Éditeur(s) : HAL CCSD
Résumé : International audience
Field trip Guidebook, CorseAlp 2011 Meeting of Geology

hal-00604006
https://hal.archives-ouvertes.fr/hal-00604006

Éditeur(s) : HAL CCSD
Résumé :   Diplôme : DEA
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
L'étude de la répartition géographique de la diversité génétique résultant de l'histoire des populations apparaît comme fondamentale pour la conservation des espèces. Ainsi, la mise en évidence des relations phylo-géographiques au court du Quaternaire récent, au sein d'une espèce modèle Vouacapoua americana (Caesalpiniaceae), en Guyane française apporte des informations importantes sur la dynamique des populations naturelles. Dans cette étude les loci trn Q-trn S et trn Sa-trn fM sont utilisés afin de déterminer l'histoire évolutive des populations issues des refuges forestiers tropicaux. Le but principal est l'obtention des séquences après amplification PCR. L'analyse de ces séquences chez cinq populations testées a permis de mettre en évidence leur caractère hypervariable, ainsi que des régions présentant des motifs conservés répétés plusieurs fois. Les constructions phylogéographiques obtenues à partir de celles-ci accentuent la régionalisation des différents chlorotypes, existant en Guyane pour cette espèce, mise en évidence au cours de travaux précédents. Ainsi, les informations apportées par cette approche apparaissent comme complémentaires aux résultats obtenus par d'autres techniques d'analyse moléculaire.
https://hal.archives-ouvertes.fr/hal-01189224

hal-01189224
https://hal.archives-ouvertes.fr/hal-01189224
PRODINRA : 16622

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
Résumé : Diffusion du document : INRA Documentation de Centre, Domaine de Duclos, 97170 Petitt-Bourg (Guadeloupe, France) Diplôme : DEA
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
absent
https://hal.archives-ouvertes.fr/hal-01189164

hal-01189164
https://hal.archives-ouvertes.fr/hal-01189164
PRODINRA : 11017

Éditeur(s) : HAL CCSD Elsevier
Résumé : Over-exploitation and fragmentation are serious problems for tropical forests. Most sustainable forest management practices avoid clear-cuts and apply selective logging systems focused on a few commercial species. We applied a simulation model to estimate the impact of such selective logging scenarios on the genetic diversity and demography of four tropical tree species from French Guiana. The simulations used data on genetic and demographic composition, growth, phenology and pollen and seed dispersal obtained for Dicorynia guianensis, Sextonia rubra, Symphonia globulifera and Vouacapoua americana at the experimental site in Paracou. Whereas Symphonia globulifera serves as a model for a species with low logging pressure, the other three species represent the most exploited tree species in French Guiana. In simulations with moderate logging, typical for French Guiana, with large cutting diameter (>60 cm diameter) and long cutting cycles (65 years), the two species V. americana and Sextonia rubra were not able to recover their initial stock at the end of the rotation period, with a large decrease in the number of individuals and in basal area. Under a more intensive logging system (cutting diameter >45 cm diameter, cutting cycles of 30 years) that is common practice in the Brazilian Amazon, only Symphonia globulifera showed no negative impact. Generally, the differences between the genetic parameters in the control scenarios without logging and the logging scenarios were surprisingly small. The main reasons for this were the overlapping of generations and the effective dispersal ability of gene vectors in all species, which guarantee relative homogeneity of the genetic structure in different age classes. Nevertheless, decreasing the population size by logging reduced the number of genotypes and caused higher genetic distances between the original population and the population at the end of the logging cycles. Sensitivity analysis showed that genetic changes in the logging scenarios were principally determined by the growth, densities and cutting diameter of each species, and only to a very small extent by the reproductive system including factors such as pollen and seed dispersal and flowering phenology
ISSN: 0006-3207

hal-01032050
https://hal.archives-ouvertes.fr/hal-01032050
DOI : 10.1016/j.biocon.2006.02.014

Éditeur(s) : HAL CCSD Wiley
Résumé :  
Drier periods from the late Pleistocene and early Holocene have been hypothesized to have caused the disappearance of various rainforest species over large geographical areas in South America and restricted the extant populations to mesic sites. Subsequent improvement in climatic conditions has been associated with recolonization. Changes in population size associated with these extinction-recolonization events should have affected genetic diversity within species. However, these historical hypotheses and their genetic consequences have rarely been tested in South America. Here, we examine the diversity of the chloroplast and nuclear genomes in a Neotropical rainforest tree species, Vouacapoua americana (Leguminosae, Caesalpinioideae) in French Guiana. The chloroplast diversity was analyzed using a polymerase chain reaction-restriction fragment length polymorphism method (six pairs of primers) in 29 populations distributed over most of French Guiana, and a subset of 17 populations was also analyzed at nine polymorphic microsatellite loci. To determine whether this species has experienced extinction-recolonization, we sampled populations in areas supposedly not or only slightly affected by climatic changes, where the populations would not have experienced frequent extinction, and in areas that appear to have been recently recolonized. In the putatively recolonized areas, we found patches of several thousands of hectares homogeneous for chloroplast variation that can be interpreted as the effect of recolonization processes from several geographical origins. In addition, we observed that, for both chloroplast and nuclear genomes, the populations in newly recolonized areas exhibited a significantly smaller allelic richness than others. Controlling for geographic distance, we also detected a significant correlation between chloroplast and nuclear population differentiation. This result indicates a cytonuclear disequilibrium that can be interpreted as a historical signal of a genetic divergence between fragmented populations. In conclusion, the spatial genetic structure of contemporary V. americana populations shows evidence that this species has experienced large extinction-recolonization events, which were possibly caused by past climatic change.
ISSN: 0014-3820

hal-01032194
https://hal.archives-ouvertes.fr/hal-01032194
DOI : 10.1111/j.0014-3820.2003.tb01517.x

Éditeur(s) : HAL CCSD Wiley
Résumé :  
The chloroplast genome has been widely used to describe genetic diversity in plant species. Its maternal inheritance in numerous angiosperm species and low mutation rate are suitable characters when inferring historical events such as possible recolonization routes. Here we have studied chloroplast DNA variation using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) with seven pairs of primers and four restriction enzymes in 14 populations of Vouacapoua americana (Caesalpiniaceae) a neotropical tree sampled throughout French Guiana. Population diversity (Hs), total gene diversity (Ht) and differentiation among populations (GST) were estimated using Nei's method as 0.09, 0.87 and 0.89, respectively. This is consistent with the limited gene flow associated with synzoochory in this species. The genetic structure observed in the north of French Guiana suggests that historical events such as contractions and recent recolonizations have had a large impact on the distribution of genetic diversity in this species.
ISSN: 0962-1083

hal-01032176
https://hal.archives-ouvertes.fr/hal-01032176
DOI : 10.1046/j.1365-294x.2000.01027.x

Éditeur(s) : HAL CCSD Wiley
Résumé : The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies
ISSN: 0962-1083

hal-01031603
https://hal.archives-ouvertes.fr/hal-01031603
DOI : 10.1111/j.1365-294X.2005.02785.x

Éditeur(s) : HAL CCSD
Résumé :   Diplôme : DEA
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
absent
https://hal.archives-ouvertes.fr/hal-01189525

hal-01189525
https://hal.archives-ouvertes.fr/hal-01189525
PRODINRA : 45292

Éditeur(s) : HAL CCSD
Résumé : CorseAlp 2011 was held in April 2011. A link to the website is here: CorseAlp 2011. The CorseAlp field trips were designed to introduce the participants to the general features of the geology of Alpine Corsica and to recent specific discoveries. The three-day post-workshop field trip (Field trip 2) focused on the general architecture of Alpine Corsica in an EW transect between the Balagne region and Bastia. First day: The internal zones of Alpine Corsica: from Bastia to Saint Florent. Intinerary: Saint Florent, Serra di Pigno, Cima Malaspina, Patrimonio, Saint Florent. Second day: The Tenda massif and its eastern margin. Intinerary: Saint Florent, Casta, Fontana Porragghia, Rue de Morello, Fontana a Murello quarry; Fornali. Third day: The external zones of Alpine Corsica in the Balagne region. Intineray: Saint Florent, Colle di U'Vezzu, Ostriconi, Belgodere, San Sebastiano Chapel, San Colombano, Ponte Leccia, Francardo, Bastia.
Journal of the Virtual Explorer

hal-00688971
https://hal.archives-ouvertes.fr/hal-00688971