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Author |
Maron, P.A.; Schimann, H.; Ranjard, L.; Brothier, E.; Domenach, A.M.; Lensi, R.; Nazaret, S. |
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Title |
Evaluation of quantitative and qualitative recovery of bacterial communities from different soil types by density gradient centrifugation |
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Journal Article |
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Year |
2006 |
Publication |
European Journal of Soil Biology |
Abbreviated Journal |
Eur. J. Soil Biol. |
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Volume |
42 |
Issue |
2 |
Pages |
65-73 |
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Keywords |
bacterial community; soil; density gradient; DNA fingerprint |
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Abstract |
Extracting and purifying a representative fraction of bacteria from soil is necessary for the application of many techniques of microbial ecology. Here the influence of different soil types on the quantitative and qualitative recovery of bacteria by soil grinding and Nycodenz density gradient centrifugation was investigated. Three soils presenting contrasted physicochemical characteristics were used for this study. For each soil, the total (AODC: acridine orange direct count) and culturable (cfa: colony-forming units) bacterial densities were measured in three distinct fractions: (i) the primary soil, (ii) the soil pellet (soil remaining after centrifugation), and (iii) the extracted cells. The automated-ribosomal intergenic spacer analysis (A-RISA) was used to characterize the community structure directly from the DNA extracted from each fraction. The physicochemical characteristics of soils were found to influence both the efficiency of bacterial cell recovery and the representativeness of the extracted cells in term of community structures between the different fractions. Surprisingly, the most representative extracted cells were obtained from the soil exhibiting the lowest efficiency of cell recovery. Our results demonstrated that quantitative and qualitative cell recovery using Nycodenz density gradient centrifugation are not necessarily related and could be differentially biased according to soil type. (c) 2006 Elsevier SAS. All rights reserved. |
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Univ Lyon 1, CNRS, UMR 5557, Ctr Microbial Ecol, F-69622 Villeurbanne, France, Email: nazaret@biomserv.univ-lyon1.fr |
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ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER |
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1164-5563 |
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ISI:000238534500001 |
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Call Number |
EcoFoG @ eric.marcon @ |
Serial |
181 |
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Author |
Veron, V.; Caron, H.; Degen, B. |
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Title |
Gene flow and mating system of the tropical tree Sextonia rubra |
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Journal Article |
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Year |
2005 |
Publication |
Silvae Genetica |
Abbreviated Journal |
Silvae Genet. |
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Volume |
54 |
Issue |
6 |
Pages |
275-280 |
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Keywords |
genetic diversity; gene flow; heterozygosity; microsatellites; mixed mating; tropical tree; twogener |
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Abstract |
In this paper we report a study of the mating system and gene flow of Sextonia rubra, a hermaphroditic, insect pollinated tropical tree species with a geographic distribution in the Guyana Plateau and the Amazon. Using five microsatellites we analysed 428 seeds of 27 open pollinated families at the experimental site “Paracou” in French Guiana. We observed, compared to other tropical tree species, a high level of genetic diversity. We estimated parameters of the mating system and gene flow by using the mixed mating model and the TwoGener approach. The estimated multilocus outcrossing rate, t(m), was 0.992 indicating nearly complete outcrossing. A significant level of biparental inbreeding and a:small proportion. of full-sibs were estimated for the 27 seed arrays. The differentiation of allelic frequencies among the pollen pools was (Phi(FT) = 0.061. We estimated mean pollen dispersal distances between 65 m and 89 m according to the dispersal models used. The joint estimation of pollen dispersal and density of reproductive trees gave an effective density estimate of 2.1-2.2 trees/ha. |
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INRA, UMR, ECOFOG, Kourou 9738, French Guiana, Email: b.degen@holz.uni-hamburg.de |
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J D SAUERLANDERS VERLAG |
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0037-5349 |
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ISI:000235239400005 |
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EcoFoG @ eric.marcon @ |
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182 |
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Hardy, O.J.; Maggia, L.; Bandou, E.; Breyne, P.; Caron, H.; Chevallier, M.H.; Doligez, A.; Dutech, C.; Kremer, A.; Latouche-Halle, C.; Troispoux, V.; Veron, V.; Degen, B. |
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Title |
Fine-scale genetic structure and gene dispersal inferences in 10 Neotropical tree species |
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Journal Article |
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Year |
2006 |
Publication |
Molecular Ecology |
Abbreviated Journal |
Mol. Ecol. |
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Volume |
15 |
Issue |
2 |
Pages |
559-571 |
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Keywords |
French Guiana; gene dispersal; seed dispersal; spatial genetic structure; tropical trees |
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Abstract |
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. |
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Address |
Univ Libre Bruxelles, Serv Ecoethol Evolut, B-1050 Brussels, Belgium, Email: ohardy@ulb.ac.be |
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BLACKWELL PUBLISHING |
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0962-1083 |
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Notes |
ISI:000235045500021 |
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no |
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EcoFoG @ eric.marcon @ |
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183 |
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Picard, N.; Gourlet-Fleury, S.; Sist, P. |
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Title |
Using process-dependent groups of species to model the dynamics of a tropical rainforest |
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Journal Article |
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Year |
2003 |
Publication |
Modelling Forest Systems |
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Pages |
237-248 |
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The high tree species diversity in tropical forests is difficult to take into account in models. The usual solution consists of defining groups of species and then adjusting a set of parameters for each group. In this study, we address this issue by allowing a species to move from one species group to another, depending on the biological process that is concerned. We developed this approach with a matrix model of forest dynamics, for a tropical rainforest in French Guiana, at Paracou, focusing on the methodological aspects. The forest dynamics is split into three components: recruitment, growth and mortality. We then built five recruitment groups, five growth groups and five mortality groups. One species is characterized by a combination of the three groups, thus yielding in total 5 X 5 X 5 = 125 possibilities, out of which 43 are actually observed. The resulting matrix model provides a better view of the floristic composition of the forest, and does not have more parameters than it would have with five global species groups. However, its predictions are no more precise than those of the matrix model based on five global groups. |
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Address |
Cirad Foret, Montpellier, France |
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Publisher |
CABI PUBLISHING |
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ISI:000231866400021 |
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no |
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EcoFoG @ eric.marcon @ |
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249 |
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Author |
Baraloto, C.; Forget, P.M.; Goldberg, D.E. |
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Title |
Seed mass, seedling size and neotropical tree seedling establishment |
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Journal Article |
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Year |
2005 |
Publication |
Journal of Ecology |
Abbreviated Journal |
J. Ecol. |
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Volume |
93 |
Issue |
6 |
Pages |
1156-1166 |
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Keywords |
French Guiana; life-history trade-offs; microhabitat; path analysis; regeneration strategy; relative growth rate; seedling survival; shade tolerance |
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Abstract |
1 We examined among- and within-species effects of seed mass for seedling establishment from seed to 5 years of age in a field experiment at Paracou, French Guiana. 2 Six seeds of each of eight species were weighed and planted into each of 120 plots (1 m(2)) throughout closed-canopy forest along 12 100-m transects in 1998. 3 We described the microhabitat of each planting site using principal components derived from measurements of light availability, soil moisture, carbon and nitrogen content, and soil phosphorus availability. Although both survival and relative growth rate (RGR) increased with increasing light availability, no other microhabitat variable significantly affected seedling performance. Nor did the magnitude of microhabitat effects on survival or RGR differ among species. 4 Larger-seeded species were more likely to survive from germination to 1 year as well as from 1 to 5 years of age. RGR for seedling height during the first year post-germination was not related to seed mass, but smaller-seeded species did grow slightly faster thereafter. Path analyses revealed that correlations between seed mass and performance were explained in part because larger seeds produced larger initial seedlings, which tended to survive better but grow more slowly. 5 We also analysed within-species effects of seed mass for the larger-seeded Eperua grandiflora and Vouacapoua americana (both Caesalpiniaceae). Larger seeds produced larger seedlings in both species, but larger seeds survived better only for Eperua. Larger seedlings grew more slowly in both species, but did not offset the early (Eperua) and later (Vouacapoua) positive direct effects of seed mass on RGR that may represent contrasting strategies for reserve deployment. 6 Our results demonstrate that seed size influences performance within and among species in part because of indirect effects of initial seedling size. However, we suggest that traits tightly correlated with seed mass at the species level, such as specific leaf area, leaf longevity and photosynthetic capacity, may also contribute to interspecific performance differences. |
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Address |
Museum Natl Hist Nat, Dept Ecol & Gest Biodivers, UMR 5176, CNRS, Brunoy, France, Email: baraloto.c@kourou.cirad.fr |
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BLACKWELL PUBLISHING |
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0022-0477 |
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ISI:000233287500012 |
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no |
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EcoFoG @ eric.marcon @ |
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250 |
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Author |
Fouquet, A.; Dubut, V.; Hataway, R.; Scotti-Saintagne, C.; Scotti, I.; Noonan, B. |
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Isolation and characterisation of 19 microsatellite loci from the Amazonian frog Adenomera andreae (Amphibia: Anura: Leptodactylidae) |
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Journal Article |
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Year |
2009 |
Publication |
Conservation Genetics Resources |
Abbreviated Journal |
Conserv. Genet. Res. |
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Volume |
1 |
Issue |
1 |
Pages |
217-220 |
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Keywords |
Biomedicine |
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Abstract |
Nineteen novel microsatellite loci were isolated from Adenomera andreae, a widespread Amazonian frog considered to be a species complex. Three multiplex kits were optimized. Genetic diversity was assessed in 66 individuals sampled in three populations along the West of the Approuague River catchment (French Guiana). We also tested the multiplex kits in four other Adenomera and nine Leptodactylus species with 43.4 and 17.5% success respectively. |
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Springer Netherlands |
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1877-7252 |
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EcoFoG @ eric.marcon @ |
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185 |
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Author |
Leroy, C.; Corbara, B.; Dejean, A.; Céréghino, R. |
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Title |
Potential sources of nitrogen in an ant-garden tank-bromeliad |
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Journal Article |
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Year |
2009 |
Publication |
Plant Signaling and Behavior |
Abbreviated Journal |
Plant. Signal. Behav. |
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Volume |
4 |
Issue |
9 |
Pages |
868-870 |
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Keywords |
Aechmea mertensii Camponotus femoratus nitrogen nitrogen stable isotope Pachycondyla goeldii plant-insect interactions phytotelmata |
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Abstract |
Epiphytic plants in general and bromeliads in particular live in a water and nutrient-stressed environment often limited in nitrogen. Thus, these plants have developed different ways to survive in such an environment. We focused on Aechmea mertensii (Bromeliaceae), which is both a tank-bromeliad and an ant-garden (AG) epiphyte initiated by either the ants Camponotus femoratus or Pachycondyla goeldii. By combining a study of plant morphology and physiology associated with aquatic insect biology, we demonstrate that the ant species influences the leaf structure of the bromeliad, the structure of the aquatic community in its tank, and nutrient assimilation by the leaves. Based on nitrogen and nitrogen stable isotope measurements of the A. mertensii leaves, the leaf litter inside of the tank and the root-embedded carton nest, we discuss the potential sources of available nitrogen for the plant based on the ant partner. We demonstrate the existence of a complex ant-plant interaction that subsequently affects the biodiversity of a broader range of organisms that are themselves likely to influence nutrient assimilation by the A. mertensii leaves in a kind of plant-invertebrate-plant feedback loop. |
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Potential sources of nitrogen in an ant-garden tank-bromeliad |
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EcoFoG @ eric.marcon @ 12 |
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186 |
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Author |
Gonzalez, M.A.; Baraloto, C.; Engel, J.; Mori, S.A.; Petronelli, P.; Riera, B.; Roger, A.; Thebaud, C.; Chave, J. |
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Title |
Identification of Amazonian Trees with DNA Barcodes |
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Journal Article |
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Year |
2009 |
Publication |
PLoS One |
Abbreviated Journal |
PLoS One |
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Volume |
4 |
Issue |
10 |
Pages |
e7483 |
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Background: Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests. Methodology/Principal Findings: Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS), matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone) to 96% (morphology and molecular) of the individuals assigned to a known tree taxon. Conclusion/Significance: We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs. |
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PUBLIC LIBRARY SCIENCE |
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1932-6203 |
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ISI:000270880700009 |
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EcoFoG @ eric.marcon @ |
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189 |
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Author |
Coste, S.; Roggy, J.C.; Imbert, P.; Born, C.; Bonal, D.; Dreyer, E. |
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Title |
Leaf photosynthetic traits of 14 tropical rain forest species in relation to leaf nitrogen concentration and shade tolerance |
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Journal Article |
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Year |
2005 |
Publication |
Tree Physiology |
Abbreviated Journal |
Tree Physiol. |
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Volume |
25 |
Issue |
9 |
Pages |
1127-1137 |
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functional diversity; leaf carbon; leaf nitrogen; nitrogen-use efficiency; photosynthetic capacity; tropical rain forest |
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Abstract |
Variability of leaf traits related to photosynthesis was assessed in seedlings from 14 tree species growing in the tropical rain forest of French Guiana. Leaf photosynthetic capacity (maximum rate of carboxylation and maximum rate of electron transport) was estimated by fitting a biochemical model of photosynthesis to response curves of net CO2 assimilation rate versus intercellular CO2 mole fraction. Leaf morphology described by leaf mass per unit leaf area (LMA), density and thickness, as well as area- and mass-based nitrogen (N) and carbon (C) concentrations, were recorded on the same leaves. Large interspecific variability was detected in photosynthetic capacity as well as in leaf structure and leaf N and C concentrations. No correlation was found between leaf thickness and density. The correlations between area- and mass-based leaf N concentration and photosynthetic capacity were poor. Conversely, the species differed greatly in relative N allocation to carboxylation and bioenergetics. Principal component analysis (PCA) revealed that, of the recorded traits, only the computed fraction of total leaf N invested in photosynthesis was tightly correlated to photosynthetic capacity. We also used PCA to test to what extent species with similar shade tolerances displayed converging leaf traits related to photosynthesis. No clear-cut ranking could be detected among the shade-tolerant groups, as confirmed by a one-way ANOVA. We conclude that the large interspecific diversity in photosynthetic capacity was mostly explained by differences in the relative allocation of N to photosynthesis and not by leaf N concentration, and that leaf traits related to photosynthetic capacity did not discriminate shade-tolerance ranking of these tropical tree species. |
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Address |
CNRS Ecol Forets Guyane, INRA, ENGREF,CIRAD, Unite Mixte Rech, Kourou 97387, French Guiana, Email: roggy.j@cirad.fr |
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Publisher |
HERON PUBLISHING |
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0829-318X |
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ISI:000231555200005 |
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EcoFoG @ eric.marcon @ |
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230 |
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Author |
Foucaud, J.; Orivel, J.; Fournier, D.; Delabie, J.H.C.; Loiseau, A.; Le Breton, J.; Cerdan, P.; Estoup, A. |
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Title |
Reproductive system, social organization, human disturbance and ecological dominance in native populations of the little fire ant, Wasmannia auropunctata |
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Journal Article |
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Year |
2009 |
Publication |
Molecular Ecology |
Abbreviated Journal |
Mol. Ecol. |
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Volume |
18 |
Issue |
24 |
Pages |
5059-5073 |
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Keywords |
biological invasion; clonality; human disturbance; parthenogenesis; social organization; Wasmannia auropunctata |
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Abstract |
The invasive ant species Wasmannia auropunctata displays both ecologically dominant and non-dominant populations within its native range. Three factors could theoretically explain the ecological dominance of some native populations of W. auropunctata: (i) its clonal reproductive system, through demographic and/or adaptive advantages; (ii) its unicolonial social organization, through lower intraspecific and efficient interspecific competition; (iii) the human disturbance of its native range, through the modification of biotic and abiotic environmental conditions. We used microsatellite markers and behavioural tests to uncover the reproductive modes and social organization of dominant and non-dominant native populations in natural and human-modified habitats. Microsatellite and mtDNA data indicated that dominant and non-dominant native populations (supercolonies as determined by aggression tests) of W. auropunctata did not belong to different evolutionary units. We found that the reproductive system and the social organization are neither necessary nor sufficient to explain W. auropunctata ecological dominance. Dominance rather seems to be set off by unknown ecological factors altered by human activities, as all dominant populations were recorded in human-modified habitats. The clonal reproductive system found in some populations of W. auropunctata may however indirectly contribute to its ecological dominance by allowing the species to expand its environmental niche, through the fixation over time of specific combinations of divergent male and female genotypes. Unicoloniality may rather promote the range expansion of already dominant populations than actually trigger ecological dominance. The W. auropunctata model illustrates the strong impact of human disturbance on species' ecological features and the adaptive potential of clonal reproductive systems. |
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Address |
[Foucaud, Julien; Fournier, Denis; Loiseau, Anne; Estoup, Arnaud] Montpellier SupAgro, Cirad, IRD, INRA,UMR CBGP, F-34988 Montferrier Sur Lez, France, Email: julien.foucaud@legs.cnrs-gif.fr |
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WILEY-BLACKWELL PUBLISHING, INC |
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0962-1083 |
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ISI:000272452700009 |
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EcoFoG @ eric.marcon @ |
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191 |
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