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 Optical Society of America
Résumé : International audience
We present a theoretical simulation of the sarcomeric SHG intensity pattern (SHG-IP) that takes into account myofibrillar misalignment that is experimentally observed in SHG images of proteolysed muscles. The model predicts that myofibrillar displacement results in the conversion from one peak (1P) to two peaks (2P) sarcomeric SHG-IP in agreement with experimental results. This study suggests that sarcomeric SHG-IP is a powerful tool for mapping spatial myofibrillar displacement and its related excitation-contraction disruption that could occur during muscle physiological adaptation and disease.
ISSN: 1094-4087

hal-00820260
https://hal.archives-ouvertes.fr/hal-00820260
https://hal.archives-ouvertes.fr/hal-00820260/document
https://hal.archives-ouvertes.fr/hal-00820260/file/Studysur the_effect-accepted.pdf
DOI : 10.1364/OE.21.011404

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the diversity of fungal communities in these two compartments is partly dependent on the coverage of trees in the Neotropical rainforest. In French Guiana, a long-term plantation and a natural forest were selected to test this hypothesis. Fungal ITS1 regions were sequenced from soil and litter samples from within the vicinity of tree species. A broad range of fungal taxa was found, with 42 orders and 14 classes.Significant spatial heterogeneity in the fungal communities was found without strong variation in the species richness and evenness among the tree plots. However, tree species shaped the fungal assemblages in the soil and litter, explaining up to 18 % of the variation among the communities in the natural forest.These results demonstrate that vegetation cover has an important effect on the structure of fungal assemblages inhabiting the soil and litter in Amazonian forests, illustrating the relative impact of deterministic processes on fungal community structures in these highly diverse ecosystems.
ISSN: 0095-3628

hal-01595373
https://hal.archives-ouvertes.fr/hal-01595373
DOI : 10.1007/s00248-016-0839-0
PRODINRA : 395655
PUBMED : 27645139

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

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

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
The exchanges of carbon, water and energy between the atmosphere and the Amazon basin have global implications for the current and future climate. Here, the global atmospheric inversion system of the Monitoring of Atmospheric Composition and Climate (MACC) service is used to study the seasonal and interannual variations of biogenic CO 2 fluxes in Amazonia during the period 2002–2010. The system assimilated surface measurements of atmospheric CO 2 mole fractions made at more than 100 sites over the globe into an atmospheric transport model. The present study adds measurements from four surface stations located in tropical South America, a region poorly covered by CO 2 observations. The estimates of net ecosystem exchange (NEE) optimized by the inversion are compared to an independent estimate of NEE upscaled from eddy-covariance flux measurements in Amazonia. They are also qualitatively evaluated against reports on the seasonal and interannual variations of the land sink in South America from the scientific literature. We attempt at assessing the impact on NEE of the strong droughts in 2005 and 2010 (due to severe and longer-than-usual dry seasons) and the extreme rainfall conditions registered in 2009. The spatial variations of the seasonal and in-terannual variability of optimized NEE are also investigated. While the inversion supports the assumption of strong spatial heterogeneity of these variations, the results reveal critical limitations of the coarse-resolution transport model, the surface observation network in South America during the recent years and the present knowledge of modelling uncertainties in South America that prevent our inversion from capturing the seasonal patterns of fluxes across Amazonia. However, some patterns from the inversion seem consistent with the anomaly of moisture conditions in 2009.
ISSN: 1680-7316

hal-01557375
https://hal.univ-lorraine.fr/hal-01557375
https://hal.univ-lorraine.fr/hal-01557375/document
https://hal.univ-lorraine.fr/hal-01557375/file/acp-15-8423-2015.pdf
DOI : 10.5194/acp-15-8423-2015-supplement

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Seagrasses structure some of the world's key coastal ecosystems presently in decline due to human activities and global change. The ability to cope with environmental changes and the possibilities for shifts in distribution range depend largely on their evolvability and dispersal potential. As large-scale data usually show strong genetic structure for seagrasses, finer-grained work is needed to understand the local processes of dispersal, recruitment and colonization that could explain the apparent lack of exchange across large distances. We aimed to assess the fine-grained genetic structure of one of the most important and widely distributed seagrasses, Zostera marina, from seven meadows in Brittany, France. Both classic population genetics and network analysis confirmed a pattern of spatial segregation of polymorphism at both regional and local scales. One location exhibiting exclusively the variety 'angustifolia' did not appear more differentiated than the others, but instead showed a central position in the network analysis, confirming the status of this variety as an ecotype. This phenotypic diversity and the high allelic richness at nine microsatellites (2.33-9.67 alleles/locus) compared to levels previously reported across the distribution range, points to Brittany as a centre of diversity for Z. marina at both genetic and phenotypic levels. Despite dispersal potential of several 100 m, a significant pattern of genetic differentiation, even at fine-grained scale, revealed 'genetic patchiness'. Meadows seem to be composed of a mosaic of clones with distinct origins in space and time, a result that calls into question the accuracy of the concept of populations for such partially clonal species.
Molecular Ecology (0962-1083) (Wiley-blackwell Publishing, Inc), 2010-06 , Vol. 19 , N. 12 , P. 2394-2407

Droits : 2010 Blackwell Publishing Ltd
http://archimer.ifremer.fr/doc/00006/11690/8499.pdf
DOI:10.1111/j.1365-294X.2010.04649.x
http://archimer.ifremer.fr/doc/00006/11690/

Éditeur(s) : Elsevier
Résumé : Sea cruises were conducted for 57 days over 16 months to characterise pelagic fish aggregations around 2 moored fish aggregating devices (FADs) in Martinique (Lesser Antilles). Echosounder surveys run in a star pattern were used in conjunction with obliquely beamed sonar observations. An echo-integration-by-shoal algorithm was implemented to isolate pelagic fish shoals from sound scattering layers and to compute mean morphometric, positional and density parameters. Tree regressions were used to select and classify pelagic fish Target Strengths (TS), with reference to their spatial and temporal characteristics. The main type of pelagic fish aggregation was a large sub-surface aggregation. It was observed during all daytime periods within a radius of 400 m of the FAD. A smaller type of aggregation was observed closer to the surface and to the FAD in 65% of daytime periods. Large scattered fish were observed in 16% of daytime periods. At night, a medium-sized aggregation was detected in the sub-surface in 75% of night-time periods. The sizes of the fish inside the aggregations (determined from TS values) were lower in the small near-surface aggregation than in the large sub-surface aggregation. Mean packing densities of sub-surface medium fish and near-surface small fish aggregations (determined from TS and shoal acoustic density) were respectively 0.2 fish per m3 and 1.3 fish per m3. The acoustic methodology and results are discussed with reference to the characteristics and performance of the echosounder and to the spatial structure of pelagic fish aggregations around moored FADs in Martinique.
Fisheries Research (0165-7836) (Elsevier), 2006-06 , Vol. 82 , N. 1-3 , P. 162-175

Droits : Elsevier 2006
http://archimer.ifremer.fr/doc/2006/publication-1734.pdf
DOI:10.1016/j.fishres.2006.06.025
http://archimer.ifremer.fr/doc/00000/1734/

Éditeur(s) : Public Library Science
Résumé : Changes in phenology, the timing of seasonal activities, are among the most frequently observed responses to environmental disturbances and in marine species are known to occur in response to climate changes that directly affects ocean temperature, biogeochemical composition and sea level. We examined nesting seasonality data from long-term studies at 8 green turtle (Chelonia mydas) rookeries that include 21 specific nesting sites in the South-West Indian Ocean (SWIO). We demonstrated that temperature drives patterns of nesting seasonality at the regional scale. We found a significant correlation between mean annual Sea Surface Temperature (SST) and dates of peak nesting with rookeries exposed to higher SST having a delayed nesting peak. This supports the hypothesis that temperature is the main factor determining peak nesting dates. We also demonstrated a spatial synchrony in nesting activity amongst multiple rookeries in the northern part of the SWIO (Aldabra, Glorieuses, Mohéli, Mayotte) but not with the eastern and southern rookeries (Europa, Tromelin), differences which could be attributed to females with sharply different adult foraging conditions. However, we did not detect a temporal trend in the nesting peak date over the study period or an inter-annual relation between nesting peak date and SST. The findings of our study provide a better understanding of the processes that drive marine species phenology. The findings will also help to predict their ability to cope with climate change and other environmental perturbations. Despite demonstrating this spatial shift in nesting phenology, no trend in the alteration of nesting dates over more than 20 years was found.
Plos One (1932-6203) (Public Library Science), 2012-10 , Vol. 7 , N. 10 , P. 1-13

Droits : 2012 Dalleau et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
http://archimer.ifremer.fr/doc/00098/20940/18558.pdf
DOI:10.1371/journal.pone.0046920
http://archimer.ifremer.fr/doc/00098/20940/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Several studies have documented that more deprived populations tend to live in areas characterized by higher levels of environmental pollution. Yet, time trends and geographic patterns of this disproportionate distribution of environmental burden remain poorly assessed, especially in Europe. We investigated the spatial and temporal relationship between ambient air nitrogen dioxide (NO2) concentrations and socioeconomic and demographic data in four French metropolitan areas (Lille in the North, Lyon in the center, Marseille in the South, and Paris) during two different time periods. The geographical unit used was the census block. The dependent variable was the NO2 annual average concentration (μg/m(3)) per census block, and the explanatory variables were a neighborhood deprivation index and socioeconomic and demographic data derived from the national census. Generalized additive models were used to account for spatial autocorrelation. We found that the strength and direction of the association between deprivation and NO2 estimates varied between cities. In Paris, census blocks with the higher social categories are exposed to higher mean concentrations of NO2. However, in Lille and Marseille, the most deprived census blocks are the most exposed to NO2. In Lyon, the census blocks in the middle social categories were more likely to have higher concentrations than in the lower social categories. Despite a general reduction in NO2 concentrations over the study period in the four metropolitan areas, we found contrasting results in the temporal trend of environmental inequalities. There is clear evidence of city-specific spatial and temporal environmental inequalities that relate to the historical socioeconomic make-up of the cities and its evolution. Hence, general statements about environmental and social inequalities can be made.
ISSN: 0013-9351

hal-01063900
https://hal.archives-ouvertes.fr/hal-01063900
DOI : 10.1016/j.envres.2014.07.017
PUBMED : 25199972

Éditeur(s) : Université de la Nouvelle-Calédonie
Résumé : Estimating diversity and abundance of fish is fundamental for the understanding of community structure and dynamics of coral reefs. Observations are generally gathered using Underwater Visual Census (UVC). These informations can also be collected by underwater video techniques involving no diver and allowing a high spatial and temporal coverage. The first part of this PhD thesis is a review of publications using underwater video techniques between 1952 and 2012. The second part present two rotating video systems used to study the diversity of ichthyofauna and habitats in the lagoon of New Caledonia: the STAVIRO (for "STAtion VIdeo ROtative") and the MICADO (for "Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine"). The third part of this work is a comparison of these techniques with UVCs and an analysis of the “observer effect” for the rotating video techniques. The comparison between rotating video systems and UVC showed that: (i) fish community data collected by UVC and by STAVIRO differed significantly; (ii) species richness and density of large species were not significantly different between techniques; (iii) species richness and density of small species were higher for UVC; (iv) density of fished species was higher for STAVIRO; and (v) only UVC detected significant differences in fish assemblages structure across reef type. The comparison of fish counts obtained from the same videos by different observers showed that for a defined list of species, estimates of species richness and total abundance can be considered as similar between observers with sufficient experiences (> 6 months). The last part of this PhD is an application of rotating video techniques to the study of daily temporal variations of the ichthyofauna. Daily variations were observed depending on the time of day and the tidal state and typical patterns of variations have been described for some species groups. The outcomes of this work bring original insights of new techniques complementary to traditional techniques in order to enhance our understanding of the functioning and dynamic of coral reef.
L’estimation de la diversité et de l’abondance des espèces de poissons est fondamentale pour comprendre la structure des communautés et la dynamique des récifs coralliens. Les observations sont généralement obtenues par des recensements visuels en scaphandre autonome (UVC). Ces informations peuvent également être obtenues de manière originale grâce aux observations issues des techniques vidéo sous-marines modernes sans plongeur qui permettent des couvertures spatiales et temporelles accrues. La première phase de ce travail de thèse synthétise l’ensemble des travaux ayant été effectués avec des techniques vidéo entre 1952 et 2012. La seconde phase, présente deux systèmes vidéo rotatifs complémentaires, utilisés pour étudier la diversité de l’ichtyofaune et des habitats marins dans le lagon de Nouvelle-Calédonie : le STAVIRO (pour « STAtion VIdéo ROtative ») et le MICADO (pour « Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine »). La troisième phase de ce travail consiste à comparer ces systèmes vidéo aux UVC puis à examiner l’effet « observateur » inhérent aux techniques vidéo rotatives. Il résulte de cette étude que : (i) les observations des communautés de poissons par UVC et STAVIRO différaient significativement, (ii) la richesse spécifique et la densité des espèces de grande taille n'étaient pas significativement différentes entre les techniques, (iii) la diversité et la densité des espèces de petite taille étaient plus élevés avec les UVC; (iv) la densité des espèces pêchées était plus élevée avec les STAVIRO et (v) seuls les UVC ont détecté des différences de structure des assemblages en fonction du type de récif. L’étude de l’effet « observateur » a montré que sur une liste d’espèces définie, les dénombrements et les identifications des individus peuvent être considérées comme similaires entre observateurs ayant une expérience suffisante (> 6 mois). La dernière phase de ce travail a permis d’appliquer la technique MICADO à l’étude des variations temporelles de l’ichtyofaune d’un site corallien à l’échelle de la journée. Elle a permis de mettre en évidence des variations cycliques journalières en fonction de l’heure et de la marée et des « profils type » de variations ont pu être identifiés pour certains groupes d’espèces. Ce travail de thèse permet ainsi de participer au développement de nouvelles techniques d’observations complémentaires des techniques traditionnelles afin d’enrichir les connaissances du fonctionnement et de la dynamique des écosystèmes coralliens.

Droits : Université de la Nouvelle-Calédonie
http://archimer.ifremer.fr/doc/00189/30050/28536.pdf
http://archimer.ifremer.fr/doc/00189/30050/

Éditeur(s) : HAL CCSD Elsevier
Résumé : Over the last decades distance-based methods have been introduced and then improved in the field of spatial economics to gauge the geographic concentration of activities. There is a growing literature on this theme including new tools, discussions on their specific properties and various applications. However, there is currently no typology of distance-based methods. This paper fills that gap. The proposed classification helps understand all the properties of distance-based methods and proves that they are variations on the same framework.
ISSN: 0166-0462

hal-01606265
https://hal.archives-ouvertes.fr/hal-01606265
DOI : 10.1016/j.regsciurbeco.2016.10.004
PRODINRA : 407314

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
We conducted a survey along three belt transects located at increasing distances from the coast to determine whether a non-random arboreal ant assemblage, such as an ant mosaic, exists in the rainforest on the Masoala Peninsula, Madagascar. In most tropical rainforests, very populous colonies of territorially dominant arboreal ant species defend absolute territories distributed in a mosaic pattern. Among the 29 ant species recorded, only nine had colonies large enough to be considered potentially territorially dominant; the remaining species had smaller colonies and were considered non-dominant. Nevertheless, the null-model analyses used to examine the spatial structure of their assemblages did not reveal the existence of an ant mosaic. Inland, up to 44% of the trees were devoid of dominant arboreal ants, something not reported in other studies. While two Crematogaster species were not associated with one another, Brachymyrmex cordemoyi was positively associated with Technomyrmex albipes, which is considered an invasive species-a non-indigenous species that has an adverse ecological effect on the habitats it invades. The latter two species and Crematogaster ranavalonae were mutually exclusive. On the other hand, all of the trees in the coastal transect and at least 4 km of coast were occupied by T. albipes, and were interconnected by columns of workers. Technomyrmex albipes workers collected from different trees did not attack each other during confrontation tests, indicating that this species has formed a supercolony along the coast. Yet interspecific aggressiveness did occur between T. albipes and Crematogaster ranavalonae, a native species which is likely territorially dominant based on our intraspecific confrontation tests. These results suggest that the Masoala rainforest is threatened by a potential invasion by T. albipes, and that the penetration of this species further inland might be facilitated by the low density of native, territorially dominant arboreal ants normally able to limit its progression.
ISSN: 1932-6203

hal-00817444
https://hal.archives-ouvertes.fr/hal-00817444
https://hal.archives-ouvertes.fr/hal-00817444/document
https://hal.archives-ouvertes.fr/hal-00817444/file/Dejean2010_Spatial.pdf
DOI : 10.1371/journal.pone.0009319

Éditeur(s) : HAL CCSD Wiley
Résumé : The evolutionary potential of long-lived species, such as forest trees, is fundamental for their local persistence under climate change (CC). Genome–environment association (GEA) analyses reveal if species in heterogeneous environments at the regional scale are under differential selection resulting in populations with potential preadaptation to CC within this area. In 79 natural [i]Fagus sylvatica[/i] populations, neutral genetic patterns were characterized using 12 simple sequence repeat (SSR) markers, and genomic variation (144 single nucleotide polymorphisms (SNPs) out of 52 candidate genes) was related to 87 environmental predictors in the latent factor mixed model, logistic regressions and isolation by distance/environmental (IBD/IBE) tests. SSR diversity revealed relatedness at up to 150m intertree distance but an absence of large-scale spatial genetic structure and IBE. In the GEA analyses, 16 SNPs in 10 genes responded to one or several environmental predictors and IBE, corrected for IBD, was confirmed. The GEA often reflected the proposed gene functions, including indications for adaptation to water availability and temperature. Genomic divergence and the lack of large-scale neutral genetic patterns suggest that gene flow allows the spread of advantageous alleles in adaptive genes. Thereby, adaptation processes are likely to take place in species occurring in heterogeneous environments, which might reduce their regional extinction risk under CC
ISSN: 0028-646X

hal-01309135
https://hal.archives-ouvertes.fr/hal-01309135
PRODINRA : 343710
DOI : 10.1111/nph.13809

Éditeur(s) : HAL CCSD
Résumé : Over the last decade, distance-based methods have been introduced and then improved in the field of spatial economics to gauge the geographic concentration of activities. There is a growing literature on this theme including new tools, discussions on their specific properties and various applications. However, there is currently no typology of distance-based methods. This paper fills that gap. The proposed classification helps understand all the properties of distance-based methods and proves that they are variations on the same framework.
https://halshs.archives-ouvertes.fr/halshs-00679993

halshs-00679993
https://halshs.archives-ouvertes.fr/halshs-00679993
https://halshs.archives-ouvertes.fr/halshs-00679993v3/document

Éditeur(s) : Elsevier Science Bv
Résumé : We developed a growth model for Crassostrea gigas oyster shells based on the use of in situ temporal manganese markings to calibrate natural cathodoluminescence (CL) changes in the shell hinge sections. A 30 min to 4-h exposure period with Mn2+ (90-120 mg l(-1)) was sufficient to create a detectable mark in the shells. This makes the Mn2+ markings the fastest mollusc shells marking technique to date. The natural CL from juvenile and adult shells cultured in four standard shellfish-farming locations along the English Channel and French Atlantic coasts, exhibited a seasonal pattern (maximum CL intensity occurring during summer periods, minimum CL intensity occurring during winter). Hydrobiological data recorded at Baie des Veys site allows us to attribute the seawater temperature as the main parameter controlling CL of shells. Chlorophyll a and seawater manganese concentration were not decisive in the luminescence intensity of the shells. A relationship between oyster hinge growth and the length of shells makes the umbo investigations a promising tool for oyster-farming and/or wild stock assessments. Shell growth varied at spatial and temporal scales (higher growth rates were observed during summer-autumn and lower during the winter period), depending on seawater temperature changes. Sub-monthly Mn2+ markings support the fact that shell deposition can occur under temperatures below 6 degrees C, which has to be taken into account for both shellfish production and environmental monitoring derived from chemical compositions of the shells. Finally, our results point out the efficiency of age and shell growth rate determination by CL analysis in further shellfish ecosystem researches.
Aquaculture (0044-8486) (Elsevier Science Bv), 2010-02 , Vol. 300 , N. 1-4 , P. 206-217

Droits : 2010 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00002/11300/7912.pdf
DOI:10.1016/j.aquaculture.2009.12.018
http://archimer.ifremer.fr/doc/00002/11300/

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
Infant and neonatal mortality indicators are known to vary geographically, possibly as a result of socioeconomic and environmental inequalities. To better understand how these factors contribute to spatial and temporal patterns, we conducted a French ecological study comparing two time periods between 2002 and 2009 for three (purposefully distinct) Metropolitan Areas (MAs) and the city of Paris, using the French census block of parental residence as the geographic unit of analysis. We identified areas of excess risk and assessed the role of neighborhood deprivation and average nitrogen dioxide concentrations using generalized additive models to generate maps smoothed on longitude and latitude. Comparison of the two time periods indicated that statistically significant areas of elevated infant and neonatal mortality shifted northwards for the city of Paris, are present only in the earlier time period for Lille MA, only in the later time period for Lyon MA, and decrease over time for Marseille MA. These city-specific geographic patterns in neonatal and infant mortality are largely explained by socioeconomic and environmental inequalities. Spatial analysis can be a useful tool for understanding how risk factors contribute to disparities in health outcomes ranging from infant mortality to infectious disease-a leading cause of infant mortality.
ISSN: 1660-4601

hal-01359563
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01359563
DOI : 10.3390/ijerph13060624
PUBMED : 27338439

Éditeur(s) : HAL CCSD Wiley
Résumé : Tropical forests contain an important proportion of the carbon stored in terrestrial vegetation, but estimated aboveground biomass (AGB) in tropical forests varies two-fold, with little consensus on the relative importance of climate, soil and forest structure in explaining spatial patterns. Here, we present analyses from a plot network designed to examine differences among contrasting forest habitats (terra firme, seasonally flooded, and white-sand forests) that span the gradient of climate and soil conditions of the Amazon basin. We installed 0.5-ha plots in 74 sites representing the three lowland forest habitats in both Loreto, Peru and French Guiana, and we integrated data describing climate, soil physical and chemical characteristics and stand variables, including local measures of wood specific gravity (WSG). We use a hierarchical model to separate the contributions of stand variables from climate and soil variables in explaining spatial variation in AGB. AGB differed among both habitats and regions, varying from 78 Mg ha−1 in white-sand forest in Peru to 605 Mg ha−1 in terra firme clay forest of French Guiana. Stand variables including tree size and basal area, and to a lesser extent WSG, were strong predictors of spatial variation in AGB. In contrast, soil and climate variables explained little overall variation in AGB, though they did co-vary to a limited extent with stand parameters that explained AGB. Our results suggest that positive feedbacks in forest structure and turnover control AGB in Amazonian forests, with richer soils (Peruvian terra firme and all seasonally flooded habitats) supporting smaller trees with lower wood density and moderate soils (French Guianan terra firme) supporting many larger trees with high wood density. The weak direct relationships we observed between soil and climate variables and AGB suggest that the most appropriate approaches to landscape scale modeling of AGB in the Amazon would be based on remote sensing methods to map stand structure.
ISSN: 1354-1013

hal-01374829
https://hal.archives-ouvertes.fr/hal-01374829
DOI : 10.1111/j.1365-2486.2011.02432.x
PRODINRA : 183370

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Continuous Global Positioning System (CGPS) position time series from eastern North America constrain the pattern and magnitude of regional crustal deformation. Initial analysis delineates consistent uplift patterns, as expected from glacial isostatic adjustment (GIA) predictions, but the associated horizontal deformation is not definitive, in part due to the short time periods for a significant number of the available stations. We employ an eigenpattern decomposition in order to define a unique, finite set of deformation patterns for this continuous GPS data. Similar in nature to the empirical orthogonal functions historically employed in the analysis of atmospheric and oceanographic phenomena, the method derives the eigenvalues and eigenstates from the diagonalization of the correlation matrix using a Karhunen-Loeve expansion (KLE). The KLE technique is used to identify the important modes in both time and space for the CGPS data, modes that potentially include signals such as horizontal and vertical GIA, tectonic strain, and seasonal effects. Here we filter both the vertical and horizontal velocity patterns on different spatiotemporal scales in order to study the potential geophysical sources, after the removal of correlated and random noise. The method is successful in disaggregating the linear vertical signal from more variable and less spatially correlated signals. The vertical and horizontal results are compared to the predictions of the ICE-3G GIA loading model with a number of plausible mantle viscosity profiles. The horizontal velocity analysis allows for qualitative differentiation between several potential GIA models and suggests that, with longer time series, this technique can be employed to remove correlated noise and improve estimates of crustal strain patterns and their sources.
ISSN: 0033-4553

hal-00795454
https://hal.archives-ouvertes.fr/hal-00795454
DOI : 10.1007/s00024-011-0420-1

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known.
ISSN: 1932-6203

hal-01190764
https://hal.archives-ouvertes.fr/hal-01190764
PRODINRA : 214530
PUBMED : 22808236
DOI : 10.1371/journal.pone.0040699

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : In habitat mosaics, plant populations face environmental heterogeneity over short geographical distances. Such steep environmental gradients can induce ecological divergence. Lowland rainforests of the Guiana Shield are characterized by sharp, short-distance environmental variations related to topography and soil characteristics (from waterlogged bottomlands on hydromorphic soils to well-drained terra firme on ferralitic soils). Continuous plant populations distributed along such gradients are an interesting system to study intrapopulation divergence at highly local scales. This study tested (1) whether conspecific populations growing in different habitats diverge at functional traits, and (2) whether they diverge in the same way as congeneric species having different habitat preferences. Phenotypic differentiation was studied within continuous populations occupying different habitats for two congeneric, sympatric, and ecologically divergent tree species (Eperua falcata and E. grandiflora, Fabaceae). Over 3000 seeds collected from three habitats were germinated and grown in a common garden experiment, and 23 morphological, biomass, resource allocation and physiological traits were measured. In both species, seedling populations native of different habitats displayed phenotypic divergence for several traits (including seedling growth, biomass allocation, leaf chemistry, photosynthesis and carbon isotope composition). This may occur through heritable genetic variation or other maternally inherited effects. For a sub-set of traits, the intraspecific divergence associated with environmental variation coincided with interspecific divergence. The results indicate that mother trees from different habitats transmit divergent trait values to their progeny, and suggest that local environmental variation selects for different trait optima even at a very local spatial scale. Traits for which differentiation within species follows the same pattern as differentiation between species indicate that the same ecological processes underlie intra- and interspecific variation.
ISSN: 0305-7364

hal-01032430
https://hal.archives-ouvertes.fr/hal-01032430
DOI : 10.1093/aob/mct176