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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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Abstract |
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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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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Keywords |
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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CNRS Ecol Forets Guyane, INRA, ENGREF,CIRAD, Unite Mixte Rech, Kourou 97387, French Guiana, Email: roggy.j@cirad.fr |
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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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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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[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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Author |
Szilagyi, A.; Scheuring, I.; Edwards, D.P.; Orivel, J.; Yu, D.W. |
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Title |
The evolution of intermediate castration virulence and ant coexistence in a spatially structured environment |
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Journal Article |
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Year |
2009 |
Publication |
Ecology Letters |
Abbreviated Journal |
Ecol. Lett. |
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Volume |
12 |
Issue |
12 |
Pages |
1306-1316 |
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Keywords |
Cooperation; evolution of virulence; host-pathogen; mutualism; myrmecophyte; parasite; rock-paper-scissors; spatial games; tolerance; trade-off |
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Abstract |
Theory suggests that spatial structuring should select for intermediate levels of virulence in parasites, but empirical tests are rare and have never been conducted with castration (sterilizing) parasites. To test this theory in a natural landscape, we construct a spatially explicit model of the symbiosis between the ant-plant Cordia nodosa and its two, protecting ant symbionts, Allomerus and Azteca. Allomerus is also a castration parasite, preventing fruiting to increase colony fecundity. Limiting the dispersal of Allomerus and host plant selects for intermediate castration virulence. Increasing the frequency of the mutualist, Azteca, selects for higher castration virulence in Allomerus, because seeds from Azteca-inhabited plants are a public good that Allomerus exploits. These results are consistent with field observations and, to our knowledge, provide the first empirical evidence supporting the hypothesis that spatial structure can reduce castration virulence and the first such evidence in a natural landscape for either mortality or castration virulence. |
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[Edwards, David P.; Yu, Douglas W.] Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England, Email: dougwyu@gmail.com |
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WILEY-BLACKWELL PUBLISHING, INC |
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1461-023X |
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ISI:000271631500006 |
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EcoFoG @ eric.marcon @ |
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192 |
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Author |
Cohen, M.C.L.; Behling, H.; Lara, R.J.; Smith, C.B.; Matos, H.R.S.; Vedel, V. |
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Title |
Impact of sea-level and climatic changes on the Amazon coastal wetlands during the late Holocene |
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Journal Article |
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Year |
2009 |
Publication |
Vegetation History and Archaeobotany |
Abbreviated Journal |
Veg. Hist. Archaeobot. |
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Volume |
18 |
Issue |
6 |
Pages |
425-439 |
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Mangrove; Marajo Island; Pollen analysis; Sea-level |
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Abstract |
Wetland dynamics in northern Brazil during the Holocene were studied by pollen analysis and AMS radiocarbon dating of three cores. Near the Amazon mouth region, covered mainly by primary Amazon coastal forest and herbaceous vegetation, the pollen record indicates the dominance of mangroves between 4800 and 1100 cal yr B.P. A contraction of the mangrove area and an expansion of herbaceous and fern vegetation occurred between 1100 and 750 cal yr B.P. The period between 750 and 200 cal yr B.P. is characterized by an expansion of mangrove and a decrease in herbaceous and fern vegetation. This trend continued until the present. On Atalaia Island, the sediment core indicates a period with poor pollen preservation between 830 and 630 cal yr B.P. Between 630 and 330 cal yr B.P., mangroves expanded. Later, up to 45 cal yr B.P., the mangrove area decreased and the herbaceous vegetation expanded. During the last hundred years, the relative sea-level rise most probably favored the mangrove expansion as far as the topographically highest sector on this island, while the herbaceous vegetation decreased. The pollen data from Agua Preta Lake indicate dry conditions, as reflected by the poor pollen preservation between 390 and 240 cal yr B.P. Between 240 and 60 cal yr B.P., restinga and Amazon coastal forest with palms dominated this region. For the last 120 years, the record indicates an expansion of the mangrove area. However, recent confinement of mangrove development to the topographically highest area, and the loss of mangrove areas on the lowest surfaces have led to a net loss of mangrove coverage during the last decades. |
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[Lisboa Cohen, Marcelo Cancela; Smith, Clarisse Beltrao; Soares Matos, Hellen Rosy] Fed Univ Para, Postgrad Program Geol & Geochem, Lab Coastal Dynam, BR-66077530 Belem, PA, Brazil, Email: mcohen@ufpa.br |
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SPRINGER |
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0939-6314 |
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ISI:000271191800001 |
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no |
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EcoFoG @ eric.marcon @ |
Serial |
193 |
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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 |
Publication |
IEEE Transactions on Aerospace and Electronic Systems |
Abbreviated Journal |
IEEE Trans. Aerosp. Electron. Syst. |
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Volume |
45 |
Issue |
3 |
Pages |
1063-1072 |
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Abstract |
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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no |
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EcoFoG @ eric.marcon @ |
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194 |
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Author |
Seymour, R.S.; Gibernau, M.; Pirintsos, S.A. |
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Title |
Thermogenesis of three species of Arum from Crete |
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Journal Article |
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Year |
2009 |
Publication |
Plant Cell and Environment |
Abbreviated Journal |
Plant Cell Environ. |
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Volume |
32 |
Issue |
10 |
Pages |
1467-1476 |
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Keywords |
Araceae; arum lily; inflorescence; pollination; temperature regulation |
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Abstract |
Inflorescences of arum lilies have a three-part spadix with a scent-producing, sterile appendix above two bands of fertile male and female florets. The appendix and male florets are thermogenic, but with different temporal patterns. Heat-production was measured in Arum concinnatum, A. creticum and A. idaeum. The male florets of A. concinnatum showed a 3 d continuous episode of thermogenesis with three waves, and the appendix warmed in a single, 6 h episode. Maximum fresh-mass-specific CO2 production rate was 0.17 μmol s(-1) g(-1) to achieve a 10.9 degrees C temperature elevation by the appendix, and 0.92 μmol s(-1) g(-1) to achieve a 4.8 degrees C elevation by male florets. Reversible, physiological temperature regulation was not evident in either tissue. Respiration increased with tissue temperatures with Q(10) values of 1.8-3.9, rather than less than 1.0 as occurs in thermoregulatory flowers. Experimental step changes in temperature of appendix and male floret tissues also failed to show thermoregulatory responses. The patterns of thermogenesis therefore appear to be fixed by the temporal sequence of blooming. Thermogenesis in the alpine species, A. creticum and A. idaeum, was significantly lower than in the lowland A. concinnatum, possibly related to difficulty in raising floral temperature in their cold and windy habitat. |
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[Seymour, Roger S.] Univ Adelaide, Adelaide, SA 5005, Australia, Email: roger.seymour@adelaide.edu.au |
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WILEY-BLACKWELL PUBLISHING, INC |
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0140-7791 |
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ISI:000269592300016 |
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EcoFoG @ eric.marcon @ |
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195 |
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Gloor, M.; Phillips, O.L.; Lloyd, J.J.; Lewis, S.L.; Malhi, Y.; Baker, T.R.; Lopez-Gonzalez, G.; Peacock, J.; Almeida, S.; de Oliveira, A.C.A.; Alvarez, E.; Amaral, I.; Arroyo, L.; Aymard, G.; Banki, O.; Blanc, L.; Bonal, D.; Brando, P.; Chao, K.J.; Chave, J.; Davila, N.; Erwin, T.; Silva, J.; Di Fiore, A.; Feldpausch, T.R.; Freitas, A.; Herrera, R.; Higuchi, N.; Honorio, E.; Jimenez, E.; Killeen, T.; Laurance, W.; Mendoza, C.; Monteagudo, A.; Andrade, A.; Neill, D.; Nepstad, D.; Vargas, P.N.; Penuela, M.C.; Cruz, A.P.; Prieto, A.; Pitman, N.; Quesada, C.; Salomao, R.; Silveira, M.; Schwarz, M.; Stropp, J.; Ramirez, F.; Ramirez, H.; Rudas, A.; ter Steege, H.; Silva, N.; Torres, A.; Terborgh, J.; Vasquez, R.; van der Heijden, G. |
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Title |
Does the disturbance hypothesis explain the biomass increase in basin-wide Amazon forest plot data? |
Type |
Journal Article |
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Year |
2009 |
Publication |
Global Change Biology |
Abbreviated Journal |
Glob. Change Biol. |
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Volume |
15 |
Issue |
10 |
Pages |
2418-2430 |
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Keywords |
Amazon rainforest; carbon sink; disturbance; mortality; power law |
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Abstract |
Positive aboveground biomass trends have been reported from old-growth forests across the Amazon basin and hypothesized to reflect a large-scale response to exterior forcing. The result could, however, be an artefact due to a sampling bias induced by the nature of forest growth dynamics. Here, we characterize statistically the disturbance process in Amazon old-growth forests as recorded in 135 forest plots of the RAINFOR network up to 2006, and other independent research programmes, and explore the consequences of sampling artefacts using a data-based stochastic simulator. Over the observed range of annual aboveground biomass losses, standard statistical tests show that the distribution of biomass losses through mortality follow an exponential or near-identical Weibull probability distribution and not a power law as assumed by others. The simulator was parameterized using both an exponential disturbance probability distribution as well as a mixed exponential-power law distribution to account for potential large-scale blowdown events. In both cases, sampling biases turn out to be too small to explain the gains detected by the extended RAINFOR plot network. This result lends further support to the notion that currently observed biomass gains for intact forests across the Amazon are actually occurring over large scales at the current time, presumably as a response to climate change. |
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[Gloor, M.; Phillips, O. L.; Lloyd, J. J.; Lewis, S. L.; Baker, T. R.; Lopez-Gonzalez, G.; Peacock, J.; Feldpausch, T. R.] Univ Leeds, Sch Geog, Leeds LS2 9JT, W Yorkshire, England, Email: eugloor@googlemail.com |
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WILEY-BLACKWELL PUBLISHING, INC |
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1354-1013 |
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ISI:000269577800006 |
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no |
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EcoFoG @ eric.marcon @ |
Serial |
196 |
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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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Address |
[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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no |
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EcoFoG @ eric.marcon @ |
Serial |
197 |
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Author |
Seymour, R.S.; White, C.R.; Gibernau, M. |
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Title |
Endothermy of dynastine scarab beetles (Cyclocephala colasi) associated with pollination biology of a thermogenic arum lily (Philodendron solimoesense) |
Type |
Journal Article |
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Year |
2009 |
Publication |
Journal of Experimental Biology |
Abbreviated Journal |
J. Exp. Biol. |
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Volume |
212 |
Issue |
18 |
Pages |
2960-2968 |
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Keywords |
beetle; endothermy; pollination biology; Cyclocephala; Philodendron |
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Abstract |
Cyclocephala colasi beetles are facultative endotherms that spend most of their adult lives inside the inflorescences of Philodendron solimoesense, where ambient temperature (T-a) averages about 28 degrees C due to floral thermogenesis. Measurements of respiration within a range of T-a showed that active beetles became spontaneously endothermic at T-a below 28 degrees C but were rarely endothermic above it. There was no evidence of endothermy within the inflorescences, indicating that activities in the floral chamber can occur without the high energy expense of endothermy. Bouts of endothermy occurred at lower T-a in respirometer chambers mainly in the evening, when the insects normally fly from one inflorescence to another, and during the night, when they normally eat and mate within the inflorescence. Patterns of endothermy in individual episodes were studied in non-flying beetles with respirometry and infrared thermal imaging. Heat was generated in the thorax by oscillatory waves of respiration that were coupled with thoracic temperature (T-th) increases. Stationary beetles could regulate T-th at about 33 degrees C independently of T-a between 16 and 29 degrees C. At T-a=20 degrees C, this represents a 116-fold increase in metabolic rate over resting, ectothermic values. Endothermy was clearly a requirement for flight, and beetles departing inflorescences warmed to about 30 degrees C before take-off. During flight, T-th was dependent on T-a, decreasing from 37 to 28 degrees C at T-a of 37 to 20 degrees C, respectively. The lowest T-a at which flight could occur was about 20 degrees C. Thermal conductance of stationary, endothermic beetles increased at higher metabolic rates, probably because of increased ventilatory heat loss. |
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[Seymour, Roger S.] Univ Adelaide, Sch Earth & Environm Sci, Adelaide, SA 5005, Australia, Email: roger.seymour@adelaide.edu.au |
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COMPANY OF BIOLOGISTS LTD |
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0022-0949 |
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ISI:000269383500014 |
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EcoFoG @ eric.marcon @ |
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198 |
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