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Brousseau, L.; Tinaut, A.; Duret, C.; Lang, T.; Garnier-Gere, P.; Scotti, I. |
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Title |
High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species |
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Journal Article |
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Year |
2014 |
Publication |
BMC Genomics |
Abbreviated Journal |
BMC Genomics |
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Volume |
15 |
Issue |
238 |
Pages |
1-13 |
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454-Pyrosequencing; Polymorphism discovery; Tropical rainforest tree species |
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Abstract |
Background: The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. Results: In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.Conclusion: The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species. © 2014 Brousseau et al.; licensee BioMed Central Ltd. |
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BIOGECO, UMR 1202, University of Bordeaux, F-33400 Talence, France |
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BioMed Central Ltd. |
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14712164 (Issn) |
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Export Date: 18 April 2014; Source: Scopus; Art. No.: 238; Coden: Bgmee; Language of Original Document: English; Correspondence Address: Scotti, I.; INRA, UMR 0745 EcoFoG, Campus agronomique BP 709, F-97387 Cedex, France; email: ivan.scotti@ecofog.gf |
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EcoFoG @ webmaster @ |
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537 |
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Peguero, G.; Sardans, J.; Asensio, D.; Fernández-Martínez, M.; Gargallo-Garriga, A.; Grau, O.; Llusià, J.; Margalef, O.; Márquez, L.; Ogaya, R.; Urbina, I.; Courtois, E.A.; Stahl, C.; Van Langenhove, L.; Verryckt, L.T.; Richter, A.; Janssens, I.A.; Peñuelas, J. |
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Title |
Nutrient scarcity strengthens soil fauna control over leaf litter decomposition in tropical rainforests |
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Journal Article |
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Year |
2019 |
Publication |
Proceedings. Biological sciences |
Abbreviated Journal |
Proc. Biol. Sci. |
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Volume |
286 |
Issue |
1910 |
Pages |
20191300 |
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Keywords |
biogeochemistry; extracellular enzyme activity; litter decomposition; nutrients; soil fauna |
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Soil fauna is a key control of the decomposition rate of leaf litter, yet its interactions with litter quality and the soil environment remain elusive. We conducted a litter decomposition experiment across different topographic levels within the landscape replicated in two rainforest sites providing natural gradients in soil fertility to test the hypothesis that low nutrient availability in litter and soil increases the strength of fauna control over litter decomposition. We crossed these data with a large dataset of 44 variables characterizing the biotic and abiotic microenvironment of each sampling point and found that microbe-driven carbon (C) and nitrogen (N) losses from leaf litter were 10.1 and 17.9% lower, respectively, in the nutrient-poorest site, but this among-site difference was equalized when meso- and macrofauna had access to the litterbags. Further, on average, soil fauna enhanced the rate of litter decomposition by 22.6%, and this contribution consistently increased as nutrient availability in the microenvironment declined. Our results indicate that nutrient scarcity increases the importance of soil fauna on C and N cycling in tropical rainforests. Further, soil fauna is able to equalize differences in microbial decomposition potential, thus buffering to a remarkable extent nutrient shortages at an ecosystem level. |
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Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, 1090, Austria |
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NLM (Medline) |
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14712954 (Issn) |
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EcoFoG @ webmaster @ |
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884 |
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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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Year |
2009 |
Publication |
Evolution & Development |
Abbreviated Journal |
Evol. Dev. |
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Volume |
11 |
Issue |
4 |
Pages |
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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Vedel, V.; Apostolou, Z.; Arthur, W.; Akam, M.; Brena, C. |
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Title |
An early temperature-sensitive period for the plasticity of segment number in the centipede Strigamia maritima |
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Journal Article |
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2010 |
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Evolution & Development |
Abbreviated Journal |
Evol Dev |
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12 |
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4 |
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347-352 |
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1520-541X |
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WOS:000279440800002 |
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EcoFoG @ eric.marcon @ |
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278 |
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Dejean, A.; Grangier, J.; Leroy, C.; Orivel, J. |
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Title |
Host plant protection by arboreal ants: looking for a pattern in locally induced responses |
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Journal Article |
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2008 |
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Evolutionary Ecology Research |
Abbreviated Journal |
Evol. Ecol. Res. |
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10 |
Issue |
8 |
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1217-1223 |
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aggressiveness; ant-plant relationships; Azteca; biotic defence; induced responses |
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Background: Among arboreal ants, both territorially dominant species and plant-ants (e.g. species associated with myrmecophytes or plants housing them in hollow structures) protect their host trees against defoliators. Yet, locally induced responses, or the recruitment of nest-mates when a worker discovers it wound on its host-tree, were only noted in plant-ants. We wondered whether this might be due to the examination of the phenomenon being restricted to only six plant-ant species belonging to four genera. Based on the ant genus Azteca, a Neotropical group of arboreal species, we compared five species. The territorially dominant, carton-nester A. chartifex, three plant-ant species [A. alfari and A. ovaticeps associated with myrmecophitic Cecropia (Cecropiaceae), and A. bequaerti associated with Tococa guianensis (Melastomataceae)], and A. schimperi thought to be a temporary social parasite of true Cecropia ants. Methods: We artificially inflicted wounds to the foliage of the host tree of the different ant species. We then compared the number of workers on wounded versus control leaves. Results: We noted a locally induced response in the three plant-ant species as well as in the territorially dominant species, but very slightly so in A. schimperi. |
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[Grangier, Julien; Orivel, Jerome] Univ Toulouse 2, Lab Evolut & Diversite Biol, CNRS, UMR 5174, Toulouse, France, Email: alain.dejean@wanadoo.fr |
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EVOLUTIONARY ECOLOGY LTD |
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1522-0613 |
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ISI:000264041000008 |
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EcoFoG @ eric.marcon @ |
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119 |
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Rodrigues, A.M.; Amusant, N.; Beauchene, J.; Eparvier, V.; Lemenager, N.; Baudasse, C.; Espindola, L.S.; Stien, D. |
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Title |
The termiticidal activity of Sextonia rubra (Mez) van der Werff (Lauraceae) extract and its active constituent rubrynolide |
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Journal Article |
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Year |
2011 |
Publication |
Pest Management Science |
Abbreviated Journal |
Pest Manage. Sci. |
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Volume |
67 |
Issue |
11 |
Pages |
1420-1423 |
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Nasutitermes macrocephalus; Reticulitermes flavipes; Rubrynolide; Sextonia rubra extract; Wood preservation |
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Termites are degradation agents that inflict severe damage on wood. Some long-lasting Amazonian trees can resist these insects by producing toxic secondary metabolites. These metabolites could potentially replace synthetic termiticidal products which are becoming more restricted to use. Results: Sextonia rubra is resistant to termite-induced degradation. It has been demonstrated that this species naturally produces an ethyl-acetate-soluble termiticidal metabolite, rubrynolide, to protect its wood. Assays in the presence of tropical and invasive termites established that both rubrynolide and crude ethyl acetate extract from S. rubra wood can be used as a treatment for the protection of sensitive woods against termites. Conclusion: Rubrynolide and S. rubra extract are promising candidates for the replacement of synthetic termiticides. © 2011 Society of Chemical Industry. |
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CNRS-Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France |
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1526498x (Issn) |
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Export Date: 26 October 2011; Source: Scopus; Coden: Pmscf; doi: 10.1002/ps.2167; Language of Original Document: English; Correspondence Address: Rodrigues, A.M.; UMR Ecofog, Institut d'Enseignement Supérieur de la Guyane, BP792, 97337 Cayenne Cedex, France; email: alice.rodrigues@pop.com.br |
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EcoFoG @ webmaster @ |
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362 |
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Aili, S.R.; Touchard, A.; Petitclerc, F.; Dejean, A.; Orivel, J.; Padula, M.P.; Escoubas, P.; Nicholson, G.M. |
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Title |
Combined Peptidomic and Proteomic Analysis of Electrically Stimulated and Manually Dissected Venom from the South American Bullet Ant Paraponera clavata |
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Journal Article |
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Year |
2017 |
Publication |
Journal of Proteome Research |
Abbreviated Journal |
J. Proteome Res. |
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16 |
Issue |
3 |
Pages |
1339-1351 |
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Ants have evolved venoms rich in peptides and proteins used for predation, defense, and communication. However, they remain extremely understudied due to the minimal amount of venom secreted by each ant. The present study investigated the differences in the proteome and peptidome of the venom from the bullet ant, Paraponera clavata. Venom samples were collected from a single colony either by manual venom gland dissection or by electrical stimulation and were compared using proteomic methods. Venom proteins were separated by 2D-PAGE and identified by nanoLC-ESI-QTOF MS/MS. Venom peptides were initially separated using C18 reversed-phase high-performance liquid chromatography, then analyzed by MALDI-TOF MS. The proteomic analysis revealed numerous proteins that could be assigned a biological function (total 94), mainly as toxins, or roles in cell regulation and transport. This investigation found that ca. 73% of the proteins were common to venoms collected by the two methods. The peptidomic analysis revealed a large number of peptides (total 309) but with <20% shared by the two collection methods. There was also a marked difference between venoms obtained by venom gland dissection from different ant colonies. These findings demonstrate the rich composition and variability of P. clavata venom. |
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American Chemical Society |
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1535-3893 |
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EcoFoG @ webmaster @ |
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746 |
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Touchard, A.; Aili, S.R.; Téné, N.; Barassé, V.; Klopp, C.; Dejean, A.; Kini, R.M.; Mrinalini; Coquet, L.; Jouenne, T.; Lefranc, B.; Leprince, J.; Escoubas, P.; Nicholson, G.M.; Treilhou, M.; Bonnafé, E. |
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Venom Peptide Repertoire of the European Myrmicine Ant Manica rubida: Identification of Insecticidal Toxins |
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Journal Article |
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Year |
2020 |
Publication |
Journal of proteome research |
Abbreviated Journal |
J. Proteome Res. |
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Volume |
19 |
Issue |
4 |
Pages |
1800-1811 |
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glycosylated toxin; peptidome; polycationic α-helix; predation; pyroglutamate; reversible neurotoxicity |
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Using an integrated transcriptomic and proteomic approach, we characterized the venom peptidome of the European red ant, Manica rubida. We identified 13 “myrmicitoxins” that share sequence similarities with previously identified ant venom peptides, one of them being identified as an EGF-like toxin likely resulting from a threonine residue modified by O-fucosylation. Furthermore, we conducted insecticidal assays of reversed-phase HPLC venom fractions on the blowfly Lucilia caesar, permitting us to identify six myrmicitoxins (i.e., U3-, U10-, U13-, U20-MYRTX-Mri1a, U10-MYRTX-Mri1b, and U10-MYRTX-Mri1c) with an insecticidal activity. Chemically synthesized U10-MYRTX-Mri1a, -Mri1b, -Mri1c, and U20-MYRTX-Mri1a irreversibly paralyzed blowflies at the highest doses tested (30-125 nmol·g-1). U13-MYRTX-Mri1a, the most potent neurotoxic peptide at 1 h, had reversible effects after 24 h (150 nmol·g-1). Finally, U3-MYRTX-Mri1a has no insecticidal activity, even at up to 55 nmol·g-1. Thus, M. rubida employs a paralytic venom rich in linear insecticidal peptides, which likely act by disrupting cell membranes. |
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VenomeTech, 473 Route des Dolines – Villa 3, Valbonne, 06560, France |
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NLM (Medline) |
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15353907 (Issn) |
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Export Date: 20 April 2020 |
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EcoFoG @ webmaster @ |
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927 |
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Mouillot, D.; Bellwood, D.R.; Baraloto, C.; Chave, J.; Galzin, R.; Harmelin-Vivien, M.; Kulbicki, M.; Lavergne, S.; Lavorel, S.; Mouquet, N.; Paine, C.E.T.; Renaud, J.; Thuiller, W. |
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Title |
Rare Species Support Vulnerable Functions in High-Diversity Ecosystems |
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Journal Article |
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2013 |
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PLoS Biology |
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PloS Biol. |
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11 |
Issue |
5 |
Pages |
e1001569 |
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Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across spatial scales. As such, they are likely to insure against future uncertainty arising from climate change and the ever-increasing anthropogenic pressures on ecosystems. Our results call for a more detailed understanding of the role of rarity and functional vulnerability in ecosystem functioning. © 2013 Mouillot et al. |
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Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom |
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15449173 (Issn) |
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Export Date: 12 June 2013; Source: Scopus; Art. No.: e1001569; Coden: Pblib; :doi 10.1371/journal.pbio.1001569; Language of Original Document: English; Correspondence Address: Mouillot, D.; Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS)-UM2, Institut français de recherche pour l'exploitation de la mer (IFREMER), Institute for Research and Development (IRD) 5119 ECOSYM, Université Montpellier 2 cc 093, Montpellier, France; email: david.mouillot@univ-montp2.fr |
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EcoFoG @ webmaster @ |
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492 |
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Hamadi, A.; Borderies, P.; Albinet, C.; Koleck, T.; Villard, L.; Ho Tong Minh, D.; Le Toan, T.; Burban, B. |
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Title |
Temporal coherence of tropical forests at P-band: Dry and rainy seasons |
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Journal Article |
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Year |
2015 |
Publication |
IEEE Geoscience and Remote Sensing Letters |
Abbreviated Journal |
IEEE Geosci. Remote Sens. Lett. |
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Volume |
12 |
Issue |
3 |
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557-561 |
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Biomass mission; forest scattering; ground-based experiment; P-band; range impulse response; temporal coherence |
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In this letter, the temporal coherence of tropical forest scattering at P-band is addressed by means of a ground-based experiment. The study is based on the TropiScat campaign in French Guiana, designed to support the Biomass mission, which will be the ESA 7th Earth Explorer mission. For Biomass, temporal coherence is a crucial parameter for coherent processing of polarimetric synthetic aperture radar (SAR) interferometry and SAR tomography in repeat-pass acquisitions. During the experiment, data were continuously collected for six months during both the rainy and dry seasons. For the rain-free days in both seasons, the coherence exhibits a daily cycle showing a high decorrelation during daytime, which is likely due to motion in the canopy. Up to a 20-day baseline, the coherence is much higher in the dry season than in the rainy season (> 0.8). From 20 to 40 days, it presents the same order of magnitude in both seasons [0.6, 0.7]. For larger temporal baselines, it becomes lower in the dry season. The results can be used to assess the long-term coherence of repeat-pass observations over a tropical forest. However, an extension of this study to several years and over other forest spots would be necessary to draw more general conclusions. |
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EcoFogKourou, France |
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Institute of Electrical and Electronics Engineers Inc. |
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1545598x (Issn) |
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Export Date: 21 October 2014; Correspondence Address: Hamadi, A.; Centre d'Etudes Spatiales de la BiosphèreFrance; Funding Details: ESA, European Space Agency |
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EcoFoG @ webmaster @ |
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563 |
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