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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 |
Campillo, F.; Rossi, V. |
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Title |
Convolution Particle Filter for Parameter Estimation in General State-Space Models |
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Journal Article |
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Year |
2009 |
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IEEE Transactions on Aerospace and Electronic Systems |
Abbreviated Journal |
IEEE Trans. Aerosp. Electron. Syst. |
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45 |
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3 |
Pages |
1063-1072 |
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The state-space modeling of partially observed dynamical systems generally requires estimates of unknown parameters. The dynamic state vector together with the static parameter vector can be considered as an augmented state vector. Classical filtering methods, such as the extended Kalman filter (EKF) and the bootstrap particle filter (PF), fail to estimate the augmented state vector. For these classical filters to handle the augmented state vector, a dynamic noise term should be artificially added to the parameter components or to the deterministic component of the dynamical system. However, this approach degrades the estimation performance of the filters. We propose a variant of the PF based on convolution kernel approximation techniques. This approach is tested on a simulated case study. |
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IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC |
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0018-9251 |
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ISI:000270225500017 |
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EcoFoG @ eric.marcon @ |
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194 |
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Vedel, V.; Brena, C.; Arthur, W. |
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Title |
Demonstration of a heritable component of the variation in segment number in the centipede Strigamia maritima |
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Journal Article |
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2009 |
Publication |
Evolution & Development |
Abbreviated Journal |
Evol. Dev. |
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11 |
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4 |
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434-440 |
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Here we address the question of how arthropod segment number may evolve by reporting the results of further work on the model system Strigamia maritima. Recently, we showed that there was a plastic component of the variation in segment number within this species; now we demonstrate that there is also a heritable component. This is important because it enables a connection to be made between the known latitudinal trend among species of geophilomorph centipedes ( more segments at lower latitudes) and the parallel trend within them. This latter trend is best documented in S. maritima but is also known in several other species. However, while a general connection between the inter- and intraspecific trends can now be made, deciding upon a specific hypothesis of the nature of the selection involved is still problematic. We provide two alternative hypotheses, one based on the temperature-related plasticity in segment number being adaptive, the other based on it being nonadaptive. |
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[Vedel, Vincent; Arthur, Wallace] Natl Univ Ireland, Dept Zool, Sch Nat Sci, Galway, Ireland, Email: wallace.arthur@nuigalway.ie |
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WILEY-BLACKWELL PUBLISHING, INC |
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1520-541X |
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ISI:000267659600011 |
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EcoFoG @ eric.marcon @ |
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200 |
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Baraloto, C.; Ferreira, E.; Rockwell, C.; Walthier, F. |
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Title |
Limitations and Applications of Parataxonomy for Community Forest Management in Southwestern Amazonia |
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Journal Article |
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Year |
2007 |
Publication |
Ethnobotany Research & Applications |
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5 |
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77-84 |
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We examined the limitations of parataxonomic inventories for developing management plans for woody plant resources in tropical rain forests of southwestern Amazonia. Using compilations of herbarium labels, forest personnel interviews and published species descriptions, we assessed the accuracy of common names as parataxonomic units (PUs). We identified 384 common names for 310 harvested woody plant species in the Brazilian state of Acre, of which only 50% were unique to a single taxonomic species. About 10% of common names referred to more than one species, more than half of which included multiple genera. For the 106 species from the Acre sample common to the MAP region including Madre de Dios, Peru and Pando, Bolivia, we identified 198 common names. Splitting was much more frequent in this sample, with more than 80% of species having more than one common name. When the Acre sample was expanded to 131 species from the Brazilian Amazon region, including the states of Amazonas and Para, we identified 740 common names, with nearly 90% of species being represented by more than one common name. Errors and inaccuracy of parataxonomy may contribute to market instability if product orders can not be homogenized within regional markets, and to unsustainable harvests if species are mistakenly lumped into single parataxonomic units. We discuss several programs currently being implemented by our collaborative team in the region to address this issue, including field guides based on digital photography, field courses, and workshops featuring discussions between regional inventory personnel and botanists. |
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2008; Limitations and Applications of Parataxonomy for Community Forest Management in Southwestern Amazonia |
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EcoFoG @ eric.marcon @ 14 |
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214 |
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Author |
Clair, B.; Almeras, T.; Yamamoto, H.; Okuyama, T.; Sugiyama, J. |
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Title |
Mechanical behavior of cellulose microfibrils in tension wood, in relation with maturation stress generation |
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Journal Article |
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Year |
2006 |
Publication |
Biophysical Journal |
Abbreviated Journal |
Biophys. J. |
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Volume |
91 |
Issue |
3 |
Pages |
1128-1135 |
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Abstract |
A change in cellulose lattice spacing can be detected during the release of wood maturation stress by synchrotron x-ray diffraction experiment. The lattice strain was found to be the same order of magnitude as the macroscopic strain. The fiber repeat distance, 1.033 nm evaluated for tension wood after the release of maturation stress was equal to the conventional wood values, whereas the value before stress release was larger, corresponding to a fiber repeat of 1.035 nm, nearly equal to that of cotton and ramie. Interestingly, the fiber repeat varied from 1.033 nm for wood to 1.040 nm for algal cellulose, with an increasing order of lateral size of cellulose microfibrils so far reported. These lines of experiments demonstrate that, before the stress release, the cellulose was in a state of tension, which is, to our knowledge, the first experimental evidence supporting the assumption that tension is induced in cellulose microfibrils. |
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Kyoto Univ, Res Inst Sustainable Humanosphere, Uji, Kyoto, Japan, Email: sugiyama@rish.kyoto-u.ac.jp |
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BIOPHYSICAL SOCIETY |
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0006-3495 |
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ISI:000239086800039 |
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no |
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EcoFoG @ eric.marcon @ |
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224 |
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Delaval, M.; Henry, M.; Charles-Dominique, P. |
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Title |
Interspecific competition and niche partitioning: Example of a neotropical rainforest bat community |
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Journal Article |
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Year |
2005 |
Publication |
Revue d'Ecologie (La Terre et la Vie) |
Abbreviated Journal |
Rev. Ecol.-Terre Vie |
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60 |
Issue |
2 |
Pages |
149-165 |
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To understand the organization of a bat community and the coexistence of sympatric species, it is essential to understand how species use and share common resources. First, we describe a bat community in a primary rainforest of French Guiana. The presence of particular roosting sites, such as caves, and the absence of disturbances are important local factors in structuring communities. In the course of this study, we focused on the three most common species of three vegetarian bat guilds (understorey frugivores, canopy frugivores and nectarivores). The local coexistence of these species is possible thanks to space, food and/or time partitioning. Space partitioning is consistent with the hypothesis that smaller bats with a more manoeuvrable flight tend to occupy more cluttered space less attractive to their competitors and have smaller home range. We observed a time partitioning that is likely to reduce competition among some frugivorous bat species by reducing direct interference during foraging. Besides an interest for the field community ecology, this study of a community living in a primary forest can be used as a reference for non disturbed habitat for conservation purposes. |
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Dept Ecol & Gestion Biodivers, UMR 5176, F-91800 Brunoy, France, Email: marguerite.delaval@wanadoo.fr |
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SOC NATL PROTECTION NATURE ACCLIMATATION FRANCE |
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0249-7395 |
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ISI:000230973300005 |
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no |
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EcoFoG @ eric.marcon @ |
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231 |
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Author |
Scotti-Saintagne, C.; Mariette, S.; Porth, I.; Goicoechea, P.G.; Barreneche, T.; Bodenes, K.; Burg, K.; Kremer, A. |
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Title |
Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q petraea (Matt.) Liebl.] |
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Journal Article |
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Year |
2004 |
Publication |
Genetics |
Abbreviated Journal |
Genetics |
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168 |
Issue |
3 |
Pages |
1615-1626 |
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Interspecific differentiation values (G(ST)) between two closely related oak species (Quercus petraea and Q. robur) were compiled across different studies with the aim to explore the distribution of differentiation at the genome level. The study was based on a total set of 389 markers (isozymes, AFLPs, SCARs, microsatellites, and SNPs) for which allelic frequencies were estimated in pairs of populations sampled throughout the sympatric distribution of the two species. The overall distribution of GST values followed an L-shaped curve with most markers exhibiting low species differentiation (G(ST) < 0.01) and only a few loci reaching >10% levels. Twelve percent of the loci exhibited significant G(ST) deviations to neutral expectations, suggesting that selection contributed to species divergence. Coding regions expressed higher differentiation than noncoding regions. Among the 389 markers, 158 could be mapped on the 12 linkage groups of the existing Q. robur genetic map. Outlier loci with large G, values were distributed over 9 linkage groups. One cluster of three outlier loci was found within 0.51 cM; but significant autocorrelation of GST was observed at distances <2 cM. The size and distribution of genomic regions involved in species divergence are discussed in reference to hitchhiking effects and disruptive selection. |
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INRA, UMR Biodivers Genes & Ecosyst, F-33612 Cestas, France, Email: kremer@pierronton.inra.fr |
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GENETICS |
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0016-6731 |
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ISI:000225767400041 |
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no |
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EcoFoG @ eric.marcon @ |
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258 |
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Scotti-Saintagne, C.; Bodenes, C.; Barreneche, T.; Bertocchi, E.; Plomion, C.; Kremer, A. |
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Title |
Detection of quantitative trait loci controlling bud burst and height growth in Quercus robur L |
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Journal Article |
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Year |
2004 |
Publication |
Theoretical and Applied Genetics |
Abbreviated Journal |
Theor. Appl. Genet. |
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Volume |
109 |
Issue |
8 |
Pages |
1648-1659 |
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Abstract |
Genetic variation of bud burst and early growth components was estimated in a full-sib family of Quercus robur L. comprising 278 offspring. The full sibs were vegetatively propagated, and phenotypic assessments were made in three field tests. This two-generation pedigree was also used to construct a genetic linkage map (12 linkage groups, 128 markers) and locate quantitative trait loci (QTLs) controlling bud burst and growth components. In each field test, the date of bud burst extended over a period of 20 days from the earliest to the latest clone. Bud burst exhibited higher heritability (0.15-0.51) than growth components (0.04-0.23) and also higher correlations across field tests. Over the three tests there were 32 independent detected QTLs (Pless than or equal to5% at the chromosome level) controlling bud burst, which likely represent at least 12 unique genes or chromosomal regions controlling this trait. QTLs explained from 3% to 11% of the variance of the clonal means. The number of QTLs controlling height growth components was lower and varied between two and four. However the contribution of each QTL to the variance of the clonal mean was higher (from 4% to 19%). These results indicate that the genetic architecture of two important fitness-related traits are quite different. On the one hand, bud burst is controlled by several QTLs with rather low to moderate effects, but contributing to a high genetic (additive) variance. On the other hand, height growth depends on fewer QTLs with moderate to strong effects, resulting in lower heritabilities of the trait. |
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INRA, UMR Biodivers Genes & Ecosyst, F-33612 Cestas, France, Email: antoine.kremer@pierroton.inra.fr |
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SPRINGER |
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0040-5752 |
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ISI:000225054800012 |
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EcoFoG @ eric.marcon @ |
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260 |
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Author |
Rahali, H.; Ghanem, N.; Griffe, L.; Rahali, R.; Stien, D. |
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Title |
A general approach to the quantification of resin-bound functional groups by NMR |
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Journal Article |
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Year |
2004 |
Publication |
New Journal of Chemistry |
Abbreviated Journal |
New J. Chem. |
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28 |
Issue |
11 |
Pages |
1344-1346 |
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There has been a continuing need for sensitive, accurate and rapid methods to monitor functional loading of insoluble supports for solid phase synthesis. The present articles reports our findings regarding functional group loading quantification using H-1 NMR. Results obtained for supported amino, hydroxyl and NH-Fmoc groups are in agreement with those calculated using well-established methods and demonstrate that the strategy of looking, either at the excess reagent left in solution (NH2 and OH), or at the protecting group derivatives released from the polymer (Fmoc), is a viable approach to resin loading quanti. cation. |
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Univ Montpellier 2, CNRS, UMR 5810, Lab Aminoacides Peptides & Prot, F-34095 Montpellier 05, France, Email: didier.stien@guyane.cnrs.fr |
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ROYAL SOC CHEMISTRY |
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1144-0546 |
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ISI:000224894700013 |
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EcoFoG @ eric.marcon @ |
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261 |
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Stien, D.; Gastaldi, S. |
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Design of polyaromatic hydrocarbon-supported tin reagents: A new family of tin reagents easily removable from reaction mixtures |
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Journal Article |
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Year |
2004 |
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Journal of Organic Chemistry |
Abbreviated Journal |
J. Org. Chem. |
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69 |
Issue |
13 |
Pages |
4464-4470 |
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We report in this paper the preparation and use of stannanes 11, 12a, and 12b, compounds whose 3-pyrenylpropyl side chain affinity for activated carbon simplifies tin removal and product isolation. Our pyrene-supported reagents can be used for radical reductions and cyclizations (11), radical and cationic allylations (12a), and Stille couplings (12b) in much the same way as tributyltin derivatives. |
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CNRS UPS 2561, Cayenne 97300, French Guiana, Email: didier.stien@guyane.cnrs.fr |
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AMER CHEMICAL SOC |
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0022-3263 |
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ISI:000222187200022 |
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EcoFoG @ eric.marcon @ |
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263 |
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