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Author |
Campillo, F.; Rakotozafy, R.; Rossi, V. |
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Title |
Parallel and interacting Markov chain Monte Carlo algorithm |
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Journal Article |
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Year |
2009 |
Publication |
Mathematics and Computers in Simulation |
Abbreviated Journal |
Math. Comput. Simul. |
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Volume |
79 |
Issue |
12 |
Pages |
3424-3433 |
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Keywords |
Markov chain Monte Carlo method; Interacting chains; Hidden Markov model |
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Abstract |
In many situations it is important to be able to propose N independent realizations of a given distribution law. We propose a strategy for making N parallel Monte Carlo Markov chains (MCMC) interact in order to get an approximation of an independent N-sample of a given target law. In this method each individual chain proposes candidates for all other chains. We prove that the set of interacting chains is itself a MCMC method for the product of N target measures. Compared to independent parallel chains this method is more time consuming. but we show through examples that it possesses many advantages. This approach is applied to a biomass evolution model. (C) 2009 IMACS. Published by Elsevier B.V. All rights reserved. |
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[Rossi, Vivien] CIRAD, Res Unit, Montpellier, France, Email: Fabien.Campillo@inria.fr |
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ELSEVIER SCIENCE BV |
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0378-4754 |
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ISI:000269289100006 |
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EcoFoG @ eric.marcon @ |
Serial |
197 |
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Author |
Flores, O.; Rossi, V.; Mortier, F. |
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Title |
Autocorrelation offsets zero-inflation in models of tropical saplings density |
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Journal Article |
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Year |
2009 |
Publication |
Ecological Modelling |
Abbreviated Journal |
Ecol. Model. |
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Volume |
220 |
Issue |
15 |
Pages |
1797-1809 |
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Keywords |
Hierarchical Bayesian Modelling; Conditional Auto-Regressive model; Variable selection; Zero-Inflated Poisson; Posterior predictive; Paracou; French Guiana |
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Abstract |
Modelling the local density of tropical saplings can provide insights into the ecological processes that drive species regeneration and thereby help predict population recovery after disturbance. Yet, few studies have addressed the challenging issues in autocorrelation and zero-inflation of local density. This paper presents Hierarchical Bayesian Modelling (HBM) of sapling density that includes these two features. Special attention is devoted to variable selection, model estimation and comparison. We developed a Zero-Inflated Poisson (ZIP) model with a latent correlated spatial structure and compared it with non-spatial ZIP and Poisson models that were either autocorrelated (Spatial Generalized Linear Mixed, SGLM) or not (generalized linear models, GLM). In our spatial models, local density autocorrelation was modeled by a Conditional Auto-Regressive (CAR) process. 13 explicative variables described ecological conditions with respect to topography, disturbance, stand structure and intraspecific processes. Models were applied to six tropical tree species with differing biological attributes: Oxandra asbeckii, Eperua falcata, Eperua grandiflora, Dicorynia guianensis, Qualea rosea, and Tachigali melinonii. We built species-specific models using a simple method of variable selection based on a latent binary indicator. Our spatial models showed a close correlation between observed and estimated densities with site spatial structure being correctly reproduced. By contrast, the non-spatial models showed poor fits. Variable selection highlighted species-specific requirements and susceptibility to local conditions. Model comparison overall showed that the SGLM was the most accurate explanatory and predictive model. Surprisingly, zero-inflated models performed less well. Although the SZIP model was relevant with respect to data distribution, and more flexible with respect to response curves, its model complexity caused marked variability in parameter estimates. In the SUM, the spatial process alone accounted for zero-inflation in the data. A refinement of the hypotheses employed at the process level could compensate for distribution flaws at the data level. This study emphasized the importance of the HBM framework in improving the modelling of density-environment relationships. (C) 2008 Elsevier B.V. All rights reserved. |
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Address |
[Flores, O.] CNRS, Ctr Ecol Fonct & Evolut, UMR 5175, F-34293 Montpellier 5, France, Email: olivierflores@free.fr |
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ELSEVIER SCIENCE BV |
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0304-3800 |
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ISI:000267585400007 |
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EcoFoG @ eric.marcon @ |
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201 |
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Author |
Rockwell, C.; Kainer, K.A.; Marcondes, N.; Baraloto, C. |
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Title |
Ecological limitations of reduced-impact logging at the smallholder scale |
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Journal Article |
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Year |
2007 |
Publication |
Forest Ecology and Management |
Abbreviated Journal |
For. Ecol. Manage. |
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Volume |
238 |
Issue |
1-3 |
Pages |
365-374 |
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Keywords |
community forest management; forest inventories; liana cutting; sustained yield; timber management; tropical forest conservation |
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Reduced-impact logging (RIL) has many demonstrated benefits to the industrial logging operations for which they were developed. It is less clear whether these gains remain consistent in smallholder forest systems that increasingly play an important role in global conservation and that target a broader suite of outputs in their management schemes. We evaluate potential ecological consequences of five RIL components (pre-harvest inventories, harvest intensity, cutting cycles, skid trail planning, and liana cutting) when applied to small-scale operations in the Brazilian Amazon and provide suggestions for modifications to RIL guidelines for smallholder systems. Rapid assessment inventories of the entire landholding should be a part of crop tree selection to minimize inbreeding and recruitment failure. Additionally, while community-based taxonomists accurately identify species to common names, botanical samples must be verified with herbarium specimens to avoid market and ecological problems when multiple species share a single common name. We advocate that smallholder managers move beyond an emphasis on RIL guidelines, while still incorporating its basic tenets into practical application. Based on our analysis, this would include evaluating benefits of particular RIL components and assessing potential advantages that smallholders have over industrial operations. We suggest incorporating anthropogenically-generated forest patches of varying sizes and successional stages into a more formalized management system, incorporating and expanding on traditional ecological knowledge acquired over generations, and integrating enrichment plantings and tending of regeneration. (c) 2006 Published by Elsevier B.V. |
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Univ Florida, Sch Forest Resources & Conservat, Gainesville, FL 32611 USA, Email: crockwel@ufl.edu |
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ELSEVIER SCIENCE BV |
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0378-1127 |
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ISI:000243761700033 |
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EcoFoG @ eric.marcon @ |
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220 |
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Author |
Phillips, P.D.; Thompson, I.S.; Silva, J.N.M.; van Gardingen, P.R.; Degen, B. |
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Title |
Scaling up models of tree competition for tropical forest population genetics simulation |
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Journal Article |
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Year |
2004 |
Publication |
Ecological Modelling |
Abbreviated Journal |
Ecol. Model. |
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Volume |
180 |
Issue |
2-3 |
Pages |
419-434 |
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Keywords |
tropical rain; forest; population genetics; model SYMFOR; eco-gene; scaling up; competition |
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Abstract |
Understanding the effects of logging activity on genetic diversity is an important aspect of establishing the sustainability of selective logging management operations in tropical forests. Genetic variation is affected by selective logging directly, through the removal of and damage to trees within the population, and indirectly, through a change in the forest structure and environment in which the remaining population lives. Eco-Gene is a population genetics model applied to tropical forests over a scale of hundreds of hectares. SYMFOR is a modelling framework for individual-based spatially explicit ecological and management models applied to tropical forests over a scale of 0.25 4 ha. We have linked the models to enable simulations using processes involved in both models. To overcome problems of scale, the spatially explicit competition index calculated in SYMFOR simulations has been modelled such that it can be applied at scales representing much larger areas for which the data are not available, as required by Eco-Gene. The competition index is modelled as a distribution on a grid-square basis, and implemented in the linked Eco-Gene/SYMFOR system. Each tree within a grid-square is given a “relative competition” within the distribution, biased according to species. A competition index value is obtained for the tree by transforming the grid-square distribution to be relevant to the size of the tree, and extracting a value according to the tree's relative competition within the distribution. The distribution and each tree's relative competition within it change according to the effects of growth, mortality and logging activity. The model was calibrated using data from the Tapajos region of the Eastern Amazon forest. This paper describes the model, its calibration and validation and the implications of scaling up from an explicit representation to a modelled quantity. (C) 2004 Elsevier B.V. All rights reserved. |
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Address |
Embrapa Amazonia Oriental, BR-66095100 Belem, Para, Brazil, Email: paul.phillips@envams.co.uk |
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ELSEVIER SCIENCE BV |
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0304-3800 |
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ISI:000224635700012 |
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no |
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EcoFoG @ eric.marcon @ |
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234 |
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Phillips, P.D.; de Azevedo, C.P.; Degen, B.; Thompson, I.S.; Silva, J.N.M.; van Gardingen, P.R. |
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Title |
An individual-based spatially explicit simulation model for strategic forest management planning in the eastern Amazon |
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Journal Article |
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Year |
2004 |
Publication |
Ecological Modelling |
Abbreviated Journal |
Ecol. Model. |
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Volume |
173 |
Issue |
4 |
Pages |
335-354 |
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Keywords |
model; individual; tropical forest; tree; spatial; Brazil; Amazon; competition; species grouping; management; certification; regulation |
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Abstract |
A model to simulate the ecological processes of tree growth, mortality and recruitment, and the processes of forest management, in the terra firme forests of the eastern Amazon is described. It is implemented within the SYMFOR (http://www.symfor.org) framework. It is based on measurements of all trees that have a diameter greater than 5 cm from experimental plots in the Jari Cellulose and Tapajos National Forest areas over a 16-year period. Ten species groups are used to describe the natural processes affecting tree behaviour. Growth rates are calculated for each species group using the tree diameter and a competition index. Mortality and recruitment are simulated as stochastic processes. Recruitment probability is based on the predicted growth rate of a hypothetical tree. Options exist to vary the human interaction with the forest reflecting forest management decisions, as for other SYMFOR models. Model evaluation compares the performance of the model with data describing forest recovery for 16 years following logging. The model was applied to simulate current forest management practice in the Brazilian Amazon, with 40 m(3) ha(-1) of timber extracted with a cutting cycle of 30 years. Results show that yields are sustained for three harvests following the first logging of primary forest, but that the composition of timber moves towards lightwooded species rather than hardwooded. The predicted size of extracted trees decreases and the number of trees extracted increases with successive harvests, leading to a prediction of increased costs and lower profits for the logging company despite constant yields. The standing volume of all trees just before harvest is reduced by 15% over 150 years, with pioneer species becoming increasingly prevalent in the stand. The model, in the SYMFOR framework, can be used to help understand the differences between alternative forest management strategies in the Brazilian Amazon. Such knowledge is required to improve forest management, regulation and certification, and help to conserve the worlds largest remaining tropical forest. (C) 2003 Elsevier B.V. All rights reserved. |
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Address |
EMBRAPA Amazonia Oriental, BR-69011970 Manaus, Amazonas, Brazil, Email: Paul.Phillips@envams.co.uk |
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ELSEVIER SCIENCE BV |
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0304-3800 |
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ISI:000220392200002 |
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no |
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EcoFoG @ eric.marcon @ |
Serial |
238 |
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Author |
Gourlet-Fleury, S.; Comu, G.; Jesel, S.; Dessard, H.; Jourget, J.G.; Blanc, L.; Picard, N. |
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Title |
Using models to predict recovery and assess tree species vulnerability in logged tropical forests: A case study from French Guiana |
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Journal Article |
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Year |
2005 |
Publication |
Forest Ecology and Management |
Abbreviated Journal |
For. Ecol. Manage. |
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Volume |
209 |
Issue |
1-2 |
Pages |
69-86 |
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Keywords |
matrix model; individual-based spatially explicit model; regeneration; recruitment; long-term population dynamics |
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Abstract |
A major challenge for forest managers is to define the optimal cutting cycle to ensure that the resource is sustained in the long term. Matrix models of forest dynamics allow time-projection of diameter-class distributions and thus assessment of the time needed, after logging, to recover a given part of the exploitable stock. They are easy to build and they only require, as input variables, the diameter structure of the population(s) under scope. However, such models are based on a coarse description of tree population dynamics and must be used with caution. In particular, as trees are only described from a diameter threshold (usually 10 cm dbh), recruitment of a new tree cannot be linked with the preceding generation since too much time elapsed between seed dispersal and the installation of a 10-cm recruit. This causes predictions of matrix models to be highly questionable in the long term when ingrowth to larger dbh classes greatly depends on the way recruitment has been modelled. We used a case study from French Guiana to test whether or not a simple matrix model is reliable enough to help forest managers choose between management alternatives. We focused on the major timber species Dicorynia guianensis Amshoff (Caesalpiniaceae) harvested under a selective cutting regime. We compared predictions of D. guianensis stock recovery in the short and long term provided by two models: StoMat, a non-regulated matrix model, and SELVA, a single-tree distance dependent model explicitly simulating the entire species life cycle. Both models were independently calibrated on data from Paracou permanent sample plots. We showed that: (i) the short-term recovery of the exploitable stock predicted by StoMat is reliable for a large range of disturbance conditions; (ii) recruitment implementation in StoMat does not influence projections until the third felling cycle; (iii) for shared initial stand conditions SELVA and StoMat give consistent mid- and long-term predictions: the simple recruitment model used into StoMat could efficiently summarise the regeneration processes of the species under low felling intensity. Our results indicate that the current felling regime used in French Guiana may not be sustainable on a long-term basis. In any case, no more than 60% of the initial stock would be recovered after logging. We conclude that simple models can provide as reliable predictions as more complicated ones. They may be sufficient to assess the recovery of a species' exploitable stock even in the long term, or at least assess the (un)sustainability of particular harvesting regimes. (c) 2005 Elsevier B.V. All rights reserved. |
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Address |
CIRAD, Dept Forets, F-34398 Montpellier 5, France, Email: sylvie.gourlet-fleury@cirad.fr |
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ELSEVIER SCIENCE BV |
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0378-1127 |
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ISI:000228504600007 |
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EcoFoG @ eric.marcon @ |
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257 |
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Author |
Melieres, M.A.; Pourchet, M.; Charles-Dominique, P.; Gaucher, P. |
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Title |
Mercury in canopy leaves of French Guiana in remote areas |
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Journal Article |
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Year |
2003 |
Publication |
Science of the Total Environment |
Abbreviated Journal |
Sci. Total Environ. |
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Volume |
311 |
Issue |
1-3 |
Pages |
261-267 |
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Keywords |
mercury; canopy; rainforest; Hg atmosphere soil transfer |
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A study of total Hg concentration in the foliage of the canopy was carried out in two remote areas in French Guiana. The sampled canopy is representative of the French Guiana canopy. The concentration in the foliage, 64+/-14 ng g(-1) (dry wt.), is used to estimate the annual input of total Hg to the soil through the litterfall, found to be 45+/-10 mug m(-2) y(-1). As translocation is negligible, mercury in the canopy originates mainly from atmospheric uptake by the leaves and this litterfall deposit represents a direct atmospheric input from the background atmospheric load into the soil. (C) 2003 Elsevier Science B.V. All rights reserved. |
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Address |
Univ Grenoble 1, CNRS, Lab Glaciol & Geophys Environm, F-38402 St Martin Dheres, France, Email: melieres@glaciog.ujf-grenobic.fr |
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ELSEVIER SCIENCE BV |
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0048-9697 |
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ISI:000184091300019 |
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EcoFoG @ eric.marcon @ |
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271 |
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Konig, A.O.; Ziegenhagen, B.; van Dam, B.C.; Csaikl, U.M.; Coart, E.; Degen, B.; Burg, K.; de Vries, S.M.G.; Petit, R.J. |
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Title |
Chloroplast DNA variation of oaks in western Central Europe and genetic consequences of human influences |
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Journal Article |
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Year |
2002 |
Publication |
Forest Ecology and Management |
Abbreviated Journal |
For. Ecol. Manage. |
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Volume |
156 |
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1-3 |
Pages |
147-166 |
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Keywords |
Q. robur; Q. petraea; PCR-RFLPs; haplotypes; spatial genetic patterns; genetic differentiation; deforestation; seed transfer |
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Abstract |
Oak chloroplast DNA (cpDNA) variation was studied in a grid-based inventory in western Central Europe, including Belgium, The Netherlands, Luxembourg, Germany, the Czech Republic, and the northern parts of Upper and Lower Austria. A total of 2155 trees representing 426 populations of Quercus robur L. and Q. petraea (Matt.) Liebl. were screened for polymorphism in up to four PCR-amplified cpDNA fragments. Eleven haplotypes belonging to four lineages were detected; these lineages were formerly restricted to glacial refugia in the Iberian Peninsula, the Apennine Peninsula and the Balkan Peninsula. The haplotypes originating from the Apennines are particularly well represented in the study region, but there is also a significant contribution from the other refugia, which explain the high overall level of cpDNA diversity. The strong human impact in western Central Europe during the past centuries, which has resulted in the clearance of most forests, was followed by reforestation, sometimes involving seed transfers. Despite this strong human impact, broad geographic patterns of lineages and haplotypes could still be detected. To evaluate further the consequences of the former human activities on the present day oak cpDNA genetic structure, four regions where increasingly strong human impact was anticipated (ranging from hilly regions in southern Germany to roadsides plantations in The Netherlands) were selected. There, a comparison of the levels of intrapopulation cpDNA diversity and spatial structuring was made. Over the whole area, within stand diversity was significantly higher in Q. robur than in Q. petraea (h(S) = 0.24 vs. 0.16). Since total diversity is identical for both species, this results in a significantly lower level of fixation for Q. robur than for Q. petraea (G(ST) = 0.68 vs. 0.79). The analyses also reveal a decrease of fixation with increasing human impact on oak populations. The Dutch roadside plantations (Q. robur) exhibit a very low level of fixation (G(ST) = 0.28) as compared to Q. petraea in southern Germany (G(ST) = 0.91). The significance of the spatial genetic structure was tested using geostatistical methods. For the complete data set, a strong spatial genetic structure is confirmed, with higher than average genetic similarities between populations distant from up to 270 km, whereas there is no spatial structure in the roadside plantations in The Netherlands or in the northern German lowlands. These results should help to differentiate introduced from autochthonous populations, and provide a framework for the identification of the geographic origin of seed lots. (C) 2002 Elsevier Science B.V. All rights reserved. |
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Address |
Inst FOrstgenet & Forstpflanzenzuchtung, BFH, D-22927 Grosshansdorf, Germany |
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ELSEVIER SCIENCE BV |
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0378-1127 |
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ISI:000174149400010 |
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EcoFoG @ eric.marcon @ |
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276 |
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Rutishauser, E.; Barthelemy, D.; Blanc, L.; Nicolini, E.A. |
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Title |
Crown fragmentation assessment in tropical trees: Method, insights and perspectives |
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Journal Article |
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Year |
2011 |
Publication |
Forest Ecology and Management |
Abbreviated Journal |
For. Ecol. Manage. |
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Volume |
261 |
Issue |
3 |
Pages |
400-407 |
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Keywords |
Crown assessment; Crown fragmentation; Tree mortality; Forest dynamics |
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Abstract |
Decreasing growth rate (Feeley et al., 2007) and large die-back due to drought (Phillips et al., 2009) suggest that tropical forests are suffering recent climate changes. Forest vulnerability to external factors (e.g. air pollution, acid rain) is widely studied in northern countries, while only a few attempts have investigated crown integrity in the Tropics. The method needs to be generic enough to account for the large number of species and crown shapes encountered in tropical forests. In the present study, we developed and tested a novel field method that estimates crown fragmentation (main branch mortality (MB) and secondary branch mortality (SB)), liana infestation (LI) and crown position (CP) in the canopy. The relationship between crown fragmentation and annual growth rate (agr) was investigated through multiple regression. Six out of eight canopy tree species showed significant growth decline with increasing crown fragmentation. Higher probability of death was also found in trees with severe crown fragmentation. The capacity of such crown assessment to depict tree vitality in a forest stand is discussed along with potential applications in both forest science and management. (C) 2010 Elsevier B.V. All rights reserved. |
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Address |
[Rutishauser, Ervan; Eric-Andre, Nicolini] Cirad UMR AMAP, F-34398 Montpellier 5, France, Email: er.rutishauser@gmail.com |
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ELSEVIER SCIENCE BV |
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ISI:000287333000009 |
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EcoFoG @ webmaster @ |
Serial |
293 |
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Author |
Lecante, A.; Robert, F.; Blandinieres, P.A.; Roos, C. |
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Title |
Anti-corrosive properties of S. tinctoria and G. ouregou alkaloid extracts on low carbon steel |
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Journal Article |
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Year |
2011 |
Publication |
Current Applied Physics |
Abbreviated Journal |
Curr. Appl. Phys. |
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Volume |
11 |
Issue |
3 |
Pages |
714-724 |
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Keywords |
Low carbon steel; Acidic media; Corrosion inhibitor; Plant extract; EIS |
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Abstract |
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. (C) 2010 Elsevier B.V. All rights reserved. |
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Address |
[Lecante, A.; Robert, F.; Blandinieres, P. A.; Roos, C.] UAG UMR ECOFOG, Lab Mat & Mol Milieu Amazonien, F-97337 Cayenne, French Guiana, France, Email: florent.robert@guyane.univ-ag.fr |
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Publisher |
Elsevier Science Bv |
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ISSN |
1567-1739 |
ISBN |
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Notes |
ISI:000288183300088 |
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no |
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Call Number |
EcoFoG @ webmaster @ |
Serial |
300 |
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