components: (1) the number of species, (2) rarity, (3) evenness and (4) taxonomic diversity. Principal component analysis based on Spearman's correlation coefficients was carried out to investigate empirical relationships between the selected indices. Our results showed not only that a single diversity index cannot provide a complete view of the groundfish diversity along the east coast of Corsica, but also that-in some cases-one index cannot even encapsulate a complete description of a specific diversity component. We also found that the nature and the number of independent diversity components slightly varied from one bathymetric stratum to another. The main differences-which mainly occurred in the deepest bathymetric stratum-might be associated with lower density of individuals and lower dominance of some species at deeper depths. Finally, this study is the first dealing with groundfish diversity in this area, which is currently characterized by one of the lowest fishing intensity rates in the northern Mediterranean Sea. It might be considered as a first '' reference state '' with a view to monitoring the spatio-temporal changes in species diversity patterns along the east coast of Corsica in the future. (C) 2007 Elsevier B.V. All rights reserved.
Fisheries Research (0165-7836) (Elsevier), 2007-12 , Vol. 88 , N. 1-3 , P. 120-132

Droits : 2007 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2007/publication-3512.pdf
DOI:10.1016/j.fishres.2007.08.003
http://archimer.ifremer.fr/doc/00000/3512/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The effects of biodiversity on the transmission of infectious diseases now stand as a cornerstone of many public health policies. The upper Amazonia and Guyana shield are hot-spots of biodiversity that offer genuine opportunities to explore the relationship between the risk of transmission of Chagas disease and the diversity of its triatomine vectors. Over 730 triato-mines were light-trapped in four geomorphological landscapes shaping French-Guiana, and we determined their taxonomic status and infection by Trypanosoma cruzi. We used a model selection approach to unravel the spatial and temporal variations in species abundance , diversity and infection. The vector community in French-Guiana is typically made of one key species (Panstrongylus geniculatus) that is more abundant than three secondary species combined (Rhodnius pictipes, Panstrongylus lignarius and Eratyrus mucronatus), and four other species that complete the assemblage. Although the overall abundance of adult triatomines does not vary across French-Guiana, their diversity increases along a coastal-inland gradient. These variations unravelled a non-monotonic relationship between vector biodiversity and the risk of transmission of Chagas disease, so that intermediate biodiversity levels are associated with the lowest risks. We also observed biannual variations in triatomine abundance, representing the first report of a biannual pattern in the risk of Cha-gas disease transmission. Those variations were highly and negatively correlated with the average monthly rainfall. We discuss the implications of these patterns for the transmission of T. cruzi by assemblages of triatomine species, and for the dual challenge of controlling Amazonian vector communities that are made of both highly diverse and mostly intrusive species.
ISSN: 1935-2727

Droits : http://creativecommons.org/licenses/by/
hal-01298091
https://hal-univ-perp.archives-ouvertes.fr/hal-01298091
https://hal-univ-perp.archives-ouvertes.fr/hal-01298091/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01298091/file/journal.pntd.0004427.PDF
DOI : 10.1371/journal.pntd.0004427

Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
Ecological connectivity is important for effective marine planning and biodiversity conservation. Our aim was to identify factors important in influencing variation in benthic community structure on shallow rocky reefs in 2 regions of the Mediterranean Sea with contrasting oceanographic regimes. We assessed beta (β) diversity at 146 sites in the littoral and shallow sub-littoral from the Adriatic/Ionian Seas (eastern region) and Ligurian/Tyrrhenian Seas (western region) using a null modelling approach to account for variation in species richness. The distance decay relationship between species turnover within each region and geographic distance by sea was determined using generalised linear models. Mantel tests were used to examine correlations between β diversity and connectivity by ocean currents, estimated from Lagrangian dispersal simulations. Variation in β diversity between sites was partitioned according to environmental and spatial components using a distance-based redundancy approach. Species turnover along a gradient of geographic distance was greater by a factor of 3 to 5 in the western region than the eastern region, suggesting lower con-nectivity between sites. β diversity was correlated with connectivity by ocean currents at both depths in the eastern region but not in the western region. The influence of spatial and environmental predictors of β diversity varied considerably between regions, but was similar between depths. Our results highlight the interaction of oceanographic, spatial and environmental processes influencing benthic marine β diversity. Persistent currents in the eastern region may be responsible for lower observed β diversity compared to the western region, where patterns of water circulation are more variable.
Marine Ecology Progress Series

Droits : http://creativecommons.org/licenses/by/
hal-01357935
https://hal-univ-perp.archives-ouvertes.fr/hal-01357935
https://hal-univ-perp.archives-ouvertes.fr/hal-01357935/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01357935/file/m553p001.pdf
DOI : 10.3354/meps11783

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.
ISSN: 0168-6496

hal-01383722
http://hal.upmc.fr/hal-01383722
http://hal.upmc.fr/hal-01383722/document
http://hal.upmc.fr/hal-01383722/file/Forster_2016_Benthic_protists.pdf
DOI : 10.1093/femsec/fiw120

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Tropical plant diversity is extraordinarily high at both local and regional scales. Many studies have demonstrated that natural enemies maintain local diversity via negative density dependence, but we know little about how natural enemies influence beta-diversity across habitats and/or regions. One way herbivores could influence plant beta-diversity is by driving allocation trade-offs that promote habitat specialization across resource gradients. We therefore predicted that increasing resource availability should be accompanied by increasing herbivory rates and decreasing plant allocation to defense. Second, relative abundances within plant lineages are predicted to reflect patterns of habitat specialization and allocation trade-offs. A phylogenetic context is vital not only to compare homologous plant traits (including defense strategies) across habitat types, but also to connect evolutionary trade-offs to patterns of species diversification in each phylogenetic lineage. We tested these predictions for trees in white-sand, clay terra firme, and seasonally flooded forests in Peru and French Guiana that represent the range of soil fertility, forest structure, and floristic compositions found throughout the Amazon region. We established 74 0.5-ha plots in these habitats and sampled all trees. Within 12 representative plots we marked newly expanding leaves of 394 saplings representing 68 species, including the most abundant species in each plot in addition to species from five focal lineages: Swartzia and Inga (Fabaceae), Protieae (Burseracaeae), Bombacoideae (Malvaceae), and Micropholis (Sapotaceae). We measured total leaf production rates for each sapling and calculated relative herbivory impact as the ratio between herbivory rate and leaf production rate. Herbivory rates averaged 2.1% per month, did not correlate with leaf production rate, and were similar across habitats. Relative herbivore impacts exceeded leaf production rates for most species. Leaf production rate averaged 2.8%, was significantly higher in seasonally flooded forests than the other two habitats, and exhibited significant correlations with specific leaf area. Species with high herbivory rates exhibited significantly lower relative abundances in terra firme forests. Overall, focal species within lineages present contrasting patterns regarding their herbivory rates and leaf production rate within habitats. These results highlight why a lineage-based approach is necessary when attempting to connect hypotheses regarding evolutionary trade-offs to community assembly patterns.
ISSN: 0012-9658

hal-01032418
https://hal.archives-ouvertes.fr/hal-01032418

Éditeur(s) : HAL CCSD
Résumé : International audience
Over the past decade, much attention has been devoted to the development of forest biomass estimation methods at a stand scale, leading to the establishment of allometric models (Chave et al., 2014). These allometric equations use a unique wood specific gravity value (WSG) per species, but neglect the within tree variations of WSG found by others (Wiemann & Williamson, 1989).The main objectives of this study are (1) to illustrate the diversity of radial (from pith to bark) and longitudinal (from bottom to top) patterns of WSG variation within and between species, (2) to highlight different trends of WSG radial variations and the possible misinterpretations of these trends due to the effect of heartwood and (3) to link these variations and patterns to the successional status of the species (from pioneer to sciaphilic species).We sampled 33 small trees (10 Wood sciences underpinning tropical ecology and management. International closing symposium of the XYLAREDD project.
Tervuren, Belgium

hal-01188894
https://hal-sde.archives-ouvertes.fr/hal-01188894

Éditeur(s) : EDP Sciences
Résumé : Twelve diel surveys were carried out in three reservoirs of Sri Lanka viz. Minneriya, Udawalawe and Victoria, to investigate diel feeding patterns, daily ration and relative food consumption in fish populations. Stomach content weights of different size classes of various fish species in the three reservoirs in 12 diel surveys were analysed using an iterative method, MAXIMS. Predominantly herbivorous or detritivorous fish species such as Amblypharyngodon melettinus and Oreochromis niloticus exhibited one peak in the diel feeding pattern. Two peak feeding periods were evident in predominantly insectivores and/or zooplanktivores (e. g., Puntius chola and Rasbora daniconius) and interestingly in macrophyte feeders (i.e., Etroplus suratensis, Puntius filamentosus and Tilapia rendalli). It might be possible that all species with two feeding peaks in diel feeding patterns rely on vision for feeding. Food consumption per biomass (Q/B ratio) defined as amount of food consumed per unit weight of an age-structured population of fish was estimated on the basis of the average quantities of food consumed over a long period of time by various size classes in order to minimize the bias of estimates.
Douze séries d'échantillonnage ont été effectuées dans trois lacs-réservoirs du Sri Lanka : Minneriya, Udawalawe et Victoria, afin d'étudier le modèle journalier d'alimentation, les rations journalières et à la consommation relative des populations de poissons. Les poids des contenus stomacaux de différentes classes de taille ont ainsi été analysés en utilisant une méthode itérative, MAXIMS. Les espèces herbivores ou détritivores telles que Amblypharyngodon melettinus et Oreochromis niloticus montrent un pic dans l'activité de nutrition. Tandis que les espèces détrivores et/ou zooplanctivores en présentent deux (ex., Puntius chola et Rasbora daniconius) de même que des espèces se nourrissant de macrophytes (ex., Etroplus suratensis, Puntius filamentosus et Tilapia rendalli). Il est possible que la vision joue un rôle chez ces espèces présentant deux pics journaliers d'alimentation. La consommation de nourriture par rapport à la biomasse (le rapport Q/B) est défini comme la quantité d'aliment consommé par unité de poids d'une population de poissons structurée en âge, sur la base de quantités moyennes de nourriture consommée sur une longue période de temps et par diverses classes de taille, afin de minimiser les biais dans les estimations.
Aquatic Living Resources (0990-7440) (EDP Sciences), 2006-07 , Vol. 19 , N. 3 , P. 229-237

Droits : 2006 EDP
http://archimer.ifremer.fr/doc/2006/publication-2134.pdf
DOI:10.1051/alr:2006023
http://archimer.ifremer.fr/doc/00000/2134/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Cnidarians living in symbiosis with photosynthetic dinoflagellates (commonly named zooxanthellae) are exposed to high concentrations of reactive oxygen species (ROS) upon illumination. To quench ROS production, both the cnidarian host and zooxanthellae express a full suite of antioxidant enzymes. Studying antioxidative balance is therefore crucial to understanding how symbiotic cnidarians cope with ROS production. We characterized glutathione peroxidases (GPx) in the symbiotic cnidarian Anemonia viridis by analysis of their isoform diversity, their activity distribution in the three cellular compartments (ectoderm, endoderm and zooxanthellae) and their involvement in the response to thermal stress. We identified a GPx repertoire through a phylogenetic analysis showing 7 GPx transcripts belonging to the A. viridis host and 4 GPx transcripts strongly related to Symbiodinium sp. The biochemical approach, used for the first time with a cnidarian species, allowed the identification of GPx activity in the three cellular compartments and in the animal mitochondrial fraction, and revealed a high GPx electrophoretic diversity. The symbiotic lifestyle of zooxanthellae requires more GPx activity and diversity than that of free-living species. Heat stress induced no modification of GPx activities. We highlight a high GPx diversity in A. viridis tissues by genomic and biochemical approaches. GPx activities represent an overall constitutive enzymatic pattern inherent to symbiotic lifestyle adaptation. This work allows the characterization of the GPx family in a symbiotic cnidarian and establishes a foundation for future studies of GPx in symbiotic cnidarians.
ISSN: 0300-9084

hal-01404424
http://hal.upmc.fr/hal-01404424
http://hal.upmc.fr/hal-01404424/document
http://hal.upmc.fr/hal-01404424/file/Pey_Characterization_of.pdf
DOI : 10.1016/j.biochi.2016.10.016

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Genetic diversity is crucial for species' maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.
ISSN: 0962-1083

hal-01681650
https://hal.archives-ouvertes.fr/hal-01681650
DOI : 10.1111/mec.14389

Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
Sphaeroma serratum is a marine isopod species that inhabits seashores from Europe to West Africa. The individuals live under stones in direct contact with reduced sediments and harbour a diverse bacterial community on the cuticle of their pleopods. We investigated the diversity of these epibiotic bacteria on male (pubescent and senescent) and female specimens with electron microscopic obser vations and molecular tools. The microbial community of S. serratum was shown to be composed of at least 5 bacterial morphotypes observed on the pleopodal cuticle in all male specimens. Using fluorescence in situ hybridization, we identified 5 major phylogenetic groups (α-, β-, γ- and δ-Proteobacteria and Archaea) whereas denaturing gradient gel electro - phoresis (DGGE) of PCR-amplified 16S rRNA gene fragments of epibiotic bacteria revealed 50 bands. The bacterial community associated with S. serratum seems more diverse than in other marine crustaceans, such as Rimicaris. The relative diversity of this bacterial community was also studied in relation to the molt cycle. The comparison of DGGE band patterns of several individuals from female, pubescent male and senescent male groups revealed that the bacterial community diversity was dependent on the sex and the age of the individuals and more generally on the molt status.
Marine Ecology Progress Series

hal-00743743
https://hal.univ-antilles.fr/hal-00743743
DOI : 10.3354/meps09711

Éditeur(s) : HAL CCSD Paris : Muséum national d'histoire naturelle
Résumé : International audience
Coral reefs are one of the most diverse ecosystems on Earth and sustain millions of people worldwide.However, coral reefs are temporally dynamic and fragile systems subject to ever increasing disturbancesof anthoropogenic and natural origins. Understanding the patterns and trajectories of changes through time isurgently needed to estimate the resilience of coral reefs. To ascertain these patterns, we depend on the availabilityof long-term datasets, which are seldom available. In this study, we present the data set which allowed us to analysethe long-term trends of coral and fish assemblages for the island of Moorea (French Polynesia) from 1983to 2014, a dataset spanning 32 years, comprising two Acanthaster planci outbreaks (1987 and 2006) and severalhurricanes (1982, 1983, 1991 and 2010), on three permanent monitoring sites (quadrats of 50 × 2 m2) located onboth fringing and barrier reefs as well as on the outer slope. Coral cover oscillated significantly over time, particularlyon the outer slope where it suffered greatly from the effects of A. planci outbreaks and hurricanes. Totalfish and commercial fish abundances varied significantly across the three habitats. Prior to 2000, both total fishand herbivorous fish abundances increased on the barrier reef while after this time, numbers began to drop significantlyalong the outer slope. Species richness for total, commercialized and herbivorous fish increased over thesampling period for all three habitats. There were varied responses amongst species to disturbances on the outerslope over the sampling period: while some tended to disappear for a while before reappearing, others showed apeak in abundance in the middle of the sampling period, and still others increased or decreased continuously orwere stable over time. Our results support the view that coral reefs are highly dynamic systems and that differentfunctional groups show different temporal trajectories. While disturbance is probably the major driver for coralcover dynamics, its impact is less obvious for fish, possibly due to their mobility and population dynamics whichmay mask the effect of disturbance.
Les récifs coralliens sont des systèmes dynamiques et diversifiés régulièrement soumis à des perturbationsnaturelles et anthropiques, sources d’hétérogénéité spatiale et temporelle dans la structure et la dynamique deces communautés d’organismes que sont, entre autres, les poissons et les coraux. Récemment, il a été démontréque les activités humaines pouvaient modifier les régimes naturels de perturbations des récifs coralliens en transformantles événements ponctuels en perturbations persistantes ou en stress chronique, soit en introduisant denouveaux types de perturbations, soit en ajoutant ou altérant certaines perturbations naturelles nécessaires au bonmaintien de la dynamique inhérente aux récifs. Dans cette étude, nous présentons la base de données qui nouspermettra d’analyser les tendances à long-terme des assemblages de poissons et de coraux de l’île de Moorea(Polynésie française) entre 1983 et 2014 sur une période de 32 ans, comprenant deux proliférations d’Acanthasterplanci (1987 et 2006) et plusieurs cyclones (1982, 1983, 1991 et 2010), sur trois sites de suivi permanents(quadrats de 50 × 2 m2) sur les récifs barrière et frangeant ainsi que sur la pente externe. La couverture corallienneprésente de fortes oscillations, en particulier sur la pente externe où elle a répondu fortement à la proliférationd’A. planci et des cyclones. Les abondances des poissons totaux et des poissons commercialisés montrent destendances contrastées sur les trois habitats, avec, plus particulièrement, une augmentation sur le récif barrière etune diminution sur la pente externe après 2000. Ces tendances se retrouvent chez les poissons herbivores dansces deux habitats. La richesse spécifique des poissons totaux, commerciaux et herbivores, augmente de façoncontinue au cours de la période d’étude dans les trois habitats. Des groupes particuliers d’espèces répondentdifféremment aux perturbations de la pente externe au cours du suivi : alors que certaines espèces ont tendanceà disparaître pendant quelques années avant de réapparaître, d’autres présentent un pic en terme d’abondanceen milieu de suivi ; d’autres espèces ont des abondances qui augmentent ou diminuent de façon continue, etd’autres encore montrent des abondances stables. Ceci indique que les récifs coralliens sont des systèmes trèsdynamiques dans lesquels les perturbations naturelles peuvent affecter les espèces de façon différente. Alors quele régime de perturbations naturelles semble être important pour la dynamique de la couverture corallienne danscertains habitats, cela se retrouve beaucoup moins pour les poissons. Cette atténuation des fluctuations spatialeset temporelles peut être due aux aptitudes de dispersion de nombreuses espèces de poissons, capables de chercherun autre habitat favorable en cas de perturbation de l’habitat corallien d’origine.
ISSN: 0399-0974

hal-01282378
https://hal-univ-perp.archives-ouvertes.fr/hal-01282378

Éditeur(s) : HAL CCSD Elsevier Elsevier Masson
Résumé : Thalattosuchia was a diverse clade of marine crocodylomorphs known from the Early Jurassic to the Early Cretaceous. Recent studies have hypothesized that their extinction was two-phased: (1) habitat loss near/at the Jurassic-Cretaceous boundary heavily reduced their morphofunctional diversity, particularly in Europe, while (2) climate change and a shift in marine fauna during the Early Cretaceous (either at the Valanginian-Hauterivian boundary or during the early Hauterivian) finished off the already stressed clade. Unfortunately, the Cretaceous fossil record of thalattosuchians is poor, with only one putative “teleosaurid” specimen and approximately ten metriorhynchid specimens. Here we re-describe the youngest known teleosaurid from the Cretaceous (Valanginian of south-eastern France). Originally considered to be a teleosaurid (possibly Steneosaurus), we demonstrate that it belongs to Metriorhynchidae, and a newly discovered subclade, Plesiosuchina. It differs from Plesiosuchus in the pattern of tooth enamel ornamentation and the variation in dentary alveoli size. Referring this specimen to Metriorhynchidae means there are no definitive Cretaceous teleosaurid specimens. Furthermore, it suggests that both durophagous and piscivorous teleosaurids became extinct at the end of the Jurassic. Interestingly, this is the fourth metriorhynchid lineage known to cross the Jurassic-Cretaceous boundary. As such, it would appear that the two thalattosuchian families responded very differently to the lowering sea levels at the end of the Jurassic: teleosaurids possibly became extinct, while metriorhynchids were seemingly unaffected.
ISSN: 0753-3969

hal-01122803
https://hal.archives-ouvertes.fr/hal-01122803
DOI : 10.1016/j.annpal.2014.01.002

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
1. Our understanding of the contribution of interspecific interactions to functional diversity in nature lags behind our knowledge of spatial and temporal patterns. Although two-species mutualisms are found in all types of ecosystems, the study of their ecological influences on other community members has mostly been limited to third species, while their influence on entire communities remains largely unexplored. 2. We hypothesized that mutualistic interactions between two respective ant species and an epiphyte mediate the biological traits composition of entire invertebrate communities that use the same host plant, thereby affecting food webs and functional diversity at the community level. 3. Aechmea mertensii (Bromeliaceae) is both a phytotelm ('plant-held water') and an ant-garden epiphyte. We sampled 111 bromeliads (111 aquatic invertebrate communities) associated with either the ant Pachycondyla goeldii or Camponotus femoratus. The relationships between ants, bromeliads and invertebrate abundance data were examined using a redundancy analysis. Biological traits information for invertebrates was structured using a fuzzy-coding technique, and a co-inertia analysis between traits and abundance data was used to interpret functional differences in bromeliad ecosystems. 4. The vegetative traits of A. mertensii depended on seed dispersion by C. femoratus and P. goeldii along a gradient of local conditions. The ant partner selected sets of invertebrates with traits that were best adapted to the bromeliads' morphology, and so the composition of the biological traits of invertebrate phytotelm communities depends on the identity of the ant partner. Biological traits suggest a bottom-up control of community structure in C. fenaoratus-associated phytotelmata and a greater structuring role for predatory invertebrates in P. goeldii-associated plants. 5. This study presents new information showing that two-species mutualisms affect the functional diversity of a much wider range of organisms. Most biological systems form complex networks where nodes (e.g. species) are more or less closely linked to each other, either directly or indirectly, through intermediate nodes. Our observations provide community-level information about biological interactions and functional diversity, and perspectives for further observations intended to examine whether large-scale changes in interacting species/community structure over broad geographical and anthropogenic gradients affect ecosystem functions.
Functional Ecology

hal-01096909
https://hal-agroparistech.archives-ouvertes.fr/hal-01096909
DOI : 10.1111/j.1365-2435-2011.01863.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : Analyses of tree diversity and community composition in tropical rain forests are usually based either on general herbarium data or on a restricted number of botanical plots. Despite their high taxonomic accuracy, both types of data are difficult to extrapolate to landscape scales. Meanwhile, forestry surveys provide quantitative occurrence data on large areas, and are thus increasingly used for landscape-scale analyses of tree diversity. However, the reliability of these approaches has been challenged because of the ambiguity of the common (vernacular) names used by foresters and the complexity of tree taxonomy in those hyper-diverse communities.We developed and tested a novel approach to evaluate taxonomic reliability of forestry surveys and to propagate the resulting uncertainty in the estimates of several diversity indicators (alpha and beta entropy, Fisher-alpha and Sørensen similarity). Our approach is based on Monte-Carlo processes that simulate communities by taking into account the expected accuracy and reliability of common names. We tested this method in French Guiana, on 9 one-hectare plots (4279 trees – DBH ⩾ 10 cm) for which both common names and standardized taxonomic determinations were available. We then applied our method of community simulation on large forestry inventories (560 ha) at the landscape scale and compared the diversity indices obtained for 10 sites with those computed from precise botanical determination situated at the same localities.We found that taxonomic reliability of forestry inventories varied from 22% (species level) to 83% (family level) in this Amazonian region. Indices computed directly with raw forestry data resulted in incorrect values, except for Gini–Simpson beta-diversity. On the contrary, our correction method provides more accurate diversity estimates, highly correlated with botanical measurements, for almost all diversity indices at both regional and local scales. We obtained a robust ranking of sites consistent with those shown by botanical inventories.These results show that (i) forestry inventories represent a significant part of taxonomic information, (ii) the relative diversity of regional sites can be successfully ranked using forestry inventory data using our method and (iii) forestry inventories can valuably contribute to the detection of large-scale diversity patterns when biases are well-controlled and corrected.The tools we developed as R-functions are available in supplementary material and can be adapted with local parameters to be used for forest management and conservation issues in other regional contexts
ISSN: 0378-1127

hal-01204219
https://hal.archives-ouvertes.fr/hal-01204219
DOI : 10.1016/j.foreco.2014.05.045
PRODINRA : 286554

Éditeur(s) : HAL CCSD
Résumé : Tropical forests are a biodiversity hotspot, with the coexistence of numerous species until a fine spatial scale. Particularly, 16.000 tree species coexist in Amazonia, 1.800 in Frenche Guiana and between 120 and more than 200 tree species per hectare. However, there are some uncertainties in maintaining diversity in regard to global changes. Hence before predicting the diversity evolution face of global changes, fundamental studies are needed to understand which assembly processes are involved in the maintenance of diversity. These fundamental studies still relevant given the lack of consensus on the relative importance of assembly processes. This thesis is a continuation of these fundamental studies, using innovative integrative approach, at multi-scale, to address three types of diversity: taxonomic diversity, functional and phylogenetic. Our results challenge the importance of environmental filtering for hydrological and chemical properties of soils, versus the importance of biotic interactions on community assembly. Furthermore, our results suggest that species distributions could be affected by forest dynamics related to falling trees and therefore by light availability. Finally, we have highlighted the importance of dispersal limitation on community assembly.
Les forêts tropicales représentent un ‘hotspot’ de diversité avec un nombre considérable d’espèces qui coexistent jusqu’à une échelle locale fine. Plus particulièrement, 16 000 espèces d’arbres coexistent en Amazonie, 1 800 en Guyane française et entre 120 et plus de 200 espèces d’arbres par hectare. Cependant, le maintien de cette diversité face aux changements globaux actuels et à venir (qu’ils soient anthropiques ou climatiques…) est incertain. Avant de pouvoir prédire l’évolution de la diversité face aux changements globaux, un travail fondamental est nécessaire afin de comprendre les processus d’assemblage des communautés, processus qui maintiennent cette diversité. Ce travail est réalisé depuis de nombreuses années en écologie et reste d’actualité vu l’absence de consensus quant à l’importance relative des processus d’assemblage. Cette thèse s’inscrit dans la continuité de ce travail fondamental en utilisant une approche intégrative innovante, qui aborde de manière multi-échelle trois types de diversité : diversité taxonomique, fonctionnelle et phylogénétique. Nos résultats questionnent sur l'importance du filtrage environnemental quant aux propriétés hydrologiques et chimiques des sols, et sur celle des interactions biotiques dans l’assemblage de la communauté étudiée. Par ailleurs, nos résultats suggèrent que les distributions d’espèces puissent être influencées par la dynamique forestière en lien avec les chutes d’arbres et donc avec la disponibilité en lumière. Enfin, nous avons mis en évidence l’importance de la limitation de dispersion.
https://tel.archives-ouvertes.fr/tel-01418447

NNT : 2016YANE0003
tel-01418447
https://tel.archives-ouvertes.fr/tel-01418447
https://tel.archives-ouvertes.fr/tel-01418447/document
https://tel.archives-ouvertes.fr/tel-01418447/file/these.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Geographical distribution of parasite species can provide insights into the evolution and diversity of parasiticcommunities. Biogeography of marine parasites is poorly known, especially because it requires anunderstanding of host-parasite interactions, information that is rare, especially over large spatial scales.Here, we have studied the biogeographical patterns of dactylogyrid parasites of chaetodontids, one of themost well-studied fish families, in the tropical Indo-west Pacific region. Dactylogyrid parasites were collectedfrom gills of 34 butterflyfish species (n = 560) at nine localities within an approximate area of62 million km2. Thirteen dactylogyrid species were identified, with richness ranging from 6 to 12 speciesat individual localities. Most dactylogyrid communities were dominated by Haliotrema angelopterum orHaliotrema aurigae, for which relative abundance was negatively correlated (q = !0.59). Parasite richnessand diversity were highest in French Polynesia and the Great Barrier Reef (Australia) and lowest in Palau.Three biogeographic regions were identified based on dactylogyrid dissimilarities: French Polynesia,characterised by the dominance of H. angelopterum, the western Pacific region dominated by H. aurigae,and Ningaloo Reef (Australia), dominated by Euryhaliotrema berenguelae. Structure of host assemblageswas the main factor explaining the dissimilarity (turnover and nestedness components of the Bray-Curtis dissimilarity and overall Bray-Curtis dissimilarity) of parasite communities between localities,while environment was only significant in the turnover of parasite communities and overall dissimilarity.Spatial structure of localities explained only 10% of the turnover of parasite communities. The interactionof the three factors (host assemblages, environment and spatial structure), however, explained the highestamounts of variance of the dactylogyrid communities, indicating a strong colinearity between the factors.Our findings show that spatial arrangement of chaetodontid dactylogyrids in the tropical Indo-westPacific is primarily characterised by the turnover of the main Haliotrema spp., which is mainly explainedby the structure of host assemblages.
ISSN: 0020-7519

hal-01562156
https://hal-univ-perp.archives-ouvertes.fr/hal-01562156
DOI : 10.1016/j.ijpara.2017.01.006

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow.
ISSN: 0737-4038

hal-01032153
https://hal.archives-ouvertes.fr/hal-01032153
DOI : 10.1093/molbev/msp043