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Marcon, E., Traissac, S., & Lang, G. (2013). A Statistical Test for Ripley’s Function Rejection of Poisson Null Hypothesis. ISRN Ecology, 2013(Article ID 753475), 9.
Abstract: Ripley’s K function is the classical tool to characterize the spatial structure of point patterns. It is widely used in vegetation studies. Testing its values against a null hypothesis usually relies on Monte-Carlo simulations since little is known about its distribution.
We introduce a statistical test against complete spatial randomness (CSR). The test returns the p-value to reject the null hypothesis of independence between point locations. It is more rigorous and faster than classical Monte-Carlo simulations. We show how to apply it to a tropical forest plot. The necessary R code is provided.
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Mortier, F., Rossi, V., Guillot, G., Gourlet-Fleury, S., & Picard, N. (2013). Population dynamics of species-rich ecosystems: The mixture of matrix population models approach. Methods Ecol. Evol., 4(4), 316–326.
Abstract: Matrix population models are widely used to predict population dynamics, but when applied to species-rich ecosystems with many rare species, the small population sample sizes hinder a good fit of species-specific models. This issue can be overcome by assigning species to groups to increase the size of the calibration data sets. However, the species classification is often disconnected from the matrix modelling and from the estimation of matrix parameters, thus bringing species groups that may not be optimal with respect to the predicted community dynamics. We proposed here a method that jointly classified species into groups and fit the matrix models in an integrated way. The model was a special case of mixture with unknown number of components and was cast in a Bayesian framework. An MCMC algorithm was developed to infer the unknown parameters: the number of groups, the group of each species and the dynamics parameters. We applied the method to simulated data and showed that the algorithm efficiently recovered the model parameters. We applied the method to a data set from a tropical rain forest in French Guiana. The mixture matrix model classified tree species into well-differentiated groups with clear ecological interpretations. It also accurately predicted the forest dynamics over the 16-year observation period. Our model and algorithm can straightforwardly be adapted to any type of matrix model, using the life cycle diagram. It can be used as an unsupervised classification technique to group species with similar population dynamics. © 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society.
Keywords: Bayesian; Clustering; Mixture models; Population dynamics; Reversible jump Markov chain Monte Carlo; Species-rich ecosystems; Tropical rain forests
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Hibert, F., Taberlet, P., Chave, J., Scotti-Saintagne, C., Sabatier, D., & Richard-Hansen, C. (2013). Unveiling the Diet of Elusive Rainforest Herbivores in Next Generation Sequencing Era? The Tapir as a Case Study. PLoS ONE, 8(4), e60799.
Abstract: Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem. © 2013 Hibert et al.
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Tritsch, I., Gond, V., Oszwald, J., Davy, D., & Grenand, P. (2012). Territorial dynamics in the wayãpi and teko amerindian communities of the middle oyapock, camopi, French Guiana. Bois Forets Tropiques, 66(311), 49–61.
Abstract: Amerindian populations have been experiencing major socio-economic changes for several decades, in a context of rapid demographic growth. This article addresses the ways in which the Amerindian populations of French Guiana have adapted their land use and natural resource management systems to cope with the pressures exerted on their lands and lifestyles. The aim was to investigate the resilience of their systems for land and natural resource use. The concentration of Amerindian habitats around the town of Camopi, which is linked to the availability of health and school infrastructure and to efforts to promote a sedentary lifestyle, is a factor of increasing natural resource scarcity and social alienation. The system is adapting by fragmenting the Amerindian habitat into peripheral villages and extending farmlands along rivers to access to more space. These villages replicate patterns of spatial organisation that are similar to those found in traditional Wayãpi and Teko villages, except that habitation is sedentary, as families hope to have their villages equipped with at lEast drinking water and electrification. Habitat fragmentation is spatially limited by the time taken for daily journeys to school, and therefore by school bus services (dugout), which means that land use is effectively conditioned by services and infrasrtucture. Other living quarters are maintained at a distance from the village, so that the habitat is bi-local: families have a main home where services and infrastructure are available, and a secondary itinerant home further away, which is chosen according to the quality of farmland, the hunting yield of hunting resources, the history of the location and family networks. These distant homes are kept up by spending income from social assistance on transport. It's thus shown that these Amerindian systems for land and natural resource uses are highly adaptable, in that their sustainability is guaranteed by the reconstruction of a circular pattern of mobility in accordance with the intensity of resource use.
Keywords: Amerindian populations; French Guiana; Protected area; Slash-and-burn cultivation; System of natural resource use; Territorial management
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Ntienoue, J. K., Reguer, A., Robert, F., Nait-Rabah, O., & Roos, C. (2013). Electrochemical behaviour of a super austenitic stainless steel in amazonian aqueous environment. Int.J.Electrochem.Sci., 8(4), 4761–4775.
Abstract: The electrochemical behaviour of 254 SMO super austenitic stainless steel in natural seawater collected from river mouth of French Guiana was investigated. A comparative study of samples immersed during 22 days in this environment was made including influences of scraped biofilm introduced in experiments and of stirring. Electrochemical measurements – open circuit potential (OCP), electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV) and linear polarisation (LP) – are used to characterize the metal/medium interface included biofilms adhesion. The EDX analysis (EDAX system) shows that the chemical composition of adhered biofilm consists mostly of iron, oxygen, silicon and aluminium and seem preferentially bind on metal defects. © 2013 by ESG.
Keywords: Cyclic voltammetry; Eis; Esem; Passive films; Stainless steel
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Arranz, S. E., Avarre, J. - C., Balasundaram, C., Bouza, C., Calcaterra, N. B., Cezilly, F., et al. (2013). Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2012-31 January 2013. Mol. Ecol. Resour., 13(3), 546–549.
Abstract: This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba. © 2013 Blackwell Publishing Ltd.
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Baraloto, C., Molto, Q., Rabaud, S., Herault, B., Valencia, R., Blanc, L., et al. (2013). Rapid simultaneous estimation of aboveground biomass and tree diversity across neotropical forests: A comparison of field inventory methods. Biotropica, 45(3), 288–298.
Abstract: A standardized rapid inventory method providing information on both tree species diversity and aboveground carbon stocks in tropical forests will be an important tool for evaluating efforts to conserve biodiversity and to estimate the carbon emissions that result from deforestation and degradation (REDD). Herein, we contrast five common plot methods differing in shape, size, and effort requirements to estimate tree diversity and aboveground tree biomass (AGB). We simulated the methods across six Neotropical forest sites that represent a broad gradient in forest structure, tree species richness, and floristic composition, and we assessed the relative performance of methods by evaluating the bias and precision of their estimates of AGB and tree diversity. For a given sample of forest area, a 'several small' (< 1 ha) sampling strategy led to a smaller coefficient of variation (CV) in the estimate of AGB than a 'few large' one. The effort (person-days) required to achieve an accurate AGB estimate (< 10% CV), however, was greater for the smallest plots (0.1 ha) than for a compromise approach using 0.5 ha modified Gentry plots, which proved to be the most efficient method to estimate AGB across all forest types. Gentry plots were also the most efficient at providing accurate estimates of tree diversity (< 10% CV of Hill number). We recommend the use of the 0.5 ha modified Gentry plot method in future rapid inventories, and we discuss a set of criteria that should inform any choice of inventory method. © 2012 The Author(s) Journal compilation © 2012 by The Association for Tropical Biology and Conservation.
Keywords: Biodiversity assessment; carbon stocks; Monitoring; Permanent plot; Survey; Tropical rain forest
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Aubry-Kientz, M., Herault, B., Ayotte-Trépanier, C., Baraloto, C., & Rossi, V. (2013). Toward Trait-Based Mortality Models for Tropical Forests. PLoS ONE, 8(5), e63678.
Abstract: Tree mortality in tropical forests is a complex ecological process for which modelling approaches need to be improved to better understand, and then predict, the evolution of tree mortality in response to global change. The mortality model introduced here computes an individual probability of dying for each tree in a community. The mortality model uses the ontogenetic stage of the tree because youngest and oldest trees are more likely to die. Functional traits are integrated as proxies of the ecological strategies of the trees to permit generalization among all species in the community. Data used to parametrize the model were collected at Paracou study site, a tropical rain forest in French Guiana, where 20,408 trees have been censused for 18 years. A Bayesian framework was used to select useful covariates and to estimate the model parameters. This framework was developed to deal with sources of uncertainty, including the complexity of the mortality process itself and the field data, especially historical data for which taxonomic determinations were uncertain. Uncertainty about the functional traits was also considered, to maximize the information they contain. Four functional traits were strong predictors of tree mortality: wood density, maximum height, laminar toughness and stem and branch orientation, which together distinguished the light-demanding, fast-growing trees from slow-growing trees with lower mortality rates. Our modelling approach formalizes a complex ecological problem and offers a relevant mathematical framework for tropical ecologists to process similar uncertain data at the community level. © 2013 Aubry-Kientz et al.
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Vedel, V., & Lalague, H. (2013). Standardized sampling protocol for spider community assessment in the Neotropical rainforest. J. Entomol. Zool. Stud., 2(1), 18–34.
Abstract: We described, here, a standardized protocol to collect the maximum number of spiders per unit of effort from the different strata of a tropical forestry habitat. This would allow quantifying the richness of a site and would allow spatial and temporal comparisons between sites. This protocol was tested and applied in a pilot study at four sites representing three different forestry habitats of the natural reserve of La Trinité (French Guiana). Results showed every feeding guild was well represented and most of the 30 families found are represented by several individuals. Indices of species richness, number of singletons, species richness estimators from the accumulation curves and diversity and similarity indices were also calculated and all indicated that La Trinité is a rich and diverse site for spiders. The standardized protocol showed here its efficiency and its wide cover of micro-habitats and is, therefore, recommended for any impact assessment or diversity of spider study in tropical forestry environment.
Keywords: Araneae; Biodiversity; French Guiana; Guianese Shield; Impact Assessment
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Foucaud, J., Rey, O., Robert, S., Crespin, L., Orivel, J., Facon, B., et al. (2013). Thermotolerance adaptation to human-modified habitats occurs in the native range of the invasive ant Wasmannia auropunctata before long-distance dispersal. Evol. Appl., 6(4), 721–734.
Abstract: Key evolutionary events associated with invasion success are traditionally thought to occur in the introduced, rather than the native range of species. In the invasive ant Wasmannia auropunctata, however, a shift in reproductive system has been demonstrated within the native range, from the sexual non-dominant populations of natural habitats to the clonal dominant populations of human-modified habitats. Because abiotic conditions of human- modified habitats are hotter and dryer, we performed lab experiments on workers from a set of native and introduced populations, to investigate whether these ecological and genetic transitions were accompanied by a change in thermotolerance and whether such changes occurred before establishment in the introduced range. Thermotolerance levels were higher in native populations from human-modified habitats than in native populations from natural habitats, but were similar in native and introduced populations from human-modified habitats. Differences in thermotolerance could not be accounted for by differences in body size. A scenario based on local adaptation in the native range before introduction in remote areas represents the most parsimonious hypothesis to account for the observed phenotypic pattern. These findings highlight the importance of human land use in explaining major contemporary evolutionary changes. © 2013 The Authors.
Keywords: Adaptation; Heat shock; Invasive species; Natural selection and contemporary evolution; Thermotolerance
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