Éditeur(s) : Paris : Librairie militaire L. Fournier

Droits : Domaine public
Provenance : Université de Nantes. Service commun de la documentation
Permalien : http://www.manioc.org/patrimon/NAN13041
NAN13041

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
In a study of a 15-year-old pasture in Martinique (French West Indies), abundance and organization of microarthropod communities were correlated with the spatial distribution of the earthworm Polypheretima elongata (Megascolecidae). In patches of high earthworm density (133 individuals m-2), microarthropod density was significantly higher (80 000 individuals m-2) than in patches with few earthworms (31 worms m-2 and 49 000 microarthropods m-2). The diversity of microarthropod communities followed a similar pattern, the Shannon index for Collembola communities being, respectively, 3.12 and 1.82 in and outside earthworm patches. These results suggest that mesofauna abundance and diversity might be at least partly determined by the activity of larger invertebrates, as a result of the dramatic effects that the latter group exerts upon soil structure, pore distribution and food resources.
ISSN: 0178-2762

hal-00505427
https://hal.archives-ouvertes.fr/hal-00505427
https://hal.archives-ouvertes.fr/hal-00505427/document
https://hal.archives-ouvertes.fr/hal-00505427/file/Loranger_et_al._1998b.pdf
DOI : 10.1007/s003740050394

Éditeur(s) : HAL CCSD Muséum national d'histoire naturelle
Résumé :  
Le rôle déterminant de la faune dans les processus de dissémination, de prédation des graines et de régénération naturelle des arbres en forêt tropicale américaine a été mis en évidence par de nombreuses études menées notamment en Guyane française. Nombreux sont les arbres qui offrent des ressources alimentaires aux animaux frugivores et granivores et sont également des essences recherchées par les exploitants forestiers de ce département d'Outre-Mer. Les pistes forestières ouvertes pour l'exploitation du bois sont des voies facilitant l'accès de la forêt aux chasseurs, professionnels ou non, lorsque ce ne sont pas les exploitants eux-mêmes qui exercent une forte pression cynégétique. La question se pose alors de savoir si, dans l'optique d'une meilleure gestion des formations forestières pour une utilisation à long terme de la ressource bois, il ne faut pas se soucier sérieusement de la préservation de cette faune, maillon indispensable au maintien de la diversité en forêt. Autrement dit, les deux activités, exploitation forestière et chasse, sont-elles compatibles avec le maintien des processus de régénération forestière ?
ISSN: 0183-5173

hal-01032077
https://hal.archives-ouvertes.fr/hal-01032077

Éditeur(s) : HAL CCSD Wiley
Résumé :  
Aims: Astrocaryum sciophilum (Miq.) Pulle (Arecaceae) is an understorey palm, endemic to north-eastern South America with a patchy distribution. We tested the hypothesis that the spatial distribution of this palm species is not in equilibrium but is slowly colonizing the forest understorey. Location: Inventories and seed dispersal studies were conducted in the undisturbed tropical forest close to the Nouragues research station, French Guiana. Additional data were collected in the entire territory of French Guiana. Methods: We studied the demography of A. sciophilum on a 20-ha plot located at the edge of its distribution. The age of the palms was estimated by postulating an exponentially decreasing abundance by age class. Direct seed dispersal experiments were also conducted, to estimate dispersal parameters. The seeds of A. sciophilum were dispersed only by rodents. This information was used to parameterize a forest growth simulator, to study the spatial spread of this species. Results: Within the sampling plot, the density of A. sciophilum dropped sharply from about 500 individuals per hectare to zero. The maturation age was estimated to be 170 ± 70 years, and over 55 years with 95% confidence. Seed-dispersal experiments yielded an average seed dispersal distance of 11 m and a maximum estimated dispersal distance of 125 m across a generational span of 55 years to maturity. Therefore, the maximal estimated colonization speed is 2.3 m/y. Conclusions: Empirical results and numerical simulations suggest that the boundary of the A. sciophilum population is a colonization front, and that the range of this species is slowly expanding. The implications of this result in respect of palaeoenvironmental changes in this region are discussed.
ISSN: 1466-822X

hal-01032154
https://hal.archives-ouvertes.fr/hal-01032154
DOI : 10.1046/j.1466-822X.2003.00020.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and tem perate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylo genies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms.
ISSN: 1055-7903

hal-01359407
https://hal.archives-ouvertes.fr/hal-01359407
https://hal.archives-ouvertes.fr/hal-01359407/document
https://hal.archives-ouvertes.fr/hal-01359407/file/Postaire-etal2016MolPhylEvol_sp_delim_hydraires_HAL.pdf
DOI : 10.1016/j.ympev.2016.08.013

Éditeur(s) : HAL CCSD PeerJ
Résumé : International audience
Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction. How to cite this article Leray et al. (2015), Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 3:e1047
ISSN: 2167-8359

Droits : http://creativecommons.org/licenses/by/
hal-01174184
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01174184/file/peerj-1047.pdf
DOI : 10.7717/peerj.1047

Résumé : This catalogue deals mainly with common phytoplanktonic species found in the Channel. It is part of a bibliographical survey on pelagos and benthos. The main idea was to gather the largest possible amount of data on the eco-physiology of each species. To do so, studies were conducted in the main marine region where the species had been found and analysed. We focused on several reference ecological studies conducted in the coastal Channel, on the E.D.F. sites, by the C.N.E.X.O., the I.S.T.P.M. and some university laboratories. A great attention was also paid to the studies on seasonal cycles carried out in laboratories in Plymouth, Helgoland and in the Irish zones. (unverified OCR)
Ce catalogue se rapporte essentiellement aux espèces phytoplanctoniques les plus courantes et abondantes en Manche; il s'insère dans une synthèse bibliographique générale concernant le pélagos et le benthos. Nous nous sommes proposés de rassembler le plus grand nombre de données sur l'éco-physiologie de chaque espèce. Pour ce faire, les recherches se sont déroulées dans les principales régions maritimes où l'espèce avait été rencontrée et étudiée. Plus particulièrement, notre attention s'est portée sur les études écologiques de référence effectuées en Manche Littorale sur les sites E.D.F. par le C.N.E.X.O., l'I.S.T.P.M, et les laboratoires universitaires; d'importance aussi, furent les études de cycles saisonniers effectuées au laboratoire de Plymouth, d'Helgoland, et dans les zones irlandaises. OCR NON CONTROLE

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1984/rapport-3701.pdf
http://archimer.ifremer.fr/doc/00000/3701/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Decomposition processes in tropical semi-evergreen forests are still poorly understood. The influence of soil properties and litter quality on decomposition rate was studied in two semi-evergreen forests of Guadeloupe, a forest plantation and a secondary forest, located on different soils. Leaf litter of four tree species was enclosed in litterbags for a 14-month period. Nonlinear correlations were calculated between mass loss and the concentration of major leaf components (soluble C, N, lignin, cellulose, tannins, total soluble phenols) in order to determine the best predictor of leaf litter decomposition. Soil physico-chemical properties and ratios between some of the above-mentioned litter quality parameters were also examined as mass loss predictors. In addition, non-linear correlations were calculated between mass loss and litter quality parameters, at successive periods. Litter quality was the main determinant of litter decomposition in the studied forests. Several litter quality parameters were correlated with leaf disappearance, varying according to stages of decomposition. Between 1 month and 2.5 months, the mass loss was correlated negatively with the initial phenol content and with initial lignin:N and (lignin+phenol):N ratios. From 2.5 to 5.5 months, the mass loss was correlated negatively with the initial phenol content and positively with the initial cellulose content. At later stages of decomposition (9-14 months), the mass loss was correlated negatively with the initial tannin content. Differences in soil characteristics and fauna did not seem to be enough to affect decomposition.
ISSN: 0178-2762

hal-00499535
https://hal.archives-ouvertes.fr/hal-00499535
https://hal.archives-ouvertes.fr/hal-00499535/document
https://hal.archives-ouvertes.fr/hal-00499535/file/Article_decomposition.pdf
DOI : 10.1007/s00374-002-0467-3

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This study aimed to identify factors associated with virological response (VR) to raltegravir (RAL)-containing regimens in 468 treatment-experienced but integrase inhibitor-naive HIV-1 patients receiving a RAL-containing regimen. VR was defined at Month 6 (M6) as HIV-1 RNA viral load (VL) <50 copies/mL. The impacts on VR of baseline integrase mutations, VL, CD4 count, genotypic sensitivity score for nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors and protease inhibitors, and the number of new antiretrovirals used for the first time associated with RAL were investigated. For patients with VL >50 copies/mL at M6, integrase mutations selected were characterised. Median baseline VL was 4.2 log(10)copies/mL (IQR 3.3-4.9 log(10) copies/mL) and CD4 count was 219 cells/mm(3) (IQR 96-368 cells/mm(3)). At M6, 71% of patients were responders. In multivariate analysis, baseline VL and CD4 count and ≥ 2 new antiretrovirals among darunavir, etravirine, maraviroc and enfuvirtide were associated with VR to RAL. Neither HIV-1 subtype nor baseline integrase polymorphisms were associated with VR to RAL. Among 63 failing patients at M6, selection of ≥ 1 change in the integrase gene was observed in 49 (77.8%), and 27/63 (42.9%) were considered as RAL-associated resistance mutations. Factors independently associated with the occurrence of ≥ 1 RAL-associated resistance mutation were VL at failure >3 log(10) and having no new drugs associated with RAL. RAL showed great potency in treatment-experienced patients. The number of new drugs associated with RAL was an important factor associated with VR. HIV-1 subtype and baseline integrase polymorphisms do not influence the RAL VR.
ISSN: 0924-8579

hal-00875083
https://hal.archives-ouvertes.fr/hal-00875083
DOI : 10.1016/j.ijantimicag.2013.02.016
PUBMED : 23562640

Éditeur(s) : HAL CCSD PeerJ
Résumé : International audience
The adaptative bleaching hypothesis (ABH) states that, depending on the symbiotic flexibility of coral hosts (i.e., the ability of corals to ''switch'' or ''shuffle'' their algal symbionts), coral bleaching can lead to a change in the composition of their associated Symbiodinium community and, thus, contribute to the coral's overall survival. In order to determine the flexibility of corals, molecular tools are required to provide accurate species delineations and to detect low levels of coral-associated Symbiodinium. Here, we used highly sensitive quantitative (real-time) PCR (qPCR) technology to analyse five common coral species from Moorea (French Polynesia), previously screened using only traditional molecular methods, to assess the presence of low-abundance (background) Symbiodinium spp. Similar to other studies, each coral species exhibited a strong specificity to a particular clade, irrespective of the environment. In addition, however, each of the five species harboured at least one additional Symbiodinium clade, among clades A–D, at background levels. Unexpectedly, and for the first time in French Polynesia, clade B was detected as a coral symbiont. These results increase the number of known coral-Symbiodinium associations from corals found in French Polynesia, and likely indicate an underestimation of the ability of the corals in this region to associate with and/or ''shuffle'' different Symbiodinium clades. Altogether our data suggest that corals from French Polynesia may favor a trade-off between optimizing symbioses with a specific Symbiodinium clade(s), maintaining associations with particular background clades that may play a role in the ability of corals to respond to environmental change. How to cite this article Rouzé et al. (2017), An updated assessment of Symbiodinium spp. that associate with common scleractinian corals from Moorea (French Polynesia) reveals high diversity among background symbionts and a novel finding of clade B.
ISSN: 2167-8359

Droits : info:eu-repo/semantics/OpenAccess
hal-01430294
https://hal-sde.archives-ouvertes.fr/hal-01430294
https://hal-sde.archives-ouvertes.fr/hal-01430294/document
https://hal-sde.archives-ouvertes.fr/hal-01430294/file/Rouze-2017-PeerJ-Updated.pdf
DOI : 10.7717/peerj.2856

Éditeur(s) : HAL CCSD
Résumé : Point processes are often used as spatial or spatio-temporal distribution models of occurrences. In this PhD dissertation, we focus first on Cox processes driven by a hidden process associated with a Dirichlet process. This model corresponds to hidden occurrences influencing the stochastic intensity of observed occurrences. We generalize the notion of "Shot noise Cox process" introduced by M{o}ller and develop its bayesian analysis by a Gibbs sampler combined with a Metropolis-Hastings algorithm. We show that our MCMC method is a reversible jump one. The model takes into account a random number of hidden contributions producing effects on the observed point process intensity. Therefore the parameter space has a variable dimension. We focus the statistical inference on the estimation of the hidden contribution expected value, the hidden contribution expected number, the spatial influence and correlation parameters. The contribution equality test and contribution independence test are proposed. Applications in epidemiology and ecology are shown from extit{Rubus fruticosa} data, extit{Ibicella lutea} data and death number data in counties of Georgia, USA. Two situations are considered with respect to available data~: firstly, the spatial positions of occurrences are observed between several pairs of consecutive dates; secondly, counts are carried out over a fixed time interval in several spatial sampling units. Secondly, we focus on point processes with memory introduced by Kagan, Ogata and Vere-Jones, pioneers in statistical seismology. In fact, spatio-temporal point processes play an important role in the studies of earthquake catalogs since they consist of seismic events with their dates and spatial locations. We studied an ETAS (Epidemic Type Aftershock Sequence) model with time independent background intensity and several triggering functions taking into account previous events. We illustrate our approach with a seismicity study of the Lesser Antilles arc. A comparaison study of Gamma, Weibull, Log-Normal and modified Omori law triggering function models is also carried out. We show that the modified Omori law does not fit the Lesser Antilles seismic data and the best adjusted triggering function is the Weibull model. Consequently, the waiting time between aftershocks is weaker in the Lesser Antilles zone compared to the one in regions with seismicity described by the modified Omori law. In other words, aftershock aggregativity is higher in the Lesser Antilles region. The stochastic background intensity following a Dirichlet process centered on a spatial log-normal process is discussed.
Les processus ponctuels sont souvent utilisés comme modèles de répartitions spatiales ou spatio-temporelles d'occurrences. Dans cette thèse, nous nous intéressons tout d'abord à des processus de Cox dirigés par un processus caché associé à un processus de Dirichlet. Ce modèle correspond à des occurrences cachées influençant l'intensité stochastique des occurrences observées. Nous généralisons la notion de " Shot noise Cox process " introduite par Moller et développons le traitement bayésien par un échantillonneur de Gibbs combiné à un algorithme de Metropolis-Hastings. Nous montrons que cette méthode MCMC est à sauts réversibles. Le modèle prend en compte, en effet, un nombre aléatoire de contributions cachées influençant l'intensité du processus ponctuel observé donc a un espace paramétrique de dimension variable. Nous focalisons l'inférence statistique sur l'estimation de la valeur espérée de chaque contribution cachée, le nombre espéré de contributions cachées, le degré d'influence spatiale de ces contributions et leur degré de corrélation. Le test d'égalité des contributions et celui de leur indépendance sont ainsi développés. L'utilité en épidémiologie et en écologie est alors démontrée à partir de données de Rubus fruticosa, Ibicella lutea et de mortalité dans les cantons de Georgia, USA. En termes de données observées, deux situations sont considérées: premièrement, les positions spatiales des occurrences sont observées entre plusieurs paires de dates consécutives; deuxièmement, des comptages sont effectués, au cours d'une période fixée, dans des unités d'échantillonnage spatiales. D'autre part, nous nous intéressons aux processus ponctuels à mémoire introduits par Kagan, Ogata et Vere-Jones, précurseurs de la statistique sismologique. En effet, les processus ponctuels spatio-temporels ont une place importante dans l'étude des catalogues sismiques puisque ces derniers sont généralement constitués d'événements sismiques datés et géo-référencés. Nous avons étudié un modèle ETAS (Epidemic Type Aftershock Sequence) avec une intensité d'arrière-plan indépendante du temps et plusieurs fonctions déclenchantes permettant d'intégrer les événements antérieurs récents. Cette approche est utilisée pour étudier la sismicité de l'arc des Petites Antilles. Une étude comparative des modèles Gamma, Weibull, Log-Normal et loi d'Omori modifiée pour les fonctions déclenchantes est menée. Nous montrons que la loi d'Omori modifiée ne s'ajuste pas aux données sismiques des Petites Antilles et la fonction déclenchante la plus adaptée est le modèle de Weibull. Cela implique que le temps d'attente entre répliques dans la zone des Petites Antilles est plus faible que celui des régions à sismicité décrite par la loi d'Omori modifiée. Autrement dit, l'agrégation des répliques après un événement majeur est plus prononcée dans la zone des Petites Antilles. La possibilité d'inclure une intensité d'arrière-plan suivant un processus de Dirichlet centré sur un processus spatial log-gaussien est discutée.
https://tel.archives-ouvertes.fr/tel-00841146

Droits : info:eu-repo/semantics/OpenAccess
NNT : 2012AGUY0555
tel-00841146
https://tel.archives-ouvertes.fr/tel-00841146
https://tel.archives-ouvertes.fr/tel-00841146/document
https://tel.archives-ouvertes.fr/tel-00841146/file/these_VALMY.pdf

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
Coral spawning times have been linked to multiple environmental factors; however, to what extent these factors act as generalized cues across multiple species and large spatial scales is unknown. We used a unique dataset of coral spawning from 34 reefs in the Indian and Pacific Oceans to test if month of spawning and peak spawning month in assemblages of Acropora spp. can be predicted by sea surface temperature (SST), photosynthetically available radiation, wind speed, current speed, rainfall or sunset time. Contrary to the classic view that high mean SST initiates coral spawning, we found rapid increases in SST to be the best predictor in both cases (month of spawning: R2 = 0.73, peak: R2 = 0.62). Our findings suggest that a rapid increase in SST provides the dominant proximate cue for coral mass spawning over large geographical scales. We hypothesize that coral spawning is ultimately timed to ensure optimal fertilization success.
ISSN: 0962-8452

hal-01325704
https://hal-univ-perp.archives-ouvertes.fr/hal-01325704
DOI : 10.1098/rspb.2016.0011

Éditeur(s) : HAL CCSD
Résumé : In spatial statistics, Ripley's K function (Ripley, 1977) is a classical tool to analyse spatial point patterns. Yet, it faces two major limits: it is only pertinent for homogeneous point processes and it does not allow the weighting of points.
We generalize it to get a new function, M, which oversteps these limits and detects spatial structures of inhomogeneous populations of weighted points.
https://halshs.archives-ouvertes.fr/halshs-00372631

halshs-00372631
https://halshs.archives-ouvertes.fr/halshs-00372631
https://halshs.archives-ouvertes.fr/halshs-00372631/document
https://halshs.archives-ouvertes.fr/halshs-00372631/file/HAL_Marcon_Puech_-_GeneralizingRipleysKFunctiontoInhomogeneousPopulations.pdf

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
BACKGROUND: Surveillance of HIV-1 drug resistance in treated patients with plasma viral load (VL) >50 copies/mL. METHODS: The protease and reverse transcriptase (RT) genes were systematically sequenced in samples from 756 patients with VL >50 copies/mL in 2009. The genotyping results were interpreted for each antiretroviral drug (ARV) by using the ANRS algorithm v21. Weighted analyses were used to derive representative estimates of percentages of patients. Prevalence rates were compared with those obtained in 2004 among patients with VL >1000 copies/mL. RESULTS: Sequences were obtained for 506 patients. Sequencing was successful in 45%, 80% and 96% of samples with VL of 51-500, 501-1000 and >1000 copies/mL, respectively. Resistance or possible resistance to at least one ARV was observed in 59% of samples. Overall, 0.9% of samples contained viruses resistant to all drugs belonging to at least three drug classes. All resistance prevalence rates were significantly lower in 2009 than in 2004. CONCLUSION: In France, where 86% of patients were receiving combination antiretroviral therapy in 2009, only 15.0% of patients had a VL >50 copies/mL, suggesting that only 8.9% of treated patients could potentially transmit resistant viruses. Only 0.08% of patients harboured viruses fully resistant to at least three antiretroviral drug classes. Further studies are needed to determine whether resistance continues to decline over time.
ISSN: 0305-7453

hal-00875092
https://hal.archives-ouvertes.fr/hal-00875092
DOI : 10.1093/jac/dkt033
PUBMED : 23404192