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Csilléry, K.; Lalague, H.; Vendramin, G.G.; González-Martínez, S.C.; Fady, B.; Oddou-Muratorio, S. |
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Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations |
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Journal Article |
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2014 |
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Molecular Ecology |
Abbreviated Journal |
Molecular Ecology |
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23 |
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19 |
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4696-4708 |
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abiotic stress; budburst phenology; FST outlier; gene network; haplotype; Ohta's test; variance components of linkage disequilibrium |
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Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multilocus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes factors over many possible phase reconstructions. Epistatic selection offers a realistic multilocus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Overall populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a nonsynonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low elevations and northern or southern populations. Several haplotypes contained nonsynonymous mutations situated in genes with known functional importance for adaptation to climatic factors. |
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CIFOR-INIA, Forest Research Centre, Carretera de La Coruña km 7.5Madrid 28040, Spain |
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Export Date: 13 January 2015 |
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EcoFoG @ webmaster @ |
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579 |
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Baraloto, C.; Alverga, P.; Quispe, S.B.; Barnes, G.; Chura, N.B.; da Silva, I.B.; Castro, W.; da Souza, H.; de Souza Moll, I.E.; Del Alcazar Chilo, J.; Linares, H.D.; Quispe, J.G.; Kenji, D.; Marsik, M.; Medeiros, H.; Murphy, S.; Rockwell, C.; Selaya, G.; Shenkin, A.; Silveira, M.; Southworth, J.; Vasquez Colomo, G.H.; Perz, S. |
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Effects of road infrastructure on forest value across a tri-national Amazonian frontier |
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Journal Article |
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2015 |
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Biological Conservation |
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Biological Conservation |
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191 |
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674-681 |
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Açai; Biodiversity; Brazil nut; Carbon stocks; Connectivity; Infrastructure; Livelihood; Ntfp; Redd; Road impact; Rubber; Timber; Tropical rainforest |
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Road construction demonstrably accelerates deforestation rates in tropical forests, but its consequences for forest degradation remain less clear. We estimated a series of forest value metrics including components of biodiversity, carbon stocks, and timber and non-timber forest product resources, along the recently paved Inter-Oceanic Highway (IOH) integrating Brazil and Peru along the Bolivian border. We installed 69 vegetation plots in intact terra firme forests representative of local community holdings near and far from the IOH, and we characterized 15 components of forest value for each plot.We observed strong geographic gradients in forest value components across the region, with increases from west to east in aboveground biomass and in the abundance of timber and non-timber forest product trees and regeneration. Plots in communities in Pando, Bolivia, where the IOH remains in part unpaved, had the highest aboveground biomass, standing timber volumes and Brazil nut tree density. In contrast, communities in Madre de Dios, Peru, where settlements and unpaved portions of the IOH have existed for decades, and in Acre, Brazil, where paving of the IOH has been underway for more than a decade, were more degraded. Seven of the fifteen forest value components we measured increased with increasing distance from the IOH, although the magnitude of these effects was weak. Landscape scale remote sensing analyses showed much stronger effects of road proximity on deforestation. We suggest that remote sensing techniques including canopy spectral signatures might be calibrated to characterize multiple components of forest value, so that we can estimate landscape scale impacts of infrastructure developments on both deforestation and forest degradation in tropical regions. © 2015 Elsevier B.V. |
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International Center for Tropical Botany, Department of Earth and Environment, Florida International University, Miami, FL, United States |
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Export Date: 8 September 2015 |
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EcoFoG @ webmaster @ |
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619 |
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Baraloto, C.; Alverga, P.; Quispe, S.B.; Barnes, G.; Chura, N.B.; Da Silva, I.B.; Castro, W.; Da Souza, H.; De Souza Moll, I.; Del Alcazar Chilo, J.; Linares, H.D.; Quispe, J.G.; Kenji, D.; Medeiros, H.; Murphy, S.; Rockwell, C.A.; Shenkin, A.; Silveira, M.; Southworth, J.; Vasquez, G.; Perz, S. |
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Trade-offs among forest value components in community forests of southwestern Amazonia |
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2014 |
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Ecology and Society |
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Ecology and Society |
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19 |
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4 |
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56 |
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Açai; Biodiversity conservation; Brazil nut; Carbon stocks; Livelihood; Ntfp; Redd; Rubber; Timber; Tropical rainforest |
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Contemporary conservation interventions must balance potential trade-offs between multiple ecosystem services. In tropical forests, much attention has focused on the extent to which carbon-based conservation provided by REDD+ policies can also mitigate biodiversity conservation. In the nearly one-third of tropical forests that are community owned or managed, conservation strategies must also balance the multiple uses of forest products that support local livelihoods. Although much discussion has focused on policy options, little empirical evidence exists to evaluate the potential for trade-offs among different tropical forest value components. We assessed multiple components of forest value, including tree diversity, carbon stocks, and both timber and nontimber forest product resources, in forest communities across the trinational frontier of Brazil, Peru, and Bolivia. We installed 69 0.5-ha vegetation plots in local communities, and we characterized 15 components of forest value for each plot. Principal components analyses revealed two major axes of forest value, the first of which defined a trade-off between diversity of woody plant communities (taxonomic and functional) versus aboveground biomass and standing timber volume. The second axis described abundance of commercial species, with strong positive loadings for density of timber and nontimber forest products, including Brazil nut (Bertholletia excelsa) and copaiba oil (Copaifera spp.). The observed trade-off between different components of forest value suggests a potential for management conflicts prioritizing biodiversity conservation versus carbon stocks in the region. We discuss the potential for integrative indices of forest value for tropical forest conservation. |
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Department of Sociology and Criminology and Law, University of Florida, United States |
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Export Date: 23 March 2015 |
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EcoFoG @ webmaster @ |
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589 |
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Faustin, M.; Maciuk, A.; Salvin, P.; Roos, C.; Lebrini, M. |
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Corrosion inhibition of C38 steel by alkaloids extract of Geissospermum laeve in 1M hydrochloric acid: Electrochemical and phytochemical studies |
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Journal Article |
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2015 |
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Corrosion Science |
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Corrosion Science |
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92 |
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287-300 |
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A. C38 steel; B. Eis; B. Sem; C. Acid corrosion; C. Anodic protection; C. Cathodic protection |
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Corrosion inhibition by alkaloids extract (AE) from Geissospermum laeve on C38 steel in 1. M HCl is investigated with electrochemical studies. Inhibition efficiency of 92% is reached with 100. mg/L of AE at 25. °C. Potentiodynamic polarization showed that the extract behaves as mixed-type inhibitors. The Nyquist plots showed that increasing AE concentration, charge-transfer resistance increased and double-layer capacitance decreased, involving increased inhibition efficiency. Adsorption of the inhibitor molecules corresponds to Langmuir adsorption isotherm. Immersion time and temperature effects were investigated using EIS and potentiodynamic polarization. SEM and EDX supported the adsorption conclusions. The active compound responsible for the corrosion inhibition is geissospermine. |
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Laboratoire de Pharmacognosie-Chimie des Substances Naturelles et Chimiotherapies Antiparasitaires, BioCIS, Université Paris-SudChâtenay-Malabry, France |
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Export Date: 6 February 2015 |
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EcoFoG @ webmaster @ |
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584 |
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Öpik, M.; Zobel, M.; Cantero, J.J.; Davison, J.; Facelli, J.M.; Hiiesalu, I.; Jairus, T.; Kalwij, J.M.; Koorem, K.; Leal, M.E.; Liira, J.; Metsis, M.; Neshataeva, V.; Paal, J.; Phosri, C.; Põlme, S.; Reier, Ü.; Saks, Ü.; Schimann, H.; Thiéry, O.; Vasar, M.; Moora, M. |
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Global sampling of plant roots expands the described molecular diversity of arbuscular mycorrhizal fungi |
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2013 |
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Mycorrhiza |
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23 |
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5 |
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411-430 |
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454-sequencing; Biogeography; Database; Diversity; Fungal macroecology; Glomeromycota |
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We aimed to enhance understanding of the molecular diversity of arbuscular mycorrhizal fungi (AMF) by building a new global dataset targeting previously unstudied geographical areas. In total, we sampled 96 plant species from 25 sites that encompassed all continents except Antarctica. AMF in plant roots were detected by sequencing the nuclear SSU rRNA gene fragment using either cloning followed by Sanger sequencing or 454-sequencing. A total of 204 AMF phylogroups (virtual taxa, VT) were recorded, increasing the described number of Glomeromycota VT from 308 to 341 globally. Novel VT were detected from 21 sites; three novel but nevertheless widespread VT (Glomus spp. MO-G52, MO-G53, MO-G57) were recorded from six continents. The largest increases in regional VT number were recorded in previously little-studied Oceania and in the boreal and polar climatic zones – this study providing the first molecular data from the latter. Ordination revealed differences in AM fungal communities between different continents and climatic zones, suggesting that both biogeographic history and environmental conditions underlie the global variation of those communities. Our results show that a considerable proportion of Glomeromycota diversity has been recorded in many regions, though further large increases in richness can be expected in remaining unstudied areas. © 2013 Springer-Verlag Berlin Heidelberg. |
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INRA-Joint Research Unit Ecology of Guiana Forests (Ecofog), campus agronomique, BP 709, 97387 Kourou cedex, French Guiana |
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Export Date: 25 June 2013; Source: Scopus |
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EcoFoG @ webmaster @ |
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493 |
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Brousseau, L.; Tinaut, A.; Duret, C.; Lang, T.; Garnier-Gere, P.; Scotti, I. |
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High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species |
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2014 |
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BMC Genomics |
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BMC Genomics |
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15 |
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238 |
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1-13 |
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454-Pyrosequencing; Polymorphism discovery; Tropical rainforest tree species |
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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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537 |
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Niamké, F.B.; Amusant, N.; Stien, D.; Chaix, G.; Lozano, Y.; Kadio, A.A.; Lemenager, N.; Goh, D.; Adima, A.A.; Kati-Coulibaly, S.; Jay-Allemand, C. |
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4',5'-Dihydroxy-epiisocatalponol, a new naphthoquinone from Tectona grandis L. f. heartwood, and fungicidal activity |
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2012 |
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International Biodeterioration and Biodegradation |
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Int. Biodeterior. Biodegrad. |
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74 |
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93-98 |
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4',5'-Dihydroxy-epiisocatalponol; Decay resistance; Fungicidal; Heartwood; Naphthoquinone; Tectona grandis |
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A new naphthoquinone derivative was isolated from the heartwood of the teak stem. The chemical structure of this new compound, 4',5'-dihydroxy-epiisocatalponol, was determined using 1-D and 2-D nuclear magnetic resonance experiments, vibrational circular dichroism, HRMS, and optical rotation. We showed that this new naphthoquinone derivative plays a key role in the variability of decay resistance in teak wood. A high negative correlation was found between its concentration and the mass losses of the wood samples after exposure to the brown rot Antrodia sp., the fungus that is the most virulent against teak (R = -0.9; ρ < 0.0001). In-vitro bioassays allowed us to demonstrate that 4',5'-dihydroxy-epiisocatalponol acted as a fungicide against Trametes versicolor (white rot) at 58 mg ml -1 (0.22 mM). Overall, our results demonstrated that the concentration of 4',5'-dihydroxy-epiisocatalponol could be used as a new tool to evaluate teak wood durability. © 2012 Elsevier Ltd. |
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Laboratoire de Biochimie et de Physiologie Végétales, UMR 47 DIADE – Equipe Rhizogenèse, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France |
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Export Date: 27 September 2012; Source: Scopus; Coden: Ibbie; doi: 10.1016/j.ibiod.2012.03.010; Language of Original Document: English; Correspondence Address: Amusant, N.; CIRAD, Department Environments and societies, UMR Ecology forests of French Guiana, BP 732, 97310 Kourou cedex, French Guiana; email: nadine.amusant@cirad.fr |
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435 |
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Roux, O.; Vantaux, A.; Petitclerc, F.; Orivel, J.; Dejean, A.; Billen, J. |
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Structural adaptations and mechanism of reflex bleeding in the larvae of the myrmecophilous ladybird Diomus thoracicus |
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2017 |
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Arthropod Structure and Development |
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Arthropod Structure and Development |
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46 |
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4 |
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529-536 |
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3D reconstruction; Coccinellidae; Myrmecophagous insect; Reflex bleeding; Ultrastructure |
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Reflex bleeding is an effective defensive mechanism against predators. When attacked, some insects emit hemolymph, which coagulates, quickly entangling their aggressor. Bleeding occurs at weak intersegmental membranes or through dedicated organs, which can be associated or not with glandular cells. Here, we describe the behavior and morphological structures involved in reflex bleeding in the larvae of the ladybird, Diomus thoracicus, which are intranidal parasites of the ant Wasmannia auropunctata. The larvae are tolerated by the ants thanks to odor mimicry, but some rare aggressive ant behaviors were observed that trigger reflex bleeding both at a pair of thoracic tubercles and a pair of posterodorsal abdominal humps. No glandular structure was found in association with these emission points, which suggests that the material emitted was hemolymph only. A 3D reconstruction suggested that reflex bleeding seems to be controlled by muscles whose contraction increases the internal hydrostatic pressure and pushes the hemolymph into a funnel-like structure with an opening to the outside. In D. thoracicus, the morphological structures involved in reflex bleeding are among the most complex and prominent described to date. © 2017 Elsevier Ltd |
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KU Leuven, Zoological Institute, Naamsestraat 59, box 2466, Leuven, Belgium |
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Export Date: 18 December 2017 |
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778 |
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Lambs, L.; Bompy, F.; Imbert, D.; Corenblit, D.; Dulormne, M. |
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Seawater and freshwater circulations through coastal forested wetlands on a Caribbean Island |
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2015 |
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Water |
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Water |
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7 |
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8 |
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4108-4128 |
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18O/2H stable isotope; Hydrology; Mangrove; Salinity; Swamp forest; Water level |
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Structure and composition of coastal forested wetlands are mainly controlled by local topography and soil salinity. Hydrology plays a major role in relation with tides, seaward, and freshwater inputs, landward. We report here the results of a two-year study undertaken in a coastal plain of the Guadeloupe archipelago (FWI). As elsewhere in the Caribbean islands, the study area is characterized by a micro-tidal regime and a highly seasonal climate. This work aimed at understanding groundwater dynamics and origin (seawater/freshwater) both at ecosystems and stand levels. These hydrological processes were assessed through 18O/16O and 2H/1H isotopic analyses, and from monthly monitoring of water level and soil salinity at five study sites located in mangrove (3) and swamp forest (2). Our results highlight the importance of freshwater budget imbalance during low rainfall periods. Sustained and/or delayed dry seasons cause soil salinity to rise at the mangrove/swamp forest ecotone. As current models on climate change project decreasing rainfall amounts over the inner Caribbean region, one may expect for this area an inland progression of the mangrove forest to the expense of the nearby swamp forest. © 2015 by the authors. |
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Geolab, UMR 6042, CNRS-Université Blaise Pascal, 4 rue Ledru, Clermont-Ferrand Cedex, France |
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Export Date: 8 September 2015 |
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EcoFoG @ webmaster @ |
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621 |
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Author |
Birer, C.; Tysklind, N.; Zinger, L.; Duplais, C. |
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Title |
Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: A case study with ant cuticular bacteria |
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Journal Article |
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2017 |
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Molecular Ecology Resources |
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Mol Ecol Resour |
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17 |
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6 |
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e34-e45 |
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16S rRNA; bacterial communities; cuticular microbiome; insect cuticle; metabarcoding |
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Abstract |
High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behaviour of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties of working with low bacterial DNA quantities as with individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial community characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in terms of bacterial diversity and composition for A. cephalotes (~15 mm). In contrast, greater amounts of artefactual sequences and contaminations, as well as noticeable differences in bacterial community characteristics were observed between extraction methods for P. penetrator (~5 mm). We also found that large (~15 mm) and small (~5 mm) A. cephalotes individuals harbour different bacterial communities. Our benchmark suggests that cuticular microbiota of single individual insects can be reliably retrieved provided that blank controls, appropriate data cleaning, and individual body size and functional role within insect society are considered in the experiment. |
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1755-0998 |
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no |
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EcoFoG @ webmaster @ |
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781 |
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