Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Epinephelus itajara is one of the marine fish species most threatened for extinction and it is considered to be "critically endangered" by the IUCN. The present study evaluated the genetic diversity of the species and the genetic/evolutionary relationships of its populations along the Atlantic coast of South America. The results indicate relatively reduced genetic variation, re-emphasizing the low adaptive potential of the species. One of the populations presented relatively high degrees of genetic diversity and it is evolutionary isolated from the all other populations. The evidences indicate the existence of two Evolutionarily Significant Units comprising E. itajara in the Atlantic coast of South America and the conservation prospects for the species must take these evidences into account.
Biochemical Systematics And Ecology (0305-1978) (Pergamon-elsevier Science Ltd), 2014-10 , Vol. 56 , P. 255-266

Droits : 2014 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00230/34100/34465.pdf
DOI:10.1016/j.bse.2014.06.004
http://archimer.ifremer.fr/doc/00230/34100/

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 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 European Geosciences Union
Résumé : Xylem density is a physical property of wood that varies between individuals, species and environments. It reflects the physiological strategies of trees that lead to growth, survival and reproduction. Measurements of branch xylem density, ρx, were made for 1653 trees representing 598 species, sampled from 87 sites across the Amazon basin. Measured values ranged from 218 kg m−3 for a Cordia sagotii (Boraginaceae) from Mountagne de Tortue, French Guiana to 1130 kg m−3 for an Aiouea sp. (Lauraceae) from Caxiuana, Central Pará, Brazil. Analysis of variance showed significant differences in average ρx across regions and sampled plots as well as significant differences between families, genera and species. A partitioning of the total variance in the dataset showed that species identity (family, genera and species) accounted for 33% with environment (geographic location and plot) accounting for an additional 26%; the remaining "residual" variance accounted for 41% of the total variance. Variations in plot means, were, however, not only accountable by differences in species composition because xylem density of the most widely distributed species in our dataset 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 in a predictable manner. Within the analysed taxa, exceptions to this general rule seem to be pioneer species belonging for example to the Urticaceae whose branch xylem density is more constrained than most species sampled in this study. These patterns of variation of branch xylem density across Amazonia suggest a large functional diversity amongst Amazonian trees which is not well understood.
ISSN: 1726-4170

hal-01032137
https://hal.archives-ouvertes.fr/hal-01032137

Éditeur(s) : HAL CCSD Wiley-VCH Verlag
Résumé : International audience
Deciphering the assembly history of the Milky Way is a formidable task, which becomes possible only if one can produce high-resolution chrono-chemo-kinematical maps of the Galaxy. Data from large-scale astrometric and spectroscopic surveys will soon provide us with a well-defined view of the current chemo-kinematical structure of the Milky Way, but will only enable a blurred view on the temporal sequence that led to the present-day Galaxy. As demonstrated by the (ongoing) exploitation of data from the pioneering photometric missions CoRoT, Kepler, and K2, asteroseismology provides the way forward: solar-like oscillating giants are excellent evolutionary clocks thanks to the availability of seismic constraints on their mass and to the tight age-initial-mass relation they adhere to. In this paper we identify five key outstanding questions relating to the formation and evolution of the Milky Way that will need precise and accurate ages for large samples of stars to be addressed, and we identify the requirements in terms of number of targets and the precision on the stellar properties that are needed to tackle such questions. By quantifying the asteroseismic yields expected from PLATO for red-giant stars, we demonstrate that these requirements are within the capabilities of the current instrument design, provided that observations are sufficiently long to identify the evolutionary state and allow robust and precise determination of acoustic-mode frequencies. This will allow us to harvest data of sufficient quality to reach a 10% precision in age. This is a fundamental pre-requisite to then reach the more ambitious goal of a similar level of accuracy, which will only be possible if we have to hand a careful appraisal of systematic uncertainties on age deriving from our limited understanding of stellar physics, a goal which conveniently falls within the main aims of PLATO's core science.
ISSN: 0004-6337

hal-01541393
https://hal.archives-ouvertes.fr/hal-01541393
ARXIV : 1706.3778
BIBCODE : 2017AN....338..644M
DOI : 10.1002/asna.201713385

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 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 Wiley
Résumé :  
Positive aboveground biomass trends have been reported from old-growth forests across the Amazon basin and hypothesized to reflect a large-scale response to exterior forcing. The result could, however, be an artefact due to a sampling bias induced by the nature of forest growth dynamics. Here, we characterize statistically the disturbance process in Amazon old-growth forests as recorded in 135 forest plots of the RAINFOR network up to 2006, and other independent research programmes, and explore the consequences of sampling artefacts using a data-based stochastic simulator. Over the observed range of annual aboveground biomass losses, standard statistical tests show that the distribution of biomass losses through mortality follow an exponential or near-identical Weibull probability distribution and not a power law as assumed by others. The simulator was parameterized using both an exponential disturbance probability distribution as well as a mixed exponential-power law distribution to account for potential large-scale blowdown events. In both cases, sampling biases turn out to be too small to explain the gains detected by the extended RAINFOR plot network. This result lends further support to the notion that currently observed biomass gains for intact forests across the Amazon are actually occurring over large scales at the current time, presumably as a response to climate change.
ISSN: 1354-1013

hal-01032162
https://hal.archives-ouvertes.fr/hal-01032162
DOI : 10.1111/j.1365-2486.2009.01891.x

Éditeur(s) : HAL CCSD Wiley Open Access
Résumé : Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
ISSN: 2045-7758

hal-01204216
https://hal.archives-ouvertes.fr/hal-01204216
DOI : 10.1002/ece3.1303
PRODINRA : 280886

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is < 2000 mm yr(-1) (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall < 2000 mm yr(-1).
ISSN: 1726-4170

hal-01557759
https://hal.univ-lorraine.fr/hal-01557759
https://hal.univ-lorraine.fr/hal-01557759/document
https://hal.univ-lorraine.fr/hal-01557759/file/bg-13-2537-2016.pdf
DOI : 10.5194/bg-13-2537-2016

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
ISSN: 1755-098X

hal-01094222
https://hal-agroparistech.archives-ouvertes.fr/hal-01094222
DOI : 10.1111/j.1755-0998.2010.02916.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Borborema Province of northeastern Brazil is divided into three main domains: northern, central, and southern. Several U-Pb zircon ages of plutons and orthogneisses became available in the recent years in the central and northern domains, but similar results are scarce in the southern domain. This study reports U-Pb dates for single zircon grains from one orthogneiss (Jupi orthogneiss) and two plutons (Cachoeirinha syenitic pluton and Cabanas granite) south of the East Pernambuco shear zone system (EPSZ). The results provide geochronological constraints on the timing of deformation and magmatism in this part of the southern domain and allow correlations with the central domain. The Jupi orthogneiss was emplaced and deformed during development of the regional flat-lying foliation. A Pb-206/U-238 weighted apparent mean age of 606 +/- 8 Ma is interpreted as the crystallization age of the protolith of the orthogneiss and consequently the age of high-grade Brasiliano metamorphism. The NNE-trending Cachoeirinha pluton is only locally affected by strike-slip deformation, whereas the ENE-trending Cabanas granite is intensely affected by deformation related to the EPSZ. The 587 8 Ma and 573 4 Ma ages of the Cachoeirinha pluton and Cabanas granite, respectively, bracket the main period of activity of the EPSZ. Tectonomagmatic activity in the study area is similar to the age of Brasiliano events in the central domain, north of the EPSZ. In addition, xenocrystic zircons in the Jupi orthogneiss and Cabanas granite are interpreted as inherited from Paleoproterozoic source rocks, suggesting the presence of widespread reworked old crust in the southern domain, similar to the central domain. These results support the idea that the central and southern domains belonged to the same crustal block before the onset of the Brasiliano orogeny.
ISSN: 0895-9811

hal-00411394
https://hal.archives-ouvertes.fr/hal-00411394
DOI : 10.1016/j.jsames.2007.06.003

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
ISSN: 0028-646X

hal-01092529
https://hal-agroparistech.archives-ouvertes.fr/hal-01092529