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
Résumé : Integrating ecological connectivity into marine ecosystem management and planning is important, especially in a global context of severe fish stocks depletion and growing habitat degradation. Environmental tools such as Marine Protected Areas have been proposed to protect biodiversity, restore damaged ecosystems, sustain fisheries, and rebuild overexploited stocks. The effectiveness of marine protected areas depends in part on the maintenance of connectivity between marine populations, linked by ecological processes such as larval dispersal. In this thesis, we applied a biophysical model driven by ocean currents derived from satellite altimetry to evaluate connectivity between Western Indian Ocean reefs and across the current MPA system in the Mediterranean Sea. We applied different methods of analysis such as graph-theoretic and clustering. In the Western Indian Ocean, marine connectivity analyses show that the number of connections between reefs increases with fish pelagic larval duration. It also highlights a low connectivity across the region and a high interconnectivity within several regions (Mozambique Channel, Mascarene archipelago). In the Mediterranean Sea, connectance is globally low at the regional scale. This connectance is more important in Western than Eastern Mediterranean. Moreover, the marine connectivity analyses revealed high domestic connectivity rates. Depending on the study area, priority reefs or sites for MPA implementation are proposed. Finally, implications for transboundary marine policies and regional cooperation are discussed.
Intégrer les connaissances sur la connectivité écologique dans la gestion des écosystèmes marins est essentiel, surtout dans un contexte d'appauvrissement des ressources marines et de dégradation des habitats côtiers à l'échelle mondiale. Des outils environnementaux, tels que les Aires Marines Protégées ont été mises en œuvre pour protéger la biodiversité, restaurer les écosystèmes endommagés, soutenir les pêcheries et reconstituer les stocks surexploités. Leur efficacité dépend en partie du maintien de la connectivité entre les populations marines, assurée à travers divers processus écologiques dont la dispersion larvaire. Dans le cadre de ce travail de thèse, un modèle biophysique intégrant des données de courants, issues de mesures d'altimétrie par satellite, a été utilisé pour évaluer la connectivité entre les récifs de l'océan Indien d'une part, et à travers le réseau d'AMP de Méditerranée d'autre part. Différentes méthodes d'analyse ont été utilisées, telles que la théorie des graphes et le clustering. Dans l'océan Indien occidental, l'analyse des connectivités marines montre que le nombre de connexions entre les récifs augmente avec la durée de vie larvaire des poissons. Elle met également en évidence une faible connectivité à l'échelle de la région, mais une forte inter-connectivité au sein de plusieurs sous-régions (Canal du Mozambique, Mascareignes). En Méditerranée, la connectance est globalement faible à l'échelle régionale, bien que plus importante dans le bassin occidental que le bassin oriental. L'analyse des connectivités marines montre également un taux de connectivité élevé à l'échelle d'un même pays. Selon le cas d'étude, une liste de récifs ou de sites prioritaires dans la mise en œuvre des AMP a été proposée. Enfin, les implications de ces résultats en termes de politiques transfrontalières et de coopération régionale sont discutées.
https://tel.archives-ouvertes.fr/tel-01269631

NNT : 2015LARE0003
tel-01269631
https://tel.archives-ouvertes.fr/tel-01269631
https://tel.archives-ouvertes.fr/tel-01269631/document
https://tel.archives-ouvertes.fr/tel-01269631/file/2015lare0003_ECrochelet.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Marine Protected Areas (MPAs) are increasingly used for biodiversity conservation and the management of sustainable fisheries. The use of taxonomic surrogates in routine monitoring of the reserve effects on fish assemblages may represent a promising method due to its substantial technical and economic benefits. However, higher taxonomic ranks should be used as surrogates with caution, especially for fish, where the approach is still virtually undocumented. This study aims to shed light on relationships between taxonomic relatedness and ecological similarity, which is crucial to assess the relevance of species surrogacy to reflect species-level information and detect changes in fish related to protection regimes. By analyzing data from a Mediterranean MPA, we show that rather being related to taxonomic relationships, the ability of higher taxa to reflect species-level patterns was explained in terms of aggregation level and distribution of species within taxa. Null models using random aggregations of species were created to identify the best surrogates able to depict changes in responses of assemblages to protection observed at the species-level. Comparison of null model predictions with the more classical higher-taxon approach revealed that the latter was not reliable because, unlike null model outcomes, surrogates determined empirically were not relevant for other subsequent independent monitoring. The effectiveness of species surrogates to depict changes in responses of assemblages to protection observed at the species-level depended (1) on the numerical resolution of the aggregation and (2) the magnitude of differences between protected and unprotected locations. Such findings suggest that surrogacy approaches may be applied for routine monitoring of Mediterranean reef fish communities, although mere empirical determinations of sufficient taxonomy seems to be not reliable, legitimizing the use of alternative methods based on null models. Guidelines for the careful use of species surrogacy in the ecological evaluation of MPAs on fish assemblages are provided.
ISSN: 0006-3207

hal-01174428
https://hal-univ-perp.archives-ouvertes.fr/hal-01174428
DOI : 10.1016/j.biocon.2015.06.002

Éditeur(s) : University of Tasmania, Université de Bretagne Occidentale
Résumé : Empirical evidence and the theoretical literature both point to stock sustainability and the protection of marine biodiversity as important fisheries management issues. Decision-support tools are increasingly required to operationalize the ecosystem-based approach to fisheries management. These tools need to integrate (i) ecological and socio-economic drivers of changes in fisheries and ecosystems; (ii) complex dynamics; (iii) deal with various sources of uncertainty; and (iv) incorporate multiple, rather than single objectives. The stochastic co-viability approach addresses the trade-offs associated with balancing ecological, economic and social objectives throughout time, and takes into account the complexity and uncertainty of the dynamic interactions which characterize exploited ecosystems and biodiversity. This thesis proposes an application of this co-viability approach to the sustainable management of mixed fisheries, using two contrasting case studies: the French Bay of Biscay (BoB) demersal mixed fishery and the Australian Northern Prawn Fishery (NPF). Both fisheries entail direct and indirect impacts on mixed species communities while also generating large economic returns. Their sustainability is therefore a major societal concern. A dynamic bio-economic modelling approach is used to capture the key biological and economic processes governing these fisheries, combining age- (BoB) or size- (NPF) structured models of multiple species with recruitment uncertainty, and multiple fleets (BoB) or fishing strategies (NPF). Economic uncertainties relating to input and output prices are also considered. The bioeconomic models are used to investigate how the fisheries can operate within a set of constraints relating to the preservation of Spawning Stock Biomasses (BoB) or Spawning Stock Size Indices (NPF) of a set of key target species, maintenance of the economic profitability of various fleets (BoB) or the fishery as a whole (NPF), and limitation of fishing impacts on the broader biodiversity (NPF), under a range of alternative scenarios and management strategies. Results suggest that under a status quo strategy both fisheries can be considered as biologically sustainable, while socio-economically (and ecologically in the NPF case) at risk. Despite very different management contexts and objectives, viable management strategies suggest a reduction in the number of vessels in both cases. The BoB simulations allow comparison of the trade-offs associated with different allocations of this decrease across fleets. Notably, co-viability management strategies entail a more equitable allocation of effort reductions compared to strategies aiming at maximizing economic yield. In the NPF, species catch diversification strategies are shown to perform well in controlling the levels of economic risk, by contrast with more specialized fishing strategies. Furthermore analyses emphasize the importance to the fishing industry of balancing global economic performance with inter-annual economic variability. Promising future developments based on this research involve the incorporation of a broader set of objectives including social dimensions, as well as the integration of ecological interactions, to better address the needs of ecosystem-based approaches to the sustainable harvesting of marine biodiversity.
L’objectif général de la thèse est de modéliser les principaux processus biologiques et économiques régissant des pêcheries multi-espèces et multi-flottilles afin de proposer des stratégies viables pour la gestion durable de ces pêcheries mixtes, dans un contexte stochastique et multiobjectif. Plus spécifiquement, cette thèse utilise des analyses de co-viabilité stochastique pour étudier les arbitrages entre des objectifs contradictoires de gestion (conservation, et viabilité économique et sociale) des pêcheries mixtes. Deux pêcheries mixtes sont analysées dans cette thèse: la pêcherie française mixte démersale du golfe de Gascogne et la pêcherie crevettière australienne du Nord (NPF). Ces deux pêcheries sont multi-espèces, et utilisent des stratégies multiples de pêche, induisant des impacts directs et indirects sur les écosystèmes. Cette thèse propose une application de la co-viabilité stochastique à ces deux cas, en prenant en compte leur histoire, leur contexte socio-politique et les différences dans les stratégies et objectifs de gestion. Les résultats suggèrent que le status quo peut être considéré comme une stratégie biologiquement durable mais socio économiquement à risque dans les deux pêcheries (ainsi qu’à risque écologique dans le cas de la pêcherie australienne). Les simulations réalisées pour le golfe de Gascogne permettent de comparer les arbitrages associés à différentes réductions de capacités par flottille et de montrer qu’il existe des solutions de gestion permettant la co-viabilité du système (viabilité biologique des différentes espèces considérées et viabilité socio-économique des flottilles) contrairement à des stratégies de gestion mono-spécifiques ou basées sur la maximisation de la rente. Dans la pêcherie crevettière australienne, l’analyse montre que les stratégies de diversification permettent de limiter le risque économique contrairement aux stratégies plus spécialisées.

Droits : UBO, Univ. Tasmania
http://archimer.ifremer.fr/doc/00206/31731/30134.pdf
http://archimer.ifremer.fr/doc/00206/31731/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The extent of the global human footprint [ 1 ] limits our understanding of what is natural in the marine environment. Remote, near-pristine areas provide some baseline expectations for biomass [ 2, 3 ] and suggest that predators dominate, producing an inverted biomass pyramid. The southern pass of Fakarava atoll—a biosphere reserve in French Polynesia—hosts an average of 600 reef sharks, two to three times the biomass per hectare documented for any other reef shark aggregations [ 4 ]. This huge biomass of predators makes the trophic pyramid inverted. Bioenergetics models indicate that the sharks require ∼90 tons of fish per year, whereas the total fish production in the pass is ∼17 tons per year. Energetic theory shows that such trophic structure is maintained through subsidies [ 5–9 ], and empirical evidence suggests that sharks must engage in wide-ranging foraging excursions to meet energy needs [ 9, 10 ]. We used underwater surveys and acoustic telemetry to assess shark residency in the pass and feeding behavior and used bioenergetics models to understand energy flow. Contrary to previous findings, our results highlight that sharks may overcome low local energy availability by feeding on fish spawning aggregations, which concentrate energy from other local trophic pyramids. Fish spawning aggregations are known to be targeted by sharks, but they were previously believed to play a minor role representing occasional opportunistic supplements. This research demonstrates that fish spawning aggregations can play a significant role in the maintenance of local inverted pyramids in pristine marine areas. Conservation of fish spawning aggregations can help conserve shark populations, especially if combined with shark fishing bans.
ISSN: 0960-9822

hal-01359391
https://hal-univ-perp.archives-ouvertes.fr/hal-01359391
DOI : 10.1016/j.cub.2016.05.058

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Coral bleaching events threaten coral reef habitats globally and cause severe declines of local biodiversity and productivity.Related to high sea surface temperatures (SST), bleaching events are expected to increase as a consequenceof future global warming. However, response to climate change is still uncertain as future low-latitude climatic conditionshave no present-day analogue. Sea surface temperatures during the Eocene epoch were warmer than forecastedchanges for the coming century, and distributions of corals during the Eocene may help to inform models forecastingthe future of coral reefs. We coupled contemporary and Eocene coral occurrences with information on their respectiveclimatic conditions to model the thermal niche of coral reefs and its potential response to projected climate change.We found that under the RCP8.5 climate change scenario, the global suitability for coral reefs may increase up to 16%by 2100, mostly due to improved suitability of higher latitudes. In contrast, in its current range, coral reef suitabilitymay decrease up to 46% by 2100. Reduction in thermal suitability will be most severe in biodiversity hotspots, especiallyin the Indo-Australian Archipelago. Our results suggest that many contemporary hotspots for coral reefs,including those that have been refugia in the past, spatially mismatch with future suitable areas for coral reefs posingchallenges to conservation actions under climate change.
ISSN: 1354-1013

hal-01145464
https://hal.archives-ouvertes.fr/hal-01145464
DOI : 10.1111/gcb.12868

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The Western Indian Ocean harbors one of theworld’s most diverse marine biota yet is threatened byexploitation with few conservation measures in place.Primary candidates for conservation in the region are theScattered Islands (Iles Eparses), a group of relativelypristine and uninhabited islands in the MozambiqueChannel. However, while optimal conservation strategiesdepend on the degree of population connectivity amongspatially isolated habitats, very few studies have beenconducted in the area. Here, we use highly variablemicrosatellite markers from two damselfishes (Amphiprionakallopisos and Dascyllus trimaculatus) with differing lifehistory traits [pelagic larval duration (PLD), adult habitat]to compare genetic structure and connectivity among theseislands using classic population structure indices as well asBayesian clustering methods. All classical fixation indexesFST, RST, G0ST, and Jost’s D show stronger genetic differentiationamong islands for A. akallopisos compared to D.trimaculatus, consistent with the former species’ shorterPLD and stronger adult site attachment, which may restrictlarval dispersal potential. In agreement with these results,the Bayesian analysis revealed clear genetic differentiationamong the islands in A. akallopisos, separating the southerngroup (Bassas da India and Europa) from the center(Juan de Nova) and northern (Iles Glorieuses) islands, butnot for D. trimaculatus. Local oceanographic patterns suchas eddies that occur along the Mozambique Channel appearto parallel the results reported for A. akallopisos, but suchfeatures seem to have little effect on the genetic differentiationof D. trimaculatus. The contrasting patterns ofgenetic differentiation between species within the samefamily highlight the importance of accounting for diverselife history traits when assessing community-wide connectivity,an increasingly common consideration in conservationplanning.
ISSN: 0722-4028

hal-01561992
https://hal-univ-perp.archives-ouvertes.fr/hal-01561992
DOI : 10.1007/s00338-016-1495-z

Éditeur(s) : HAL CCSD
Résumé : il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : ACTIVITY_REPORT
Understanding genomic evolution in wild populations is of particular importance because evolution is a central process in our understanding of populations’ history and their future response to global changes. In addition to fundamental knowledge, the study of populations’ evolution has wide applications such as conservation/restoration genetics or epidemiology. Indeed, genetic diversity is the ‘fuel’ for populations’ evolution and adaptation to new conditions, and estimating the extent and the geographic structure of genetic diversity, as well as identifying the evolutionary forces behind (demography, gene flow, and adaptation) are thus major challenges in the current context of global changes. [br/]A particular attention is currently devoted to the process of genetic divergence in wild populations, with emphases on gene flow, local adaptation, and their interactions. Indeed, adaptation in wild populations is supported in many species by many kinds of experiments based on both quantitative phenotypic traits and molecular data. However, the processes governing populations’ evolution are poorly understood in the tropical rainforest of Amazonia, and the relative influence of neutral and adaptive processes are continuously discussed. [br/]I am a young scientist interested in the process of genomic divergence in wild (tree) populations. I aimed at understanding how evolution structures the genetic diversity and governs molecular divergence in wild populations, with particular emphases on gene flow and local adaptation. During five years as a young scientist, I worked on answering the following questions, focusing on two tree species occupying vulnerable areas: mainly [i]Eperua falcata[/i] in Amazonia and, to a lesser extent, [i]Abies alba[/i] in the Mediterranean area.[br/][u]Scientific questions:[/u][br/]- Which evolutionary drivers are responsible of the structure of genetic diversity in wild populations occupying wide areas? This question was addressed at different geographical scales: from large (regional) to very local (microgeographic) scales. [br/]- What is the relative influence of neutral (gene flow, inbreeding) and adaptive drivers in the process of genetic divergence?[br/]- Is microgeographic adaptation possible in spite of extensive gene flow between populations occupying the extreme boundaries of an ecological gradient? [br/]- What is the extent of natural selection in the (whole) genome of wild populations? [br/][br/]My research work is at the interface between three promising disciplines: Evolutionary genomics (i.e. the study of populations evolution and the evolutionary drivers behind), Bioinformatics (i.e. the treatment of next-generation data), and Bayesian modelling (i.e. the empirical calibration of complex mechanistic model). I intend to take advantage of the recent advances in sequencing and informatic technologies to bring up to date the field of ecological genetics and evolutionary biology, by developing modern research strategies to study the process of genomic divergence in wild populations.
https://hal.archives-ouvertes.fr/hal-01204218

hal-01204218
https://hal.archives-ouvertes.fr/hal-01204218
PRODINRA : 286326

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01224215
http://hal.upmc.fr/hal-01224215
http://hal.upmc.fr/hal-01224215/document
http://hal.upmc.fr/hal-01224215/file/Genome%20Biol%20Evol-2015-Boon-505-21.pdf
DOI : 10.1093/gbe/evv002

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Different marine habitats are characterised by different soundscapes. How or which differences may be representative of the habitat characteristics and/or community structure remains however to be explored. A growing project in passive acoustics is to find a way to use soundscapes to have information on the habitat and on its changes. In this study we have successfully tested the potential of two acoustic indices, i.e. the average sound pressure level and the acoustic complexity index based on the frequency spectrum. Inside and outside marine protected areas of Moorea Island (French Polynesia), sound pressure level was positively correlated with the characteristics of the substratum and acoustic complexity was positively correlated with fish diversity. It clearly shows soundscape can be used to evaluate the acoustic features of marine protected areas, which presented a significantly higher ambient sound pressure level and were more acoustically complex than non-protected areas. This study further emphasizes the importance of acoustics as a tool in the monitoring of marine environments and in the elaboration and management of future conservation plans. Coral reef ecosystems are among the most biologically diverse and complex marine ecosystems worldwide. In addition to their biological and ecological importance, coral reefs support major economic and physical functions (e.g. food production, tourism, biotechnology development and coastal protection) that are essential for many countries 1. Unfortunately, coral reefs are severely threatened: 20% of coral reefs can no longer be defined as such, another 25% are currently endangered and another 25% will be endangered by 2050 2. The frequency and severity of natural perturbations (e.g. cyclone, outbreaks of predators, particularly the crown-of-thorns starfish [COTS] Acanthaster planci) and anthropogenic perturbations (e.g. ocean acidification, pesticides, rising seawater temperatures) on coral reefs have greatly increased worldwide in the last three decades, and, as a consequence, reef communities (fish, coral and benthic invertebrates) have suffered unprecedented levels of decline 3,4
ISSN: 2045-2322

hal-01370610
https://hal-uvsq.archives-ouvertes.fr/hal-01370610
https://hal-uvsq.archives-ouvertes.fr/hal-01370610/document
https://hal-uvsq.archives-ouvertes.fr/hal-01370610/file/2016%20Sci.Rep.pdf
DOI : 10.1038/srep33326

Éditeur(s) : HAL CCSD WILEY-BLACKWELL Wiley
Résumé : International audience
Connectivity among populations determines the dynamics and evolution of populations, and its assessment is essential in ecology in general and in conservation biology in particular. The robust basis of any ecological study is the accurate delimitation of evolutionary units, such as populations, metapopulations and species. Yet a disconnect still persists between the work of taxonomists describing species as working hypotheses and the use of species delimitation by molecular ecologists interested in describing patterns of gene flow. This problem is particularly acute in the marine environment where the inventory of biodiversity is relatively delayed, while for the past two decades, molecular studies have shown a high prevalence of cryptic species. In this study, we illustrate, based on marine case studies, how the failure to recognize boundaries of evolutionary-relevant unit leads to heavily biased estimates of connectivity. We review the conceptual framework within which species delimitation can be formalized as falsifiable hypotheses and show how connectivity studies can feed integrative taxonomic work and vice versa. Finally, we suggest strategies for spatial, temporal and phylogenetic sampling to reduce the probability of inadequately delimiting evolutionary units when engaging in connectivity studies.
ISSN: 0962-1083

hal-01218810
https://hal.archives-ouvertes.fr/hal-01218810
DOI : 10.1111/mec.13048

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
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.
ISSN: 2041-1723

hal-01282920
https://hal-univ-perp.archives-ouvertes.fr/hal-01282920
https://hal-univ-perp.archives-ouvertes.fr/hal-01282920/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01282920/file/ncomms10359.pdf
DOI : 10.1038/ncomms10359

Éditeur(s) : HAL CCSD Elsevier
Résumé : Guadua sarcocarpa and Guadua weberbaueri (Poaceae: Bambuseae) have a negative influence on tree regeneration and recruitment in bamboo-dominated forests of southwestern Amazonia. The lack of advanced regeneration and sparse canopy in this forest type present a considerable challenge for developing sustainable timber management plans. We conducted field studies in the Porto Dias Agroextractive Settlement Project in Acre, Brazil to assess influences of logging in bamboo-dominated forest sites. Taxonomic composition, stand structure, aboveground biomass, commercial timber volume, and commercial tree seedling and bamboo culm density were compared between five logged vs. unlogged sites in different landholdings, using modified 0.5 ha Gentry plots. No differences in taxonomic composition, aboveground biomass, adult and juvenile stem density, or woody seedling and bamboo culm density were detected between paired logged and unlogged sites. Commercial timber volume, however, was reduced by almost two-thirds in logged plots, suggesting that long-term timber management goals in this forest type are compromised since so few future crop trees remained onsite. Our findings indicate that in order to maximize local management objectives, community forest managers must approach logging in bamboo-dominated forests with caution. We suggest an integration of non-timber forest product extraction with low harvest intensity and low-impact logging, tending of natural regeneration, and diversification of commercial species.
ISSN: 0378-1127

hal-01204213
https://hal.archives-ouvertes.fr/hal-01204213
DOI : 10.1016/j.foreco.2013.12.022
PRODINRA : 263103

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.
ISSN: 1932-6203

hal-01608324
https://hal.archives-ouvertes.fr/hal-01608324
DOI : 10.1371/journal.pone.0182515
PRODINRA : 403154
PUBMED : 28771629

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
Measurements of branch xylem density, D_x, were made for 1466 trees representing 503 species, sampled from 80 sites across the Amazon basin. Measured values ranged from 240 kg m^?3 for a Brosimum parinarioides from Tapajos in West Pará, Brazil to 1130 kg m^?3 for an Aiouea sp. from Caxiuana, Central Pará, Brazil. Analysis of variance showed significant differences in average D_x across the sample plots as well as significant differences between families, genera and species. A partitioning of the total variance in the dataset showed that geographic location and plot accounted for 33% of the variation with species identity accounting for an additional 27%; the remaining "residual" 40% of the variance accounted for by tree to tree (within species) variation. Variations in plot means, were, however, hardly accountable at all by differences in species composition. Rather, it would seem that variations of xylem density at plot level must be explained by the effects of soils and/or climate. This conclusion is supported by the observation that the xylem density of the more widely distributed species varied systematically from plot to plot. Thus, as well as having a genetic component branch xylem density is a plastic trait that, for any given species, varies according to where the tree is growing and in a predictable manner. Exceptions to this general rule may be some pioneers belonging to Pourouma and Miconia and some species within the genera Brosimum, Rinorea and Trichillia which seem to be more constrained in terms of this plasticity than most species sampled as part of this study.
ISSN: 1810-6277

hal-00298004
https://hal.archives-ouvertes.fr/hal-00298004
https://hal.archives-ouvertes.fr/hal-00298004/document
https://hal.archives-ouvertes.fr/hal-00298004/file/bgd-5-2003-2008.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
BackgroundTree above ground biomass (AGB) is currently estimated by tree-level allometrical models that take into account, tree volume estimated from proxy variables of tree size (DBH) and species average wood specific gravity (WSG). These methods are common and realistic from a practical point of view. However, they do not take into account deviance from fixed allometrical trajectories and species or tree level WSG variations. Here, we present Xtrawood software that allows computation of tree AGB according to structure and WSG variations.MethodXtrawood reconstructs tree structure and integrates WSG variations by merging tree structure and WSG data measured at different position in trees, leading to the computation of global AGB and visualization of WSG variation along tree structure. Tree structure is measured according to stem dimensions (length, diameter) and positions within tree, and encoded in Multiscale Tree Graph format (MTG). WSG data is made of radial WSG profiles (1 measure each 0,5 cm from pith to bark) sampled at different heights within whole tree. Xtrawood output are illustrated using a dataset collected on an Amazonian forest ‘biomass dominant species’, Dicorynia guianensis Amsh., also known to exhibit substantial WSG gradients along both radial and vertical axis. 9 trees ranging from 15 to 60 cm DBH were measured by climbers. Each tree was felled and samples were collected at different positions (3 in trunk, 1 to 5 in crown) to record WSG radial profiles.ResultsXtrawood allows computation of tree volume, but also visualization of WSG variations in tree as well as inference of WSG radial profiles at different heights. Output variables are decomposed according to different tree scale and locations (axis, trunk/crown) and easy to extract. Xtrawood results will be compared to those of standard estimation method and can be used to identify positions in trees where WSG value leads to the better estimate of tree AGB.Conclusion/perspectiveXtrawood produces AGB estimate with data from intensive measurements practices. The sampling protocol, used here, remains destructive and time-consuming because Xtrawood is not directly dedicated to forest managers, but to help calibration of realistic sampling strategies. Moreover, Xtrawood offers a way to understand relationships between tree development, WSG variations within tree structure and biomass accumulation in the context of natural forests or plantations. A software demo is available at coffee break.
53rd Annual Meeting of the Association for Tropical Biology and Conservation (ATBC 2016)
Montpellier, France

Droits : http://creativecommons.org/licenses/by/
hal-01349613
https://hal.archives-ouvertes.fr/hal-01349613

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Ecological resilience assessments are an important part of resilience-based management (RBM) and can help prioritize and target management actions. Use of such assessments has been limited due to a lack of clear guidance on the assessment process. This study builds on the latest scientific advances in RBM to provide that guidance from a resilience assessment undertaken in the Commonwealth of the Northern Mariana Islands (CNMI). We assessed spatial variation in ecological resilience potential at 78 forereef sites near the populated islands of the CNMI: Saipan, Tinian/Aguijan, and Rota. The assessments are based on measuring indicators of resilience processes and are combined with information on anthropogenic stress and larval connectivity. We find great spatial variation in relative resilience potential with many high resilience sites near Saipan (5 of 7) and low resilience sites near Rota (7 of 9). Criteria were developed to identify priority sites for six types of management actions (e.g., conservation, land-based sources of pollution reduction, and fishery management and enforcement) and 51 of the 78 sites met at least one of the sets of criteria. The connectivity simulations developed indicate that Tinian and Aguijan are each roughly 10 × the larvae source that Rota is and twice as frequent a destination. These results may explain the lower relative resilience potential of Rota reefs and indicates that actions in Saipan and Tinian/Aguijan will be important to maintaining supply of larvae. The process we describe for undertaking resilience assessments can be tailored for use in coral reef areas globally and applied to other ecosystems.
ISSN: 0006-3207

Droits : http://creativecommons.org/licenses/by-nc-nd/
hal-01224905
https://hal-univ-perp.archives-ouvertes.fr/hal-01224905
https://hal-univ-perp.archives-ouvertes.fr/hal-01224905/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01224905/file/1-s2.0-S0006320715300926-main.pdf
DOI : 10.1016/j.biocon.2015.09.001

Éditeur(s) : Elsevier Science Bv
Résumé : Small-scale fisheries have traditionally received less research effort than large-scale fisheries and are generally under-studied in Europe. In spite of their comparatively low volume of catches and economic importance, small-scale fisheries are socially important and an integral part of the European coastal zone. Considering the high heterogeneity of situations and the paucity of quantitative data, we used an analytical methodology based on the comparative method. We carried out an analysis of small-scale fisheries (SSFs) in Europe based on a selection of nine case studies. Our objective was to obtain a comprehensive description of small-scale fleets covering different areas/fisheries/species, encompassing the diversity and specific conditions under which SSFs operate, in order to demonstrate the ecological and social sustainability of this often overlooked fisheries segment. A common approach formulated so that the case studies could be compared with the case histories of other competing users, required that for each set of criteria – technical, biological, socio-economic, and institutional – a set of relevant items and indicators was established. An analysis of characteristics common to the selected case studies is conducted and an attempt made to extend our comparisons to the whole of the European Union. Our results show that (as compared with large-scale fleets, their main competitor) small-scale fleets: (i) are composed of smaller vessels and, consequently, travel lower distances to fishing grounds, and are more reliant on coastal areas; (ii) have smaller crews (although the global employment figure is similar to that of large-scale fleets in Europe); (iii) use mostly, but not exclusively, passive gears; (iv) use multi-purpose fishing approaches, and can change the fish species they target during the year; (v) have lower extraction rates; (vi) have lower total capital investments (including fishing rights), turnover and costs; and (vii) have lower fuel consumption, making them less sensitive to changing oil prices. Dependence on subsidies is lower (viii). Involvement in fisheries management is variable, conservation and access regulation measures are largely local in origin. For the selected case studies, the most significant competitors are large-scale fleets, and recreational fisheries, but other sources of interaction (water quality, invasive species, etc.) cannot be ignored.
Fisheries Research (0165-7836) (Elsevier Science Bv), 2013-02 , Vol. 140 , P. 1-13

Droits : 2012 Elsevier B.V. All rights reserved
http://archimer.ifremer.fr/doc/00118/22934/20757.pdf
DOI:10.1016/j.fishres.2012.11.008
http://archimer.ifremer.fr/doc/00118/22934/

Éditeur(s) : HAL CCSD
Résumé : International audience
Semantic web standards, tools, ontologies and related technologies have considerably matured in the recent years. Nowadays, accessing a wide catalogue of biological, social, environmental, and ecological data sources helps stakeholders working on biodiversity to answer their complex questions. Will the real time access to web resources effectively support the definition of strategies to conserve and manage biodiversity? How might semantic web technologies help us to handle the complex and heterogeneous big data related to biodiversity? The workshop aims to identify the key challenges faced by the bioinformatics community, discuss potential solutions and identify the opportunities emerging from the trans-disciplinary interactions between Plant Science and Informatics experts. Therefore, we expect the bioinformatics experts to explain how they apply semantic web standards and tools to their scientific topic, from biology, agriculture, agro-ecology, genomics, environmental studies, to social sciences, citizen sciences. Research papers presenting various aspects of semantic web technologies applied to biodiversity data, ranging from position papers to implemented systems descriptions and their evaluation, will be selected. We are particularly interested in the use of the semantic technologies to design and develop systems that supports research on agricultural and wild biodiversity conservation and management for food security. Examples may include strategies for resilience to climate change pressures, sustainability of productive ecosystems, ecosystems services monitoring or territories management, rather than systems supporting only research on climate patterns or soil erosion.
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757

lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757/document

Éditeur(s) : HAL CCSD Wiley
Résumé : White-sand forests represent natural laboratories of evolution over their long history throughout Amazonia and the Guiana Shield and pose significant physiological challenges to the plants and animals they host. The study of diversification in plant lineages comprising species endemic to white-sand forest can therefore give insights into processes of evolution and community assembly in tropical forests. In this article, we synthesize recent studies of white-sand forests to integrate patterns of plant species distribution with processes of lineage diversification and community assembly in the white-sand flora. We contrast lineages that have radiated uniquely in these habitats (e.g., Pagamea, Rubiaceae), with cosmopolitan lineages comprising specialists to white-sand forests and other habitats that may have arisen via ecological speciation across habitat gradients (e.g., Protium, Burseraceae). In both cases, similar suites of functional traits have evolved, including investment in dense, long-lived tissues that are well-defended structurally and chemically. White-sand endemics, therefore, play an important role in biodiversity conservation because they represent unique combinations of functional and phylogenetic diversity. Furthermore, white-sand endemics may respond differently than other tropical forest plant species to contemporary global changes because they comprise resilient functional types that may better withstand increased drought, temperature, and invasions of exotic pests in these regions.
ISSN: 0006-3606

hal-01531635
https://hal.archives-ouvertes.fr/hal-01531635
DOI : 10.1111/btp.12301
PRODINRA : 353397