Éditeur(s) : HAL CCSD Ethnobotany Research and Applications
Résumé :  
We examined the limitations of parataxonomic inventories for developing management plans for woody plant resources in tropical rain forests of southwestern Amazonia. Using compilations of herbarium labels, forest personnel interviews and published species descriptions, we assessed the accuracy of common names as parataxonomic units (PUs). We identified 384 common names for 310 harvested woody plant species in the Brazilian state of Acre, of which only 50% were unique to a single taxonomic species. About 10% of common names referred to more than one species, more than half of which included multiple genera. For the 106 species from the Acre sample common to the MAP region including Madre de Dios, Peru and Pando, Bolivia, we identified 198 common names. Splitting was much more frequent in this sample, with more than 80% of species having more than one common name. When the Acre sample was expanded to 131 species from the Brazilian Amazon region, including the states of Amazonas and Para, we identified 740 common names, with nearly 90% of species being represented by more than one common name. Errors and inaccuracy of parataxonomy may contribute to market instability if product orders can not be homogenized within regional markets, and to unsustainable harvests if species are mistakenly lumped into single parataxonomic units. We discuss several programs currently being implemented by our collaborative team in the region to address this issue, including field guides based on digital photography, field courses, and workshops featuring discussions between regional inventory personnel and botanists.
Ethnobotany Research and Applications

hal-01032130
https://hal.archives-ouvertes.fr/hal-01032130

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.
ISSN: 1755-098X

hal-01204217
https://hal.archives-ouvertes.fr/hal-01204217
DOI : 10.1111/1755-0998.12246
PRODINRA : 283530

Éditeur(s) : HAL CCSD Embrapa Amazônia Oriental
Résumé :  
absent
Modelling and experimental research on genetic processes in tropical and temperate forests [proceedings]
Kourou, Guyane, France

hal-01032053
https://hal.archives-ouvertes.fr/hal-01032053

Éditeur(s) : HAL CCSD
Résumé :  
In tropical rainforests, the origin of the interspecific variability in trunk CO2 efflux (Et) and of seasonal variations in Et have not yet been explained. We conducted a study to test which biotic and abiotic determinants would contribute to these variations. Et and a set of wood anatomical and functional characteristics were measured on trees in two habitats (Terra Firme forest vs. seasonal flooded forest) in a Neotropical rainforest over a 18-months' period including a range of climatic and soil water conditions. The large variability in Et (0.33 to 3.15 μmol CO2 m-2 s-1 in Terra Firme forest) was associated with tree diameter and growth respiration (Eg), although maintenance respiration (Em) was the main component of Et. Neither wood properties nor sapflow density were correlated with trunk CO2 efflux. The large seasonal variations in Et were correlated with diameter growth and surface soil water content (SWC). These data underlined the absence of clearly identified biotic determinants, beside growth, to explain the interspecific variability in Et. We emphasized the fast response of growth and maintenance respiration processes to seasonal variations in SWC that potentially has consequences on the carbon cycle in the ecosystem under upcoming climatic changes.
23. New Phytologist Symposium. Carbon cycling in tropical ecosystems
Guangzhou, China

hal-01032199
https://hal.archives-ouvertes.fr/hal-01032199

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The effect of alkaloid extracts from two Amazonian trees (Guatteria ouregou and Simira tinctoria) on low carbon steel corrosion was investigated in acidic solutions by using electrochemical techniques. All of these plant extracts inhibit the corrosion of low carbon steel in 0.1 M HCl solutions. As their concentration increases to 250 mg/L, the inhibition efficiencies of S. tinctoria and G. ouregou alkaloid extracts reach approximately 92% in 0.1 M HCl solutions. The adsorption of the inhibitor molecules was in accordance with the Langmuir adsorption isotherm. The results obtained show that these plant extracts could be serve as an effective inhibitor for the corrosion of low carbon steel in hydrochloric acid media. Furthermore, harmane was identified as the main component of S. tinctoria extract and that suggests that it is the active ingredient against corrosion of low carbon steel.
ISSN: 1567-1739

hal-01096888
https://hal-agroparistech.archives-ouvertes.fr/hal-01096888
DOI : 10.1016/j.cap.2010.11.038

Éditeur(s) : HAL CCSD Ethnobotany Research and Applications
Résumé : We examined the limitations of parataxonomic inventories for developing management plans for woody plant resources in tropical rain forests of southwestern Amazonia. Using compilations of herbarium labels, forest personnel interviews and published species descriptions, we assessed the accuracy of common names as parataxonomic units (PUs). We identified 384 common names for 310 harvested woody plant species in the Brazilian state of Acre, of which only 50% were unique to a single taxonomic species. About 10% of common names referred to more than one species, more than half of which included multiple genera. For the 106 species from the Acre sample common to the MAP region including Madre de Dios, Peru and Pando, Bolivia, we identified 198 common names. Splitting was much more frequent in this sample, with more than 80% of species having more than one common name. When the Acre sample was expanded to 131 species from the Brazilian Amazon region, including the states of Amazonas and Para, we identified 740 common names, with nearly 90% of species being represented by more than one common name. Errors and inaccuracy of parataxonomy may contribute to market instability if product orders can not be homogenized within regional markets, and to unsustainable harvests if species are mistakenly lumped into single parataxonomic units. We discuss several programs currently being implemented by our collaborative team in the region to address this issue, including field guides based on digital photography, field courses, and workshops featuring discussions between regional inventory personnel and botanists.
ISSN: 1547-3465

hal-01032404
https://hal.archives-ouvertes.fr/hal-01032404

Résumé : En 2013, Le Groupe d'experts Intergouvernemental sur l'Evolution du Climat (GIEC) publie son cinquième rapport concernant les changements climatiques. Il y est souligné que le réchauffement climatique est sans équivoque, et que de nouvelles émissions de gaz à effet de serre impliqueront une poursuite du réchauffement et des changements affectant toutes les composantes du système climatique. En région tropicale, une hausse de la température, ainsi qu'une intensification des événements de sécheresse et de pluviométrie extrêmes sont à prévoir. C'est dans ce contexte que s'inscrit ce travail, dont le but est d'étudier la réponse de la forêt tropicale à ces changements climatiques prédits en Guyane Française. Pour ce faire, j'ai utilisé les données du dispositif de suivi forestier de Paracou pour construire un modèle de dynamique individuel basé sur les traits fonctionnels des arbres. Un modèle de mortalité a d'abord été réalisé puis couplé à un modèle de croissance.Le modèle couplé ainsi construit permet de modéliser la croissance et la mortalité des arbres sur un pas de temps de 2 ans tout en tenant compte de leur ontogénie et de leurs traits fonctionnels. Ce modèle a d'abord été appliqué aux essences commerciales de Guyane Française en forêt naturelle et exploitée en y ajoutant un indice de stress hydrique. Ceci permet de montrer que le stress hydrique fait baisser la croissance et augmenter la mortalité, tandis que l'exploitation a l'effet inverse. Malgré le signal commun, différentes réponses sont observées selon les espèces. Le modèle a ensuite été appliqué à la communauté en forêt naturelle pour identifier les drivers climatiques et les processus impactés. Il ressort que la croissance est impactée par le stress hydrique et la température, et que la mortalité est impactée par le stress hydrique et la pluviométrie totale.Ces résultats ont enfin permis de construire un modèle complet de dynamique forestière climat dépendant, et de simuler l'évolution d'une communauté pendant un siècle selon différents scénarios correspondant aux prédictions du GIEC. Les simulations mettent en évidence une très forte diminution de la croissance, ainsi qu'une plus faible diminution de la mortalité. Ceci entraine une diminution notable de la surface terrière, du diamètre quadratique et de la biomasse fraiche. Une analyse de sensibilité montre que ces changements sont principalement dus à l'augmentation sévère des températures prédites pour le siècle à venir. Des pistes de réflexion sur les enjeux de modélisation et les échelles considérées sont proposées en discussion de ce travail.
In 2013 the intergovernmental panel on climate change (ipcc) publishes its fifth report. This report underlines that an increase of temperature and a strengthening of drought and extreme rainfall are expected in tropical regions. This work was made in this context of climate changes, and aimed to study the response of the rainforest to predicted climate changes. To do this, i used the data from the study site of Paracou French Guiana to build an individual based dynamics model based on the functional traits of trees. This model was first applied to species with a commercial interest in French Guiana, in natural and logged forest and adding a water stress index as predictor. Water stress decreases growth and increases mortality, while logging had the opposite effect. The model was then applied to the community in natural forest for identifying potential climate drivers and impacted processes. Growth is impacted by the water stress and temperature and mortality is imp acted by the water stress and the total rainfall. These results allowed us to build a climate dependent model of forest dynamics and to run simulations of the evolution of a community under different scenarios for the next century. Simulations showed a decrease of growth and a small decrease of mortality. This resulted in a substantial decrease of basal area, squared diameter and fresh biomass.

http://www.theses.fr/2014AGUY0802/document

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Mycoheterotrophic orchids have adapted to shaded forest understory by shifting to achlorophylly and receiving carbon from their mycorrhizal fungi. In temperate forests, they associate in a highly specific way with fungi forming ectomycorrhizas on nearby trees, and exploiting tree photosynthates. However, many rainforests lack ectomycorrhizal fungi, and there is evidence that some tropical Asiatic species associate with saprotrophic fungi. To investigate this in different geographic and phylogenetic contexts, we identified the mycorrhizal fungi supporting two tropical mycoheterotrophic orchids from Mascarene (Indian Ocean) and Caribbean islands. We tested their possible carbon sources by measuring natural nitrogen (15N) and carbon (13C) abundances. Saprotrophic basidiomycetes were found: Gastrodia similis associates with a wood-decaying Resinicium (Hymenochaetales); Wullschlaegelia aphylla associates with both litter-decaying Gymnopus and Mycena species, whose rhizomorphs link orchid roots to leaf litter. The 15N and 13C abundances make plausible food chains from dead wood to G. similis and from dead leaves to W. aphylla. We propose that temperature and moisture in rainforests, but not in most temperate forests, may favour sufficient saprotrophic activity to support development of mycoheterotrophs. By enlarging the spectrum of mycorrhizal fungi and the level of specificity in mycoheterotrophic orchids, this study provides new insights on orchid and mycorrhizal biology in the tropics. New Phytologist (2009)doi: 10.1111/j.1469-8137.2009.02987.x
ISSN: 0028-646X

hal-01199356
http://hal.univ-reunion.fr/hal-01199356
DOI : 10.1111/j.1469-8137.2009.02987.x

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] [br/] The phylogeographical history of Neotropical species can be difficult to reconstruct because of superimposed Neogene and Quaternary histories, and because of taxonomic uncertainty. We analysed range-wide genetic diversity in a widespread pioneer tree species, Jacaranda copaia (Aubl.) D. Don, to characterize phylogeographical structure, date the evolutionary relationships among lineages, and evaluate the role of dispersal and vicariance in establishing the present geographical range.[br/] [br/] [br/] [b]Location[/b][br/] [br/] Guiana Shield; central, southern and western Amazon Basin; Chocó region; Central America.[br/] [br/] [br/] [b]Methods[/b][br/] [br/] We analysed nine nuclear simple sequence repeat loci (nuSSR), eight chloroplast SSRs (cpSSR), and two cpDNA intergenic sequences in 341 adult trees. Genetic differentiation at nuSSRs was inferred using Bayesian clustering. Dating of chloroplast lineage divergence was obtained using a range of published mutation rates and Bayesian coalescence analyses. Population divergence dating was performed using an isolation-with-migration model for eight loci (one cp sequence and seven nuSSRs).[br/] [br/] [br/] [b]Results[/b][br/] [br/] Nuclear SSR variation identified three geographically overlapping clusters (nu-1, nu-2, nu-3). Twelve cpDNA haplotypes were clustered into two haplogroups (cp-1, cp-2) with the central Amazon harbouring the highest diversity. Molecular dating analysis suggests that cpDNA haplotype diversification started around the end of the Pliocene (2.61 Ma on average), whereas population divergence was more recent and occurred during the mid-Quaternary (point estimates between 357 and 436 ka).[br/] [br/] [br/] [b]Main conclusions[/b][br/] [br/] The genetic variation of J. copaia in the Neotropics was shaped mainly by Pleistocene events. Chloroplast diversity did not display the expected cis/trans Andean disjunction, indicating recent dispersal. Nuclear variation revealed that separate regions share a recent history, with a centre of diversity in the central Amazon Basin. The geographical pattern of diversity is congruent with the distribution of the two subspecies, J. copaia copaia and J. copaia spectabilis, and evidence of nuSSR admixture between the two taxa supports their classification as subspecies.
ISSN: 0305-0270

hal-01032410
https://hal.archives-ouvertes.fr/hal-01032410
DOI : 10.1111/j.1365-2699.2012.02797.x

Résumé : Aujourd’hui, il est indispensable de découvrir de nouveaux agents thérapeutiques pour faire face à l’expansion des infections fongiques humaines. D’un autre côté, certains arbres amazoniens ont acquis des moyens pour se protéger contre la dégradation fongique. Ces composés d’origine végétale pourraient donc être des candidats potentiels au développement de composés antifongiques. Il est ainsi exposé dans ce travail la sélection bio-inspirée et la récolte d’espèces d’arbres amazoniens résistants à la dégradation fongique ; à partir desquelles il est proposé d’isoler, d’identifier et de valoriser les métabolites responsables de la durabilité naturelle et d’étudier leurs propriétés sur des champignons pathogènes humains. Cette étude a conduit à l’isolement de molécules inédites apportant un complément d’information chimiotaxonomique pour les espèces étudiées. De plus, il a pu être mis en avant deux molécules pouvant devenir des composés pertinents pour le développement de traitements antimycotiques.
It is now essential to discover new therapeutic agents against the increase of human fungal infections. On the other hand, some Amazonian trees have succeeded to develop a chemical defense arsenal to protect themselves against fungal degradation. These compounds of plant origin could become potential candidates for the development of antifungal compounds for the treatment of human fungal diseases. Therefore, this manuscript describes the bio-inspired selection and collection of Amazonian tree species capable of specializing a highly fungiresistant wood; from which it is proposed to isolate, identify and valorize the secondary metabolites responsible for the natural durability, and study their properties on human pathogenic fungi. Ultimately, this study led to the isolation of new compounds and providing additional important chemotaxonomic information for the species studied. In addition, it as been established that two compounds could be relevant for the development of antimitotic therapies.

http://www.theses.fr/2011AGUY0467/document

Résumé : Le maintien de ressources génétiques suffisamment larges est nécessaire pour assurer la viabilité et le potentiel évolutif des populations naturelles. Cette thèse a le principal objectif de caractériser la diversité et la variabilité génétique chez le genre Virola (Myristicaceae) pour décrire les processus évolutifs qui en sont à l'origine. Premièrement,une étude de la régénération d'un échantillonnage exhaustif de V. michelii a été menée dans une parcelle du dispositif expérimental de Paracou ayant subi une exploitation forestière de faible intensité et comparée à une parcelle témoin. La diversité génétique mesurée à partir de marqueurs AFLP (Amplified Fragment-Length Polymorphism, N=229) en zones perturbées s'est révélée être plis grande qu'en zone non-perturbées. Puis, l'adaptation locale a été étudiée à travers ces mêmes individus et certains loci (AFLP) montrent une sélection divergente pour des environnements contrastés, indiquant un signe d'adaptation. Enfin, l'étude des niveaux de divergence génétique chez trois espèces de Virola du bouclier guyanais (V. michelii, V. surinamensis et V. kwatae) montrent que deux d'entre elles (V. surinamensis et V. kwatae) montrent de fortes similarités génétiques malgré leur distribution sur des environnements contrastés. des Flux de gènes intersécifiques ont été mis en évidence chez ces deux espèces-soeurs et l'hypothèse d'une spéciation écologique est avancée. Ce travail a permis d'aborder différents processus évolutifs à l'origine de la diversité génétique actuelle chez ces espèces forestières tropicales et peut fournir une contribution pour appréhender le devenir des populations.
Genetic diversity is an essential component of biodiversity. The maintenance of sufficient genetic resources is needed to ensure the adaptive potential and the viability of natural populations. In the current context of global changes, the study of adaptation in living organisms is a key task, particularly for tropical forest trees that are dominant components (in terms of biomass and as ecological drivers) of some of the most diverse ecosystems on Earth. The main objective of this thesis is to characterize genetic diversity and genetic variability to understand the evolutionary processes that act on them. This ecological-genetic study was carried out at the interspecific and intraspecific level in the Virola genus.If overall high levels of genetic diversity are a guarantee of prosperity for the future of the species, it seems essential to perform studies on the impact of environmental disturbance on genetic diversity. In the first section, the genetic consequences of regeneration dynamics were studied in an exhaustive sample of V. michelii in a low-intensity logging plot and in a control plot at the Paracou experimental site. A greater genetic diversity, measured from AFLP markers (Amplified Fragment Length Polymorphism, N = 229), was found in perturbed areas. Because studying genetic diversity within species may be useful for understanding species adaptation to environmental changes, in the second section. I studied local adaptation in a population of V. michelii on the Paracou experimental site. A genome scan approach with AFLPs (N = 229) was conducted on 77 adult individuals and 401 juveniles to identify genetic differences between populations associated to contrasting conditions for an array of environmental variables. Some loci (N = 2) were found to be subject to divergent selection, indicating adaptation to contrasting habitats.In the third section, the study of levels of genetic divergence in three Virola species of the Guiana Shield (V. michelii, V. surinamensis and V. kwatae) was investigated for nuclear and chloroplast molecular markers. V. surinamensis and V. kwatae showed strong genetic similarities despite their contrasting habitats preferences. Coalescent analyses have revealed, on one hand, a recent divergence between these two species suggesting an ecological speciation, and one the other hand that interspecific gene flow occurs between these sister-species.This work focuses on understanding evolutionary processes shaping genetic diversity and provides a useful contribution for biodiversity conservation programs.

http://www.theses.fr/2011AGUY0480/document