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Sommeria-Klein, G.; Zinger, L.; Coissac, E.; Iribar, A.; Schimann, H.; Taberlet, P.; Chave, J. |
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Title |
Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest |
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Journal Article |
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Year |
2020 |
Publication |
Molecular Ecology Resources |
Abbreviated Journal  |
Mol. Ecol. Resour. |
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Volume |
20 |
Issue |
2 |
Pages |
371-386 |
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Keywords |
community ecology; environmental DNA; metabarcoding; OTU presence–absence; soil microbiome; topic modelling; bacterium; biodiversity; biology; classification; eukaryote; fungus; genetics; high throughput sequencing; isolation and purification; microbiology; parasitology; procedures; soil; Bacteria; Biodiversity; Computational Biology; Eukaryota; Fungi; High-Throughput Nucleotide Sequencing; Soil; Soil Microbiology |
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High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity. © 2019 John Wiley & Sons Ltd |
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Laboratoire d’Ecologie des Forêts de Guyane (EcoFoG, UMR 745), INRA, AgroParisTech, CIRAD, CNRS, University of the French West Indies, University of French Guiana, Kourou, France |
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Blackwell Publishing Ltd |
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1755098x (Issn) |
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EcoFoG @ webmaster @ |
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981 |
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Hamon, P.; Duroy, P.-O.; Dubreuil-Tranchant, C.; Mafra D'Almeida Costa, P.; Duret, C.; Razafinarivo, N.J.; Couturon, E.; Hamon, S.; De Kochko, A.; Poncet, V.; Guyot, R. |
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Title |
Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae) |
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Journal Article |
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Year |
2011 |
Publication |
Molecular Genetics and Genomics |
Abbreviated Journal |
Mol. Genet. Genomics |
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Volume |
285 |
Issue |
6 |
Pages |
447-460 |
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Keywords |
Coffea; Evolution; Genetic diversity; LTR-retrotransposons; article; coffee; controlled study; Divo; gene amplification; gene dosage; gene expression; gene insertion; gene locus; gene sequence; genetic identification; genetic polymorphism; genetic variability; molecular cloning; Nana; nonhuman; nucleotide sequence; phylogeny; plant evolution; plant gene; priority journal; Psilanthus; random amplified microsatellite; retroposon; Rubiaceae; species differentiation; tree; Ty1 copia gene; Coffea; Genes, Plant; Genome, Plant; Phylogeny; Retroelements |
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In the study, we developed new markers for phylogenetic relationships and intraspecies differentiation in Coffea. Nana and Divo, two novel Ty1-copia LTR-retrotransposon families, were isolated through C. canephora BAC clone sequencing. Nana- and Divo-based markers were used to test their: (1) ability to resolve recent phylogenetic relationships; (2) efficiency in detecting intra-species differentiation. Sequence-specific amplification polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposon-based insertion polymorphism (RBIP) approaches were applied to 182 accessions (31 Coffea species and one Psilanthus accession). Nana- and Divo-based markers revealed contrasted transpositional histories. At the BAC clone locus, RBIP results on C. canephora demonstrated that Nana insertion took place prior to C. canephora differentiation, while Divo insertion occurred after differentiation. Combined SSAP and REMAP data showed that Nana could resolve Coffea lineages, while Divo was efficient at a lower taxonomic level. The combined results indicated that the retrotransposon-based markers were useful in highlighting Coffea genetic diversity and the chronological pattern of speciation/differentiation events. Ongoing complete sequencing of the C. canephora genome will soon enable exhaustive identification of LTR-RTN families, as well as more precise in-depth analyses on contributions to genome size variation and Coffea evolution. © 2011 Springer-Verlag. |
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IRD, UMR DIADE, BP 50172, Sainte Clotilde Cedex, La Réunion 97492, France |
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16174615 (Issn) |
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Export Date: 21 October 2011; Source: Scopus; Coden: Mggoa; doi: 10.1007/s00438-011-0617-0; PubMed ID: 21505885; Language of Original Document: English; Correspondence Address: Hamon, P.; IRD, UMR DIADE, BP 64501, Montpellier Cedex 5, France; email: perla.hamon@ird.fr; Molecular Sequence Numbers: GENBANK: DV666936, HM755952, HM755953;; Chemicals/CAS: Retroelements |
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EcoFoG @ webmaster @ |
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344 |
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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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Year |
2014 |
Publication |
Molecular Ecology |
Abbreviated Journal |
Molecular Ecology |
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Volume |
23 |
Issue |
19 |
Pages |
4696-4708 |
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Keywords |
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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Marti, G.; Eparvier, V.; Litaudon, M.; Grellier, P.; Gueritte, F. |
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Title |
A New Xanthone from the Bark Extract of Rheedia acuminata and Antiplasmodial Activity of Its Major Compounds |
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Journal Article |
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Year |
2010 |
Publication |
Molecules |
Abbreviated Journal |
Molecules |
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Volume |
15 |
Issue |
10 |
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7106-7114 |
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Rheedia acuminata, Clusiaceae; xanthones; antiplasmodial activity; cytotoxicity |
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Bioassay-guided fractionation of the ethyl acetate bark extract of Rheedia acuminata led to the isolation of the new compound 1,5,6-trihydroxy-3-methoxy-7-geranyl-xanthone (1), together with four known compounds 2-5. These compounds were tested in vitro for their antiplasmodial activity on a chloroquine-resistant strain of Plasmodium falciparum (FcB1) and for their cytotoxicity against the human diploid embryonic lung cell line MRC-5. |
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[Eparvier, Veronique] CNRS, UPS2561, F-97300 Cayenne, France, Email: guillaume.marti@icsn.cnrs-gif.fr |
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MDPI AG |
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1420-3049 |
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ISI:000283587400030 |
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EcoFoG @ webmaster @ |
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282 |
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Henkel, T.W.; Wilson, A.W.; Aime, M.C.; Dierks, J.; Uehling, J.K.; Roy, M.; Schimann, H.; Wartchow, F.; Mueller, G.M. |
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Cantharellaceae of Guyana II: New species of Craterellus, new South American distribution records for Cantharellus guyanensis and Craterellus excelsus, and a key to the Neotropical taxa |
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Journal Article |
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2014 |
Publication |
Mycologia |
Abbreviated Journal |
Mycologia |
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106 |
Issue |
2 |
Pages |
307-324 |
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Cantharellales; Coccoloba; Dicymbe; Ectomycorrhizae; Guiana shield; Tropical fungi |
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Craterellus olivaceoluteus sp. nov. and Craterellus cinereofimbriatus sp. nov. are described as new to science. These fungi were collected from Guyana in association with ectomycorrhizal host trees in the genera Dicymbe (Fabaceae subfam. Caesalpinioideae) and Pakaraimaea (Dipterocarpaceae). Cantharellus guyanensis Mont., originally described from French Guiana, is redescribed from recent collections from Guyana, with additional range extensions for the species provided based on material examined from French Guiana, Venezuela, and north central, northeastern and southern Brazil, circumscribing nearly the entire Guiana Shield region and beyond. A new distribution record from French Guiana is provided for Craterellus excelsus T.W. Henkel & Aime. Macromorphological, micromorphological and habitat data are provided for the new species and C. guyanensis as well as DNA sequence data from the nuclear ribosomal regions of the internal transcribed spacer (ITS) and 28S large subunit (LSU); additional sequence data is provided for C. guyanensis and C. excelsus specimens collected outside Guyana. The relationships of these taxa within the Cantharellaceae were evaluated with phylogenetic analyses of ITS and LSU sequence data. This work brings the total number of Cantharellaceae species known from Guyana to eight. A key to the Cantharellus and Craterellus species known from the lowland Neotropics and extralimital montane Central and South America is provided. © 2014 by The Mycological Society of America. |
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Department of Biological Sciences, Boise State University, Boise, ID, 83725, United States |
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Allen Press Inc. |
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15572536 (Issn) |
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Export Date: 10 June 2014; Coden: Mycoa; Correspondence Address: Henkel, T.W.; Department of Biological Sciences, Humboldt State University, Arcata, CA 95521, United States; email: twh5@humboldt.edu; Funding Details: DEB-0732968, NSF, National Science Foundation |
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no |
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EcoFoG @ webmaster @ |
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546 |
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Bandou, E.; Lebailly, F.; Muller, F.; Dulormne, M.; Toribio, A.; Chabrol, J.; Courtecuisse, R.; Plenchette, C.; Prin, Y.; Duponnois, R.; Thiao, M.; Sylla, S.; Dreyfus, B.; Ba, A.M. |
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The ectomycorrhizal fungus Scleroderma bermudense alleviates salt stress in seagrape (Coccoloba uvifera L.) seedlings |
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Journal Article |
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Year |
2006 |
Publication |
Mycorrhiza |
Abbreviated Journal |
Mycorrhiza |
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16 |
Issue |
8 |
Pages |
559-565 |
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Coccoloba uvifera; ectomycorrhizal dependency; mineral uptake; salt stress; water status |
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The purpose of this study was to test the capacity of the ectomycorrhizal (ECM) fungus, Scleroderma bermudense, to alleviate saline stress in seagrape (Coccoloba uvifera L.) seedlings. Plants were grown over a range (0, 200, 350 and 500 mM) of NaCl levels for 12 weeks, after 4 weeks of non-saline pre-treatment under greenhouse conditions. Growth and mineral nutrition of the seagrape seedlings were stimulated by S. bermudense regardless of salt stress. Although ECM colonization was reduced with increasing NaCl levels, ECM dependency of seagrape seedlings increased. Tissues of ECM plants had significantly increased concentrations of P and K but lower Na and Cl concentrations than those of non-ECM plants. Higher K concentrations in the leaves of ECM plants suggested a higher osmoregulating capacity of these plants. Moreover, the water status of ECM plants was improved despite their higher evaporative leaf surface. The results suggest that the reduction in Na and Cl uptake together with a concomitant increase in P and K absorption and a higher water status in ECM plants may be important salt-alleviating mechanisms for seagrape seedlings growing in saline soils. |
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Univ Antilles Guyane, Fac Sci Exactes & Nat, Lab Biol & Physiol Vegetales, F-97159 Guadeloupe, France, Email: amadou.ba@univ-ag.fr |
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SPRINGER |
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0940-6360 |
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ISI:000241687200006 |
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no |
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EcoFoG @ eric.marcon @ |
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221 |
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Kenne, M.; Feneron, R.; Djieto-Lordon, C.; Malherbe, M.C.; Tindo, M.; Ngnegueu, P.R.; Dejean, A. |
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Nesting and foraging habits in the arboreal ant Atopomyrmex mocquerysi ANDRE, 1889 (Hymenoptera: Formicidae: Myrmicinae) |
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Journal Article |
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Year |
2009 |
Publication |
Myrmecological News |
Abbreviated Journal |
Myrmecol. News |
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12 |
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Pages |
109-115 |
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Cameroon; wood-excavating ant; nest site selection; pest ant; predatory behavior; rhythm of activity; life history |
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Atopomyrmex mocquerysi ANDRE, 1889 is a West-Central African wood-excavating myrmicine species whose colonies construct galleries in the main live branches of their host trees, causing the distal parts of these branches to dry out. In southeastern Cameroon, this species was mainly found in woody savannahs that are burned annually. It was also present in the canopy of a secondary forest, but was relatively rare on trees growing along forest edges and entirely absent from the canopy of an old-growth forest. It was absent from oil palm and coffee tree plantations, rare on cocoa trees. present on 0.2% to 5.3% of the avocado, guava, mango and Citrus spp. trees monitored, and frequent on safoo trees (12.4%). A fire in a mango plantation seems to have favored its presence. The colonies generally exploit Aleyrodidae, Aphididae, Coccidae, and Stictococcidae. Workers forage for prey diurnally, mostly on the ground. Their predatory behavior is characterized by detection through contact. Workers recruit nestmates at short-range (within range of an alarm pheromone), rarely at long-range, after which they spread-eagle the prey and immediately cut it up on the spot. Individual workers retrieve the prey pieces. Unlike other territorially-dominant arboreal ants, A. mocquerysi is a threat to host trees because. in addition to being a wood-excavating species, its workers only slightly protect the foliage of their host tree from herbivorous insects since they mostly hunt on the ground. |
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[Kenne, Martin; Tindo, Maurice] Univ Douala, Fac Sci, Dept Biol Organismes Anim, Douala, Cameroon, Email: medoum68@yahoo.fr |
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OESTERREICHISCHE GESELL ENTOMOFAUNISTIK, C/O NATURHISTOR MUSEUM WIEN |
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1994-4136 |
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ISI:000271357700012 |
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EcoFoG @ eric.marcon @ |
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97 |
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Orivel, J.; Leroy, C. |
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The diversity and ecology of ant gardens (Hymenoptera: Formicidae; Spermatophyta: Angiospermae) |
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Journal Article |
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Year |
2011 |
Publication |
Myrmecological News |
Abbreviated Journal |
Myrmecol. News |
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Volume |
14 |
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Pages |
73-85 |
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Ant-plant interactions; epiphytes; mutualisms; Neotropics; Paleotropics; phytotelm; parabiosis; seed dispersal; review |
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Mutualistic interactions between ants and plants are important features of many ecosystems, and they can be divided into three main categories: dispersal and protective mutualisms and myrmecotrophy. In both the Neotropics and the Southeastern Asian Paleotropics, ant gardens (AGs), a particular type of ant-plant interaction, are frequent. To initiate AGs, ants integrate the seeds of certain epiphyte species into the carton of their nest. The development of the plants leads to the formation of a cluster of epiphytes rooted in the carton. They have been defined as one of the most complex associations between ants and plants known because of the plurispecific, but also specialized nature of the association involving several phylogenetically-distant ant and plant species. The aim of this review is to provide a synthesis of the diversity and ecology of AGs, including the outcomes experienced by the partners in the interaction and the direct and indirect impacts ant-garden ants have on the plant and arthropod communities. |
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[Orivel, Jerome; Leroy, Celine] CNRS, UMR Ecol Forets Guyane, Kourou 97379, French Guiana, Email: jerome.orivel@ecofog.gf |
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OESTERREICHISCHE GESELL ENTOMOFAUNISTIK, C/O NATURHISTOR MUSEUM WIEN |
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1994-4136 |
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ISI:000286844100009 |
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EcoFoG @ webmaster @ |
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292 |
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Groc, S.; Delabie, J.H.C.; Fernández, F.; Leponce, M.; Orivel, J.; Silvestre, R.; Vasconcelos, H.L.; Dejean, A. |
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Leaf-litter ant communities in a pristine Guianese rainforest: stable functional structure versus high species turnover |
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Journal Article |
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2013 |
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Myrmecological News |
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Myrmecol. News |
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19 |
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43-51 |
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EcoFoG @ webmaster @ |
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523 |
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Groc, S.; Delabie, J.H.C.; Fernández, F.; Leponce, M.; Orivel, J.; Silvestre, R.; Vasconcelos, H.L.; Dejean, A. |
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Title |
Leaf-litter ant communities (Hymenoptera: Formicidae) in a pristine Guianese rain-forest: Stable functional structure versus high species turnover |
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Journal Article |
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2014 |
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Myrmecological News |
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Myrmecological News |
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19 |
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43-51 |
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Diversity gradient; Functional groups; Habitat heterogeneity; Litter-dwelling ant communities; Local scale; Pristine Amazonian rainforest; Taxonomic and functional structure |
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We compared the ant assemblages from four very heterogeneous habitats over a short-distance elevational gradient of vegetation (due to the presence of an inselberg) at the Nouragues Research Station, French Guiana. We focused on litter-dwelling ants, combining the use of pitfall traps and the Winkler method according to the Ants of the Leaf Litter Proto-col. This permitted us to note (1) a high leaf-litter ant diversity overall and a decreasing diversity gradient from the lowland rainforest to the top of the inselberg, and (2) differences in species density, composition and functional struc-ture. While the ant assemblages on the plateau and inselberg can be considered functionally similar and typical of an Amazonian rainforest, that of the transition forest, relatively homogenous, rather corresponded to an ant fauna typical of open areas. By contrast, the liana forest assemblage was unexpectedly richer and denser than the others, sheltering a litter-dwelling ant fauna dominated by numerous and abundant cryptic species. These taxonomical and functional dissi-milarities may reflect the influence of the environmental heterogeneity, which, through variable abiotic conditions, can contribute to maintaining a notably rich ant biodiversity in these Neotropical habitats. |
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Université de Toulouse, UPS (Ecolab), 118 route de Narbonne, 31062 Toulouse Cedex 9, France |
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Export Date: 10 March 2014; Source: Scopus; Language of Original Document: English; Correspondence Address: Groc, S.; Instituto de Biologia, Universidade Federal de Uberlândia (UFU), 38400-902 Uberlândia, Minas Gerais, Brazil; email: groc.sarah@gmail.com |
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