Éditeur(s) : HAL CCSD Hindawi Publishing Corporation
Résumé : International audience
We generalize Ripley's K function to get a new function, M, to characterize the spatial structure of a point pattern relatively to another one. We show that this new approach is pertinent in ecology when space is not homogenous and the size of objects matters. We present how to use the function and test the data against the null hypothesis of independence between points. In a tropical tree data set we detect intraspecific aggregation and interspecific competition.
ISSN: 1687-9708

hal-01502623
https://hal-agroparistech.archives-ouvertes.fr/hal-01502623
DOI : 10.1155/2012/619281

Éditeur(s) : HAL CCSD
Résumé : Guide
La mise en place de la gestion forestière en Guyane est très récente: ce n’est qu’à partir de 1990 et de la prise de conscience consécutive à la conférence de Rio qu’une véritable politique de gestion et de valorisation de la forêt guyanaise est entreprise par l’ONF sous la commande de l’Etat. Depuis ses débuts, cet effort porté par les gestionnaires forestiers publics a été accompagné par toute la communauté scientifique guyanaise sous l’égide d’un groupement d’intérêt scientifique focalisé sur le milieu forestier : le GIS SILVOLAB, aujourd’hui élargi aux autres disciplines sous le nom d’IRISTA. Les développements méthodologiques réalisés depuis 1994 avec la communauté scientifique ont déjà permis la rédaction d’un guide pratique d’aménagement spécifique à la Guyane (ONF mars 2009). Après plus de 20 ans de recherche (ce qui à l’échelle du pas de temps forestier est très peu), il demeure un manque de connaissances sur le fonctionnement de la forêt dense tropicale humide et plus particulièrement sur les effets du milieu sur la distribution des espèces et la dynamique du peuplement. En attendant que la recherche apporte des réponses aux questions qui restent posées, ce sont aujourd’hui les connaissances acquises en écologie des communautés et des populations avec nos partenaires de l’UMR Ecofog (regroupement d’AgroParisTech, de l’INRA, du CIRAD, du CNRS et l’Université des Antilles et de la Guyane) qui permettent la rédaction de ce premier guide sylvicole applicable aux forêts guyanaises. Le programme BGF «Biodiversité et Gestion Forestière» financé par le Ministère chargé de l’Environnement sur l’appel à projet ECOFOR (2006) a particulièrement contribué à la réflexion engagée pour ce document, de même que les travaux de fonds engagés depuis de nombreuses années par le CIRAD sur le site de Paracou et par l’ONF sur les forêts pilotes de Risquetout et d’Organabo (réseau de placettes permanentes GUYAFOR). Le programme DYGEPOP, financé plus récemment par l’Union Européenne (PO-FEDER) a permis de compléter et synthétiser ces résultats pour aboutir à la rédaction de ce guide. Le présent guide de sylviculture a pour objectif de synthétiser l’ensemble des connaissances scientifiques acquises au cours de ces dernières années concernant l’écologie des forêts guyanaises et leurs applications en termes de règles sylvicoles. Le guide s’accompagne d’annexes donnant des descriptifs précis des dispositifs scientifiques dont sont tirés ces résultats, ainsi qu’une revue bibliographique exhaustive des études exploitées pour asseoir ces premières bases sylvicoles qui restent évidemment largement améliorables. En complément de ce guide, sera rédigée, une note d’application régionale qui constituera une déclinaison opérationnelle des actions à mettre en œuvre qui viendra compléter ou modifier les différents processus. Nous tenons à préciser ici que ce document ne concerne que la sylviculture pour le bois d’œuvre. L’exploitation de bois énergie constitue en soi un changement d’objectif qui amène des préconisations différentes notamment dans le choix des tiges et dans le niveau de prélèvements et fera l’objet en temps et en heure d’un document spécifique.
https://hal-agroparistech.archives-ouvertes.fr/hal-01503730

hal-01503730
https://hal-agroparistech.archives-ouvertes.fr/hal-01503730

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary. We developed a method to compare genome-wide diversity estimates while taking into account-and factoring out-variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels. An approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers. RaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots. RaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).
ISSN: 1286-4560

hal-01032413
https://hal.archives-ouvertes.fr/hal-01032413
DOI : 10.1007/s13595-013-0302-z

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Questions: Several studies have described aggregated spatial patterns in tropical tree species. This study investigates aggregate dynamics of Vouacapoua americana (Aublet), a climax species whose spatial pattern is not simply related to light and soil conditions or to its short seed dispersal range. Location: Two rain forest sites: Nouragues and Paracou, in the Guiana Shield. Methods: We described the spatial pattern of tree locations and spatial autocorrelation of tree diameters, using statistics derived from Ripley's K. We particularly used methods to define analysis subplots according to local density or local mean diameter. We investigated relationships between spatial distributions of adults and saplings. Results: At both sites, populations of Vouacapoua demonstrated several nested levels of aggregation. Tree diameters were spatially autocorrelated, revealing the existence of clusters with similar diameters. In the largest aggregates, tree diameters declined from the centre to the edge. Regeneration was aggregated and occurred mainly at cluster edges and around rare isolated trees, and sapling densities and basal area of adults were negatively correlated. We show that long-distance dispersal events are rare. Conclusions: Environmental factors and seed dispersal only explain part of the observed spatial patterns. We provide two main hypotheses about Vouacapoua population dynamics. First, the lack of regeneration in aggregate centres results in the ageing of existing aggregates. We suggest that this lack of recruitment close to mature trees is due to a Janzen-Connell effect. However, aggregates can continue to grow along colonization fronts. Second, long-distance dispersal events allow the formation of new clusters and play a crucial role in the colonization process. We investigate aggregate dynamics of Vouacapoua americana (Aublet) whose spatial pattern is not simply related to environmental conditions or to its seed dispersal. Regeneration does not occur in centers of aggregate of adults. We suggest that rare long-distance dispersal events and density-dependence predation of seeds and seedlings play a crucial role in formation of new clusters and structuration of larger aggregates.
ISSN: 1100-9233

hal-01502642
https://hal-agroparistech.archives-ouvertes.fr/hal-01502642
DOI : 10.1111/jvs.12080

Éditeur(s) : HAL CCSD
Résumé : International audience
Ripley’s K function is the classical tool to characterize the spatial structure of point patterns. It is widely used in vegetation studies. Testing its values against a null hypothesis usually relies on Monte-Carlo simulations since little is known about its distribution.We introduce a statistical test against complete spatial randomness (CSR). The test returns the p-value to reject the null hypothesis of independence between point locations. It is more rigorous and faster than classical Monte-Carlo simulations. We show how to apply it to a tropical forest plot. The necessary R code is provided.
International Scholarly Research Network, ISRN Ecology

hal-01502637
https://hal-agroparistech.archives-ouvertes.fr/hal-01502637
https://hal-agroparistech.archives-ouvertes.fr/hal-01502637/document
https://hal-agroparistech.archives-ouvertes.fr/hal-01502637/file/2013_Marcon_Hindawi%20Publishing%20Corporation_%7B7A602F34-6983-47DE-924B-7CDC3B8D14F7%7D.pdf
DOI : 10.1155/2013/753475

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : International audience
Key message: Genetic diversity appears to be unaffected by disturbance in a stand of the light-demanding Neotropical treeV. michelii. Although spatial genetic structure is modified in post-disturbance cohorts, mixing of seeds from different mother trees in canopy gaps appears to efficiently maintain genetic admixture. Context: The interplay between genetic and demographic processes has major consequences on population viability. Population size affects demographic trends, while genetic diversity insures viability by reducing risks of inbreeding depression and by maintaining adaptive potential. Yet, the consequences of increases in census size (as opposed to effective size) on genetic diversity of forest populations are poorly known. Aims: We have studied the structure of genetic diversity in populations of saplings of the light-responsive tree, Virola michelii (Myristicaceae, the nutmeg family), in two plots having undergone different levels of canopy-gap opening disturbance. This allowed us to test the “intermediate disturbance” hypothesis, which generally applies to species diversity, at the intra-specific scale. Methods: Levels and distribution of genetic diversity were compared between plots and between life stages. Sapling parentage was analysed to infer each adult tree’s contribution to regeneration. Results: Genetic diversity was higher, and spatial genetic structure was stronger in the post-disturbance than in the control seedling population. Parentage analysis suggested that a limited number of parents contributed to most of the regeneration, but that efficient mixing of their progeny may have enhanced the diversity of saplings occupying canopy gaps. Conclusion: A mixture of demo-genetic processes may contribute to maintain genetic diversity in spite of, or possibly due to, ecosystem disturbance in V. michelii.
ISSN: 1286-4560

hal-01502942
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942/document
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942/file/art_10.1007_s13595-015-0508-3-1_%7B869D58F4-272C-491F-A903-DAD6CDBDC042%7D.pdf
DOI : 10.1007/s13595-015-0508-3

Éditeur(s) : HAL CCSD University of California, Los Angeles
Résumé : International audience
The dbmss package for R provides an easy-to-use toolbox to characterize the spatial structure of point patterns. Our contribution presents the state of the art of distance-based methods employed in economic geography and which are also used in ecology. Topographic functions such as Ripley’s K, absolute functions such as Duranton and Overman’s Kd and relative functions such as Marcon and Puech’s M are implemented. Their confidence envelopes (including global ones) and tests against counterfactuals are included in the package
ISSN: 1548-7660

hal-01498361
https://hal-agroparistech.archives-ouvertes.fr/hal-01498361
DOI : 10.18637/jss.v067.c03