Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few 'hyperdominant' species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region.
ISSN: 2041-1723

hal-01204225
https://hal.archives-ouvertes.fr/hal-01204225
DOI : 10.1038/ncomms7857
PRODINRA : 305614
PUBMED : 25919449

Éditeur(s) : Centro Internacional de Investigaciones para el Desarrollo ; Centro Internacional de Investigaciones para el Desarrollo Departamento de Ciencia Política, Universidad de los Andes Centro Internacional de Investigaciones para el Desarrollo ;
Résumé : (Bibliography) Includes bibliographical references.
Colombia
Colombia
Colombia
Colombia

12583831
85174104
9586080129

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Aim To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia.Location Two hundred and eighty-three c.1ha forest inventory plots from across Amazonia.Methods We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival.Results PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric.Main conclusions High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities.
ISSN: 1366-9516

hal-01557462
https://hal.univ-lorraine.fr/hal-01557462
DOI : 10.1111/ddi.12357

Éditeur(s) : HAL CCSD
Résumé : Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades, with a substantial fraction of this sink probably located in the tropics, particularly in the Amazon. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale, and is contrary to expectations based on models.
ISSN: 1476-4687

hal-01204223
https://hal.archives-ouvertes.fr/hal-01204223
DOI : 10.1038/nature14283
PRODINRA : 294797
PUBMED : 25788097

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
ISSN: 0305-1048

hal-01146849
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146849
DOI : 10.1093/nar/gkv350
PUBMED : 25897122

Éditeur(s) : HAL CCSD
Résumé : National audience
Colloque annuel du GdR MeGe
La Rochelle, France

hal-00844261
https://hal.archives-ouvertes.fr/hal-00844261

Éditeur(s) : HAL CCSD American Physical Society
Résumé : International audience
This is the first of two papers investigating the mechanical response of cemented granular materials by means of contact dynamics simulations. In this paper, a two-dimensional polydisperse sample with high-void ratio is constructed and then sheared in a simple shear numerical device at different confinement levels. We study the macroscopic response of the material in terms of mean and deviatoric stresses and strains. We show that the introduction of a local force scale, i.e., the tensile strength of the cemented bonds, causes the material to behave in a rigid-plastic fashion, so that a yield surface can be easily determined. This yield surface has a concave-down shape in the mean: deviatoric stress plane and it approaches a straight line, i.e., a Coulomb strength envelope, in the limit of a very dense granular material. Beyond yielding, the cemented structure gradually degrades until the material eventually behaves as a cohesionless granular material. Strain localization is also investigated, showing that the strains concentrate in a shear band whose thickness increases with the confining stress. The void ratio inside the shear band at the steady state is shown to be a material property that depends only on contact parameters.
ISSN: 1539-3755

hal-00523453
https://hal.archives-ouvertes.fr/hal-00523453
DOI : 10.1103/PhysRevE.82.011303

Éditeur(s) : HAL CCSD springer Link
Résumé : International audience
Experimental Astronomy

hal-01094521
https://hal.archives-ouvertes.fr/hal-01094521
BIBCODE : 2014ExA...tmp...41R
DOI : 10.1007/s10686-014-9383-4
ARXIV : 1310.0696

Éditeur(s) : HAL CCSD Elsevier
Résumé : This paper presents a numerical investigation on the mechanical behavior of cemented granular materials by means of discrete element simulations. In particular, two conceptual elements of this behavior were explored: the yield surfaces and the plastic potentials, as defined in the framework of elastoplastic constitutive models. For this purpose, we implemented a contact model that mimics the mechanical behavior of cemented bonds, we constructed a set of polydisperse samples with different solid fractions, and we tested these samples by means of a biaxial device with four rigid walls. The yield surfaces and plastic potentials were thus obtained and analyzed as functions of the solid fraction of the material, drawing interesting conclusions, confirming previous experimental findings, and, consequently, evidencing the great potential of discrete element simulations in exploring the behavior of real cemented geomaterials.
ISSN: 0266-352X

hal-00853748
https://hal.archives-ouvertes.fr/hal-00853748
DOI : 10.1016/j.compgeo.2012.11.001

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Forest successional processes following disturbance take decades to play out, even in tropical forests. Nonetheless, records of vegetation change in this ecosystem are scarce, increasing the importance of the chronosequence approach to study forest recovery. However, this approach requires accurate dating of secondary forests, which until now was a difficult and/or expensive task. Cecropia is a widespread and abundant pioneer tree genus of the Neotropics. Here we propose and validate a rapid and straightforward method to estimate the age of secondary forest patches based on morphological observations of Cecropia trees. We found that Cecropia-inferred ages were highly correlated with known ages of the forest. We also demonstrate that Cecropia can be used to accurately date disturbances and propose twenty-one species distributed all over the geographical range of the genus as potential secondary forest chronometer species. Our method is limited in applicability by the maximal longevity of Cecropia individuals. Although the oldest chronosequence used in this study was 20 years old, we argue that at least for the first four decades after disturbance, the method described in this study provides very accurate estimations of secondary forest ages. The age of pioneer trees provides not only information needed to calculate the recovery of carbon stocks that would help to improve forest management, but also provides information needed to characterize the initial floristic composition and the rates of species remigration into secondary forest. Our contribution shows how successional studies can be reliably and inexpensively extended without the need to obtain forest ages based on expensive or potentially inaccurate data across the Neotropics.
ISSN: 1932-6203

halsde-00757518
https://hal.archives-ouvertes.fr/halsde-00757518
DOI : 10.1371/journal.pone.0042643
PUBMED : 22916144

Éditeur(s) : HAL CCSD American Physical Society
Résumé : International audience
This is the second of two papers investigating the mechanical response of cemented granular materials by means of contact dynamics simulations. In this paper, a two-dimensional polydisperse sample with high void ratio is sheared in a load-controlled simple shear numerical device until the stress state of the sample reaches the yield stress. We first study the stress transmission properties of the granular material in terms of the fabric of different subsets of contacts characterized by the magnitude of their normal forces. This analysis highlights the existence of a peculiar force carrying structure in the cemented material, which is reminiscent of the bimodal stress transmission reported for cohesionless granular media. Then, the evolution of contact forces and torques is investigated trying to identify the micromechanical conditions that trigger macroscopic yielding. It is shown that global failure can be associated to the apparition of a group of particles whose contacts fulfill at least one of the local rupture conditions. In particular, these particles form a large region that percolates through the sample at the moment of failure, evidencing the relationship between macroscopic yielding and the emergence of large-scale correlations in the system.
ISSN: 1539-3755

hal-00523451
https://hal.archives-ouvertes.fr/hal-00523451
DOI : 10.1103/PhysRevE.82.011304

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
ISSN: 0022-3697

hal-00808660
https://hal.univ-antilles.fr/hal-00808660

Éditeur(s) : HAL CCSD
Résumé : International audience
In this paper, we compare the effect of rolling resistance at the contacts in granular systems composed of disks with the effect of angularity in granular systems composed of regular polygonal particles. For this purpose, we use contact dynamics simulations. By means of a simple shear numerical device, we investigate the mechanical behavior of these materials in the steady state in terms of shear strength, solid fraction, force and fabric anisotropies, and probability distribution of contact forces. We find that, based on the energy dissipation associated with relative rotation between two particles in contact, the effect of rolling resistance can explicitly be identified with that of the number of sides in a regular polygonal particle. This finding supports the use of rolling resistance as a shape parameter accounting for particle angularity and shows unambiguously that one of the main influencing factors behind the mechanical behavior of granular systems composed of noncircular particles is the partial hindrance of rotations as a result of angular particle shape.
AIP Conference Proceedings
Sydney, Australia

hal-00842799
https://hal.archives-ouvertes.fr/hal-00842799
https://hal.archives-ouvertes.fr/hal-00842799/document
https://hal.archives-ouvertes.fr/hal-00842799/file/Comparison_effects_rolling_Estrada_al.pdf

Éditeur(s) : HAL CCSD Cambridge University Press (CUP)
Résumé : Patterns of leaf production and leaf fall directly influence leaf area index and forest productivity. Here, we focused on Cecropia sciadophylla individuals inhabiting the extremes of the gradient in seasonality in rainfall at which C. sciadophylla occurs. In Colombia and French Guiana we compared the intra-annual variation in leaf production as well as the intra-annual fluctuation in internode length on a total of 69 saplings ranging in size from 1 to 2 m. The mean rate of leaf production was similar to 2 leaves mo(-1) in both populations, and the rate of leaf production was constant throughout the year. Our results showed monthly variation in internode length and the number of live leaves per sapling in the seasonal habitat and variation only in internode length in the everwet habitat. Because the rate of leaf production is constant at both localities, the difference in number of live leaves per sapling at the seasonal site must reflect seasonal variation in leaf life span. We show that in Cecropia, internode length can serve as an indicator of precipitation seasonality. Finally an open question is whether leaf production in other pioneer species is also independent of climatic seasonal cues. This information could allow us to link growth and climate of secondary forest species and better understand how past and future climate can affect plant growth trajectories.
ISSN: 0266-4674

hal-01032402
https://hal.archives-ouvertes.fr/hal-01032402
DOI : 10.1017/S0266467413000394

Éditeur(s) : HAL CCSD
Résumé : International audience
Powders and Grains 2009
Golden, United States

hal-00760571
https://hal.archives-ouvertes.fr/hal-00760571

Éditeur(s) : HAL CCSD
Résumé : Le genre Cecropia regroupe des arbres pionniers, à croissance rapide, qui colonisent les aires défrichées et les milieux ouverts à fort ensoleillement. Leur architecture est relativement simple et conforme au modèle de Rauh. Tout au long de la vie de la plante il est possible de retrouver a posteriori les cicatrices de feuille, d’inflorescences et de branches élaguées. En décrivant les axes noeuds à noeuds il est possible de construire des séquences d’événements ou l’index est le métamère et les variables associées la longueur de l’entre-noeud, la présence de fleurs, de branches, ou de leurs cicatrices. En analysant ces séquences avec des outils statistiques issus de l’analyse des séries temporelles il est possible de mettre en évidence des régularités structurelles (par ex: nombres de noeuds séparant 2 étages de branches) et de proposer une interprétation sur l’organisation dans le temps des processus de croissance, ramification et floraison qui mène à l’édification de l’architecture des représentants de cette espèces. C’est en suivant cette démarche que de récents travaux menés en Guyane française sur C. obtusa et C. sciadophylla ont démontré une forte périodicité annuelle pour les processus de croissance, de floraison et de ramification chez deux espèces. Le fait le plus remarquable est la grande régularité dans le nombre de feuilles émises chaque année avec 35 noeuds pour C. obusa et 25 noeuds pour C. sciadophylla. Cette régularité peut permettre déterminer l’âge d’un individu et de retrouver sa croissance passée. Dans ce travail nous avons voulu aborder la diversité et la plasticité de ces règles de construction en comparant des populations de C. sciadophylla ayant poussé dans des environnements variés en Guyane Française (2 populations) et en Colombie (4 populations). Les résultats montrent que le nombre de feuilles allongées chaque année est remarquablement stable pour l’ensemble des populations et est égal 25. La floraison est annuelle pour la majorité des individus mesurés mais il est cependant possible d’observer 2 floraisons par an chez certains arbres de Guyane. Les paramètres les plus variables concernent l’âge et la hauteur avant la première ramification ou la de la première floraison ainsi que les allométries entre la hauteur et le diamètre. Le lien entre cette variabilité et les conditions environnementales tel que la pluviométrie, la fertilité des sols ou la compétition seront discutés.
La plasticité phénotypique des arbres
Montpellier, France

hal-01190210
https://hal.archives-ouvertes.fr/hal-01190210
PRODINRA : 182912

Éditeur(s) : HAL CCSD American Physical Society
Résumé : International audience
Using contact dynamics simulations, we compare the effect of rolling resistance at the contacts in granular systems composed of disks with the effect of angularity in granular systems composed of regular polygonal particles. In simple shear conditions, we consider four aspects of the mechanical behavior of these systems in the steady state: shear strength, solid fraction, force and fabric anisotropies, and probability distribution of contact forces. Our main finding is that, based on the energy dissipation associated with relative rotation between two particles in contact, the effect of rolling resistance can explicitly be identified with that of the number of sides in a regular polygonal particle. This finding supports the use of rolling resistance as a shape parameter accounting for particle angularity and shows unambiguously that one of the main influencing factors behind the mechanical behavior of granular systems composed of noncircular particles is the partial hindrance of rotations as a result of angular particle shape.
ISSN: 1539-3755

hal-00594891
https://hal.archives-ouvertes.fr/hal-00594891
https://hal.archives-ouvertes.fr/hal-00594891/document
https://hal.archives-ouvertes.fr/hal-00594891/file/Estrada2010ReSubmitV2.pdf
ARXIV : 1105.4418

Éditeur(s) : HAL CCSD Landes Bioscience
Résumé : International audience
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Autophagy

hal-00735751
https://hal.archives-ouvertes.fr/hal-00735751
PUBMED : 22966490

Éditeur(s) : HAL CCSD Wiley
Résumé : Negative density dependence (NDD) and environmental filtering (EF) shape community assembly, but their relative importance is poorly understood. Recent studies have shown that seedlings mortality risk is positively related to the phylogenetic relatedness of neighbours. However, natural enemies, whose depredations often cause NDD, respond to functional traits of hosts rather than phylogenetic relatedness per se. To understand the roles of NDD and EF in community assembly, we assessed the effects on seedling mortality of functional similarity, phylogenetic relatedness and stem density of neighbouring seedlings and adults in a species-rich tropical forest. Mortality risks increased for common species when their functional traits departed substantially from the neighbourhood mean, and for all species when surrounded by close relatives. This indicates that NDD affects community assembly more broadly than does EF, and leads to the tentative conclusion that natural enemies respond to phylogenetically correlated traits. Our results affirm the prominence of NDD in structuring species-rich communities.
ISSN: 1461-023X

hal-01032429
https://hal.archives-ouvertes.fr/hal-01032429
DOI : 10.1111/j.1461-0248.2011.01705.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
An empirical relation is proposed to analyze the broad band observed in the photoluminescence spectra of CuInSe2 (CIS) due to donor-acceptor pair recombinations. This permits, together with the knowledge of the majority carrier concentration and the compensation ratio, the determination of the activation energy ED of the donor and EA of the acceptor levels and the mean distance R between D-A pairs. Values of the dielectric constant ϵ, ED and EA for CIS obtained with this model agree with reported data.
ISSN: 0167-577X

hal-00808657
https://hal.univ-antilles.fr/hal-00808657
DOI : 10.1016/S0167-577X(96)00133-4