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Mirabel, A.; Hérault, B.; Marcon, E. |
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Title |
Diverging taxonomic and functional trajectories following disturbance in a Neotropical forest |
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Journal Article |
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Year |
2020 |
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Science of The Total Environment |
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720 |
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137397 |
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Community ecology; Disturbance trajectories; Intermediate disturbance hypothesis; Mid-term resilience; Neotropical forests; Taxonomic and functional biodiversity |
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In the current global change context, it is urgent to anticipate the fate of tropical forests. This means understanding tree community response to disturbance and the underlying processes. In that respect, we aim here to clarify taxonomic and functional post-disturbance trajectories, and determine the scope of the Intermediate Disturbance Hypothesis (IDH) that remains debated in tropical forests. We analyzed community trajectories following a disturbance gradient from 10 to 60% of above-ground biomass loss in a Neotropical forest over 30 years. We considered trajectories along time of community taxonomic and functional trajectories in terms of richness, evenness, composition, and redundancy. We based on the annual botanical inventories of 75 ha of a Neotropical forest and on large trait datasets comprising seven leaf, stem, and life-history traits. We identified a decoupling between taxonomic composition, differing among communities, and functional composition, similar among communities and convergent in the functional space. The taxonomic diversity followed humped-shaped trajectories along time after disturbance depending on the initial disturbance intensity, which validated the IDH (Intermediate Disturbance Hypothesis). The functional diversity trajectories, however, were homogeneous among plots and dismissed the IDH. We explained this decoupling by the variations in community functional redundancy that mitigated the functional impact of disturbance. Although consistent, the recovery of community composition, diversity, and redundancy remained divergent from the initial state after 30 years. These results acknowledged the need of decades-long cycles without disturbance to ensure community complete recovery. |
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0048-9697 |
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EcoFoG @ webmaster @ |
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920 |
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Sommeria-Klein, G.; Zinger, L.; Coissac, E.; Iribar, A.; Schimann, H.; Taberlet, P.; Chave, J. |
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Title |
Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest |
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Journal Article |
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Year |
2020 |
Publication |
Molecular Ecology Resources |
Abbreviated Journal |
Mol. Ecol. Resour. |
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20 |
Issue |
2 |
Pages |
371-386 |
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community ecology; environmental DNA; metabarcoding; OTU presence–absence; soil microbiome; topic modelling; bacterium; biodiversity; biology; classification; eukaryote; fungus; genetics; high throughput sequencing; isolation and purification; microbiology; parasitology; procedures; soil; Bacteria; Biodiversity; Computational Biology; Eukaryota; Fungi; High-Throughput Nucleotide Sequencing; Soil; Soil Microbiology |
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High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity. © 2019 John Wiley & Sons Ltd |
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Laboratoire d’Ecologie des Forêts de Guyane (EcoFoG, UMR 745), INRA, AgroParisTech, CIRAD, CNRS, University of the French West Indies, University of French Guiana, Kourou, France |
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Blackwell Publishing Ltd |
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1755098x (Issn) |
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EcoFoG @ webmaster @ |
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981 |
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Siefert, A.; Violle, C.; Chalmandrier, L.; Albert, C.H.; Taudiere, A.; Fajardo, A.; Aarssen, L.W.; Baraloto, C.; Carlucci, M.B.; Cianciaruso, M.V.; de L. Dantas, V.; de Bello, F.; Duarte, L.D.S.; Fonseca, C.R.; Freschet, G.T.; Gaucherand, S.; Gross, N.; Hikosaka, K.; Jackson, B.; Jung, V.; Kamiyama, C.; Katabuchi, M.; Kembel, S.W.; Kichenin, E.; Kraft, N.J.B.; Lagerström, A.; Bagousse-Pinguet, Y.L.; Li, Y.; Mason, N.; Messier, J.; Nakashizuka, T.; Overton, J.M.; Peltzer, D.A.; Pérez-Ramos, I.M.; Pillar, V.D.; Prentice, H.C.; Richardson, S.; Sasaki, T.; Schamp, B.S.; Schöb, C.; Shipley, B.; Sundqvist, M.; Sykes, M.T.; Vandewalle, M.; Wardle, D.A. |
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Title |
A global meta-analysis of the relative extent of intraspecific trait variation in plant communities |
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Journal Article |
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Year |
2015 |
Publication |
Ecology Letters |
Abbreviated Journal |
Ecology Letters |
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18 |
Issue |
12 |
Pages |
1406-1419 |
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Community ecology; Functional diversity; Interspecific variation; Intraspecific variability; Leaf trait; Plant functional trait; Trait-based ecology |
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Recent studies have shown that accounting for intraspecific trait variation (ITV) may better address major questions in community ecology. However, a general picture of the relative extent of ITV compared to interspecific trait variation in plant communities is still missing. Here, we conducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits. Overall, ITV accounted for 25% of the total trait variation within communities and 32% of the total trait variation among communities on average. The relative extent of ITV tended to be greater for whole-plant (e.g. plant height) vs. organ-level traits and for leaf chemical (e.g. leaf N and P concentration) vs. leaf morphological (e.g. leaf area and thickness) traits. The relative amount of ITV decreased with increasing species richness and spatial extent, but did not vary with plant growth form or climate. These results highlight global patterns in the relative importance of ITV in plant communities, providing practical guidelines for when researchers should include ITV in trait-based community and ecosystem studies. © 2015 John Wiley & Sons Ltd/CNRS. |
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Department of Physical Geography and Ecosystem Science, Lund University, Sölvegatan 12, Lund, Sweden |
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Export Date: 16 November 2015 |
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EcoFoG @ webmaster @ |
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637 |
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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 |
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365-374 |
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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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Baraloto, C.; Hardy, O.J.; Paine, C.E.T.; Dexter, K.G.; Cruaud, C.; Dunning, L.T.; Gonzalez, M.-A.; Molino, J.-F.; Sabatier, D.; Savolainen, V.; Chave, J. |
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Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities |
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Journal Article |
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Year |
2012 |
Publication |
Journal of Ecology |
Abbreviated Journal |
J. Ecol. |
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100 |
Issue |
3 |
Pages |
690-701 |
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Competition; Determinants of plant community diversity and structure; Environmental filtering; French Guiana; Functional traits; Limiting similarity; Niche; Phylogenetic signal; Tropical forests |
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Niche theory proposes that species differences underlie both coexistence within communities and the differentiation in species composition among communities via limiting similarity and environmental filtering. However, it has been difficult to extend niche theory to species-rich communities because of the empirical challenge of quantifying niches for many species. This has motivated the development of functional and phylogeny-based approaches in community ecology, which represent two different means of approximating niche attributes. Here, we assess the utility of plant functional traits and phylogenetic relationships in predicting community assembly processes using the largest trait and phylogenetic data base to date for any set of species-rich communities. We measured 17 functional traits for all 4672 individuals of 668 tree species co-occurring in nine tropical rain forest plots in French Guiana. Trait variation was summarized into two ordination axes that reflect species niche overlap. We also generated a dated molecular phylogenetic tree based on DNA sequencing of two plastid loci (rbcL and matK) comprising 97% of the individuals and 91% of the species in the plots. We found that, on average, co-occurring species had greater functional and, to a lesser extent, phylogenetic similarity than expected by chance. We also found that functional traits and their ordination loadings showed significant, albeit weak, phylogenetic signal, suggesting that phylogenetic distance provides pertinent information on niche overlap in tropical tree communities. Synthesis. We provide the most comprehensive examination to date of the relative importance of environmental filtering and limiting similarity in structuring tropical tree communities. Our results confirm that environmental filtering is the overriding influence on community assembly in these species-rich systems. © 2012 The Authors. Journal of Ecology © 2012 British Ecological Society. |
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Royal Botanic Gardens, Kew, Richmond TW9 3DS, United Kingdom |
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00220477 (Issn) |
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Export Date: 24 April 2012; Source: Scopus; Coden: Jecoa; doi: 10.1111/j.1365-2745.2012.01966.x; Language of Original Document: English; Correspondence Address: Chave, J.; Université Paul Sabatier, CNRS, UMR 5174 Laboratoire Evolution et Diversité Biologique, 31062 Toulouse, France; email: chave@cict.fr |
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EcoFoG @ webmaster @ |
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393 |
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Vincent, G.; Caron, F.; Sabatier, D.; Blanc, L. |
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LiDAR shows that higher forests have more slender trees |
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Journal Article |
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2012 |
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Bois et Forets des Tropiques |
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Bois Forets Tropiques |
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66 |
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314 |
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51-56 |
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Competition; Fertility; French Guiana; LiDAR; Tree allometry |
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High-density Airborne Laser Scanning was used to derive the Canopy Height Model (CHM) of an experimental forest site in the neotropics (Paracou, French Guiana). Individual tree heights were computed by manually segmenting tree crowns on the CHM and then extracting the local maximum canopy height. Three hundred and ninety-six (396) height estimates were matched from dominant or emergent trees with the corresponding ground records of stem diameters sampled in two plots with different mean canopy heights (28.1 m vs. 31.3 m). Tree slenderness was found to be positively and very significantly correlated with mean canopy height at the plot level. The same correlation was observed at the species population level for the three species adequately sampled. It can therefore be concluded that stratification by canopy height is to be recommended when deriving allometric relationships in order to avoid bias in Above Ground Biomass estimations. |
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CIRAD, UMR Ecofog, 97300 Kourou, France |
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0006579x (Issn) |
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Export Date: 5 June 2013; Source: Scopus; Language of Original Document: English; Correspondence Address: IRD, UMR AMAP, 34000 Montpellier, France |
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EcoFoG @ webmaster @ |
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490 |
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Baraloto, C.; Marcon, E.; Morneau, F.; Pavoine, S.; Roggy, J.C. |
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Integrating functional diversity into tropical forest plantation designs to study ecosystem processes |
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Journal Article |
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2010 |
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Annals of Forest Science |
Abbreviated Journal |
Ann. For. Sci. |
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67 |
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3 |
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303 |
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complementarity; ecosystem function; functional groups; leaf economics spectrum; nitrogen fixation; quadratic entropy |
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The elucidation of relationships between biodiversity and ecosystem processes has been limited by the definition of metrics of biodiversity and their integration into experimental design. Functional trait screening can strengthen the performance of these designs. We suggest the use of Rao's quadratic entropy to measure both functional diversity and phylogenetic diversity of species mixtures proposed for an experimental design, and demonstrate how they can provide complementary information. We also present an index assessing the statistical performance of these independent variables in different experimental designs. Measurement of independent variables as continuous vs. discrete variables reduces statistical performance, but improves the model by quantifying species differences masked by group assignments. To illustrate these advances, we present an example from a tropical forest tree community in which we screened 38 species for nine functional traits. The proposed TropiDEP design is based on the relative orthogonality of two multivariate trait axes defined using principal component analysis. We propose that independent variables describing functional diversity might be grouped to calculate independent variables describing suites of different traits with potentially different effects on particular ecosystem processes. In other systems these axes may differ from those reported here, yet the methods of analysis integrating functional and phylogenetic diversity into experimental design could be universal. |
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[Baraloto, Christopher; Roggy, Jean-Christophe] INRA, UMR Ecol Forets Guyane, Kourou, French Guiana, Email: chris.baraloto@ecofog.gf |
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EDP SCIENCES S A |
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1286-4560 |
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ISI:000276507800004 |
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EcoFoG @ eric.marcon @ |
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62 |
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Brémaud, I.; Ruelle, J.; Thibaut, A.; Thibaut, B. |
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Changes in viscoelastic vibrational properties between compression and normal wood: Roles of microfibril angle and of lignin |
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2013 |
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Holzforschung |
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67 |
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1 |
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75-85 |
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Compression wood (CW); Damping coefficient; Ft-Ir; Internal friction; Lignin; Microfibril angle (MFA); Picea abies; Pinus pinaster; Pinus sylvestris; Specific dynamic modulus of elasticity; Viscoelastic vibrational properties |
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This study aims at better understanding the respective influences of specific gravity (γ ), microfibril angle (MFA), and cell wall matrix polymers on viscoelastic vibrational properties of wood in the axial direction. The wide variations of properties between normal wood (NW) and compression wood (CW) are in focus. Three young bent trees (Picea abies, Pinus sylvestris and Pinus pinaster ), which recovered verticality, were sampled. Several observed differences between NW and CW were highly significant in terms of anatomical, physical (γ, shrinkage, CIE Lab colorimetry), mechanical (compressive strength), and vibrational properties. The specific dynamic modulus of elasticity (E′/γ) decreases with increasing MFA, and Young's modulus (E′) can be satisfactorily explained by γ and MFA. Apparently, the type of the cell wall polymer matrix is not influential in this regard. The damping coefficient (tan δ) does not depend solely on the MFA of NW and CW. The tanδ-E′/γ relationship evidences that, at equivalent E′/γ, the tan δ of CW is approximately 34% lower than that of NW. This observation is ascribed to the more condensed nature of CW lignins, and this is discussed in the context of previous findings in other hygrothermal and time/frequency domains. It is proposed that the lignin structure and the amount and type of extractives, which are both different in various species, are partly responsible for taxonomy-related damping characteristics. Copyright © by Walter de Gruyter • Berlin • Boston. |
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Wood Laboratory, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland |
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Export Date: 25 February 2013; Source: Scopus |
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EcoFoG @ webmaster @ |
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471 |
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Christensen-Dalsgaard, K.K.; Ennos, A.R.; Fournier, M. |
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Interrelations between hydraulic and mechanical stress adaptations in woody plants |
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Journal Article |
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2008 |
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Plant Signaling and Behavior |
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Plant. Signal. Behav. |
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3 |
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7 |
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463-465 |
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Conductivity; Modulus of elasticity; Strain; Tree ecophysiology; Tropical trees; Wood anatomy; Yield stress |
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The fields of plant water relations and plant biomechanics have traditionally been studied separately even though often the same tissues are responsible for water transport and mechanical support. There is now increasing evidence that hydraulic and mechanical adaptations may influence one another. We studied the changes in the hydraulic and mechanical properties of the wood along lateral roots of two species of buttressed trees. In these roots, the mechanical contstraints quantified by strain measurements are known to decrease distally. Further, we investigated the effect of mechanical loading on the vessel anatomy in these and four other species of tropical trees. We found that as the strain decreased, the wood became progressively less stiff and strong but the conductivity increased exponentially. This was reflected in that adaptations towards re-enforcing mechanically loaded areas resulted in xylem with fewer and smaller vessels. In addition a controlled growth experiment on three tree species showed that drought adaptation may results in plants with stronger and stiffer tissue. Our results indicate that hydraulic and mechanical stress adaptations may be interrelated, and so support recent studied suggesting that physiological responses are complex balances rather than pure optimisations. ©2008 Landes Bioscience. |
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University of Alberta, Department of Renewable Resources, 4-44 Earth Science Bldg., Edmonton, AB T6G 2E3, Canada |
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15592316 (Issn) |
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Export Date: 25 January 2012; Source: Scopus; Language of Original Document: English; Correspondence Address: Christensen-Dalsgaard, K. K.; University of Alberta, Department of Renewable Resources, 4-44 Earth Science Bldg., Edmonton, AB T6G 2E3, Canada; email: kkchrist@ualberta.ca |
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EcoFoG @ webmaster @ |
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380 |
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Scotti, I.; Paglia, G.; Magni, F.; Morgante, M. |
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Population genetics of Norway spruce (Picea abies Karst.) at regional scale: sensitivity of different microsatellite motif classes in detecting differentiation |
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Journal Article |
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2006 |
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Annals of Forest Science |
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Ann. For. Sci. |
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63 |
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5 |
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485-491 |
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conifers; SSR; divergence; statistical testing; genetic distance |
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Abstract |
Four populations of Norway spruce (Picea abies Karst.) were screened using nine nuclear microsatellite markers (three trinucleotides and six dinucleotides) and four chloroplast markers (all mononucleotides). Marker classes were compared for their variability, mutation rate and ability to detect differentiation between stands. Dinucleotide markers proved to be the most variable group and chloroplast stretches the least variable, with differences in mutation rate between the former and the latter spanning over two orders of magnitude. Variability correlated to the number of repeats but not to the absolute length of the microsatellite region. The different marker classes were combined with two different measures of genetic distance in order to investigate the performance of markers and evolutionary models for the study of genetic variation in natural populations of Norway spruce. Weir and Cockeram's F-ST generally performed better in this clear-cut, four-population model study. Chloroplast haplotypes turned out to be the most sensitive marker system, being able to differentiate populations and to detect differences in genetic variability between sub-regions. |
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INRA, UMR ECOFOG, Kourou 97387, French Guiana, Email: ivan.scotti@kourou.cirad.fr |
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EDP SCIENCES S A |
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1286-4560 |
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ISI:000240514800005 |
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EcoFoG @ eric.marcon @ |
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177 |
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