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Lalague, H.; Csilléry, K.; Oddou-Muratorio, S.; Safrana, J.; de Quattro, C.; Fady, B.; González-Martínez, S.C.; Vendramin, G.G. |
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Nucleotide diversity and linkage disequilibrium at 58 stress response and phenology candidate genes in a European beech (Fagus sylvatica L.) population from southeastern France |
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2014 |
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Tree Genetics and Genomes |
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Tree Genetics and Genomes |
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10 |
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1 |
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15-26 |
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Climate adaptation; Effective population size; Forest tree; Genomic diversity; Minor allele frequency (MAF); Recombination rate; Single nucleotide polymorphism (SNP) |
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European beech (Fagus sylvatica L.) is one of the most economically and ecologically important deciduous trees in Europe, yet little is known about its genomic diversity and its adaptive potential. Here, we detail the discovery and analysis of 573 single nucleotide polymorphisms (SNPs) from 58 candidate gene fragments that are potentially involved in abiotic stress response and budburst phenology using a panel of 96 individuals from southeastern France. The mean nucleotide diversity was low (θ π = 2.2 × 10-3) but extremely variable among gene fragments (range from 0.02 to 10), with genes carrying insertion/deletion mutations exhibiting significantly higher diversity. The decay of linkage disequilibrium (LD) measured at gene fragments >800 base pairs was moderate (the half distance of r 2 was 154 bp), consistent with the low average population-scaled recombination rate (ρ = 5.4 × 10-3). Overall, the population-scaled recombination rate estimated in F. sylvatica was lower than for other angiosperm tree genera (such as Quercus or Populus) and similar to conifers. As a methodological perspective, we explored the effect of minimum allele frequency (MAF) on LD and showed that higher MAF resulted in slower decay of LD. It is thus essential that the same MAF is used when comparing the decay of LD among different studies and species. Our results suggest that genome-wide association mapping can be a potentially efficient approach in F. sylvatica, which has a relatively small genome size. © 2013 Springer-Verlag Berlin Heidelberg. |
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Department of Forest Ecology and Genetics, National Institute for Agriculture and Food Research and Technology (INIA), Forest Research Centre (CIFOR), 28040 Madrid, Spain |
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Cited By :1; Export Date: 13 January 2015 |
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EcoFoG @ webmaster @ |
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578 |
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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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2014 |
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Molecular Ecology |
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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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Réjou-Méchain, M.; Muller-Landau, H.C.; Detto, M.; Thomas, S.C.; Le Toan, T.; Saatchi, S.S.; Barreto-Silva, J.S.; Bourg, N.A.; Bunyavejchewin, S.; Butt, N.; Brockelman, W.Y.; Cao, M.; Cárdenas, D.; Chiang, J.-M.; Chuyong, G.B.; Clay, K.; Condit, R.; Dattaraja, H.S.; Davies, S.J.; Duque, A.; Esufali, S.; Ewango, C.; Fernando, R.H.S.; Fletcher, C.D.; N. Gunatilleke, I.A.U.; Hao, Z.; Harms, K.E.; Hart, T.B.; Herault, B.; Howe, R.W.; Hubbell, S.P.; Johnson, D.J.; Kenfack, D.; Larson, A.J.; Lin, L.; Lin, Y.; Lutz, J.A.; Makana, J.-R.; Malhi, Y.; Marthews, T.R.; Mcewan, R.W.; Mcmahon, S.M.; Mcshea, W.J.; Muscarella, R.; Nathalang, A.; Noor, N.S.M.; Nytch, C.J.; Oliveira, A.A.; Phillips, R.P.; Pongpattananurak, N.; Punchi-Manage, R.; Salim, R.; Schurman, J.; Sukumar, R.; Suresh, H.S.; Suwanvecho, U.; Thomas, D.W.; Thompson, J.; Uríarte, M.; Valencia, R.; Vicentini, A.; Wolf, A.T.; Yap, S.; Yuan, Z.; Zartman, C.E.; Zimmerman, J.K.; Chave, J. |
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Local spatial structure of forest biomass and its consequences for remote sensing of carbon stocks |
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2014 |
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Biogeosciences |
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Biogeosciences |
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11 |
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23 |
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6827-6840 |
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Advances in forest carbon mapping have the potential to greatly reduce uncertainties in the global carbon budget and to facilitate effective emissions mitigation strategies such as REDD+ (Reducing Emissions from Deforestation and Forest Degradation). Though broad-scale mapping is based primarily on remote sensing data, the accuracy of resulting forest carbon stock estimates depends critically on the quality of field measurements and calibration procedures. The mismatch in spatial scales between field inventory plots and larger pixels of current and planned remote sensing products for forest biomass mapping is of particular concern, as it has the potential to introduce errors, especially if forest biomass shows strong local spatial variation. Here, we used 30 large (8-50 ha) globally distributed permanent forest plots to quantify the spatial variability in aboveground biomass density (AGBD in Mg ha-1) at spatial scales ranging from 5 to 250 m (0.025-6.25 ha), and to evaluate the implications of this variability for calibrating remote sensing products using simulated remote sensing footprints. We found that local spatial variability in AGBD is large for standard plot sizes, averaging 46.3% for replicate 0.1 ha subplots within a single large plot, and 16.6% for 1 ha subplots. AGBD showed weak spatial autocorrelation at distances of 20-400 m, with autocorrelation higher in sites with higher topographic variability and statistically significant in half of the sites. We further show that when field calibration plots are smaller than the remote sensing pixels, the high local spatial variability in AGBD leads to a substantial “dilution” bias in calibration parameters, a bias that cannot be removed with standard statistical methods. Our results suggest that topography should be explicitly accounted for in future sampling strategies and that much care must be taken in designing calibration schemes if remote sensing of forest carbon is to achieve its promise. |
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Institute of Biology University of the Philippines DilimanQuezon City, Philippines |
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Cited By :1; Export Date: 30 January 2015 |
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EcoFoG @ webmaster @ |
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582 |
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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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589 |
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Barantal, S.; Schimann, H.; Fromin, N.; Hättenschwiler, S. |
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C, N and P fertilization in an Amazonian rainforest supports stoichiometric dissimilarity as a driver of litter diversity effects on decomposition |
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2014 |
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Proceedings. Biological sciences / The Royal Society |
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Proceedings. Biological sciences / The Royal Society |
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281 |
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1796 |
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20141682 |
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litter diversity; neotropical forest; nutrient addition; soil fauna; stoichiometry; trait dissimilarity |
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Plant leaf litter generally decomposes faster as a group of different species than when individual species decompose alone, but underlying mechanisms of these diversity effects remain poorly understood. Because resource C : N : P stoichiometry (i.e. the ratios of these key elements) exhibits strong control on consumers, we supposed that stoichiometric dissimilarity of litter mixtures (i.e. the divergence in C : N : P ratios among species) improves resource complementarity to decomposers leading to faster mixture decomposition. We tested this hypothesis with: (i) a wide range of leaf litter mixtures of neotropical tree species varying in C : N : P dissimilarity, and (ii) a nutrient addition experiment (C, N and P) to create stoichiometric similarity. Litter mixtures decomposed in the field using two different types of litterbags allowing or preventing access to soil fauna. Litter mixture mass loss was higher than expected from species decomposing singly, especially in presence of soil fauna. With fauna, synergistic litter mixture effects increased with increasing stoichiometric dissimilarity of litter mixtures and this positive relationship disappeared with fertilizer addition. Our results indicate that litter stoichiometric dissimilarity drives mixture effects via the nutritional requirements of soil fauna. Incorporating ecological stoichiometry in biodiversity research allows refinement of the underlying mechanisms of how changing biodiversity affects ecosystem functioning. © 2014 The Author(s) Published by the Royal Society. All rights reserved. |
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Centre d'Ecologie Fonctionnelle et Evolutive (CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE), 1919 Route de MENDE, 34293 Montpellier Cedex 5, France |
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Export Date: 24 July 2015 |
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Moore, A.L.; McCarthy, M.A.; Parris, K.M.; Moore, J.L. |
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The optimal number of surveys when detectability varies |
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2014 |
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PLoS ONE |
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PLoS ONE |
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9 |
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12 |
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e115345 |
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The survey of plant and animal populations is central to undertaking field ecology. However, detection is imperfect, so the absence of a species cannot be determined with certainty. Methods developed to account for imperfect detectability during surveys do not yet account for stochastic variation in detectability over time or space. When each survey entails a fixed cost that is not spent searching (e.g., time required to travel to the site), stochastic detection rates result in a trade-off between the number of surveys and the length of each survey when surveying a single site. We present a model that addresses this trade-off and use it to determine the number of surveys that: 1) maximizes the expected probability of detection over the entire survey period; and 2) is most likely to achieve a minimally-acceptable probability of detection. We illustrate the applicability of our approach using three practical examples (minimum survey effort protocols, number of frog surveys per season, and number of quadrats per site to detect a plant species) and test our model's predictions using data from experimental plant surveys. We find that when maximizing the expected probability of detection, the optimal survey design is most sensitive to the coefficient of variation in the rate of detection and the ratio of the search budget to the travel cost. When maximizing the likelihood of achieving a particular probability of detection, the optimal survey design is most sensitive to the required probability of detection, the expected number of detections if the budget were spent only on searching, and the expected number of detections that are missed due to travel costs. We find that accounting for stochasticity in detection rates is likely to be particularly important for designing surveys when detection rates are low. Our model provides a framework to do this. © 2014 Moore et al. |
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School of Biological Sciences, Monash University, Melbourne, VIC, Australia |
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Export Date: 8 September 2015 |
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618 |
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Bompy, F.; Lequeue, G.; Imbert, D.; Dulormne, M. |
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Increasing fluctuations of soil salinity affect seedling growth performances and physiology in three Neotropical mangrove species |
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2014 |
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Plant and Soil |
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Plant and Soil |
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380 |
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1 |
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399-413 |
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Acclimation; Avicennia germinans; Hypersalinity; Laguncularia racemosa; Leaf gas exchange; Rhizophora mangle; Salt stress |
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Background: Micro-tidal wetlands are subject to strong seasonal variations of soil salinity that are likely to increase in amplitude according to climate model predictions for the Caribbean. Whereas the effects of constant salinity levels on the physiology of mangrove species have been widely tested, little is known about acclimation to fluctuations in salinity. Aims and methods: The aim of this experiment was to characterize the consequences of the rate of increase in salinity (slow versus fast) and salinity fluctuations over time versus constant salt level. Seedling mortality, growth, and leaf gas exchange of three mangrove species, Avicennia germinans, Laguncularia racemosa, and Rhizophora mangle were investigated in semicontrolled conditions at different salt levels (0, 685, 1025, and 1370 mM NaCl). Results: Slow salinity increase up to 685 mM induced acclimation, improving the salt tolerance of A. germinans and L. racemosa, but had no effect on R. mangle. During fluctuations between 0 and 685 mM, A. germinans and R. mangle were not affected by a salinity drop to zero, whereas L. racemosa took advantage of the brief freshwater episode as shown by the durable improvement of photosynthesis and biomass production. Conclusions: This study provides new insights into physiological resistance and acclimation to salt stress. We show that seasonal variations of salinity may affect mangrove seedlings' morphology and physiology as much as annual mean salinity. Moreover, more severe dry seasons due to climate change may impact tree stature and species composition in mangroves through higher mortality rates and physiological disturbance at the seedling stage. © 2014 Springer International Publishing Switzerland. |
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EA 926 DYNECAR, UFR des Sciences Exactes et Naturelles, Université des Antilles et de la Guyane, BP 592, 97 159 Pointe-à-Pitre cedex, Guadeloupe (F.W.I.), France |
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Cited By :7; Export Date: 7 February 2017 |
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726 |
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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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Temporal coherence of tropical forests at P-band: Dry and rainy seasons |
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2015 |
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IEEE Geoscience and Remote Sensing Letters |
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IEEE Geosci. Remote Sens. Lett. |
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12 |
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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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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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Lachenaud, P.; Rossi, V.; Thevenin, J.-M.; Doaré, F. |
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The “Guiana” genetic group: A new source of resistance to cacao (Theobroma cacao L.) black pod rot caused by Phytophthora capsici |
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2015 |
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Crop Protection |
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Crop Prot. |
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67 |
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91-95 |
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Black pod; Cocoa; French guiana; Phytophthora capsici; Resistance; Phytophthora capsici; Theobroma cacao |
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Black pod rot, caused by Stramenopiles of the genus Phytophthora, leads to serious production losses in all cocoa growing zones. In order to reduce the impact of these pests, preference is given to genetic control using resistant varieties, and sources of resistance are actively being sought, particularly in wild cacao trees. Surveys were undertaken in the natural cacao tree populations of south-eastern French Guiana between 1985 and 1995 and an abundant amount of plant material belonging to a particular genetic group, the “Guiana” group, was collected. A great deal of work has shown the merits of this genetic group as a source of resistance to Phytophthora palmivora and megakarya. We describe here the results of a global study to assess the resistance of the 186 clones in the “Guiana” group “core collection” to a Guianese strain of Phytophthora capsici (strain Reg 2-6). This study, which used an efficient methodology (fifteen series of tests on leaf discs and a statistical test adapted to the ordinal nature of the basic data), showed that the “Guiana” genetic group is a major source of resistance to P.capsici. Strain Reg 2-6 proves to be particularly virulent, as the Scavina 6 control, an international reference for resistance to Phytophthora, is not resistant to it. However, 24 clones of the “Guiana” group are, and 92 have proved to be more resistant than Scavina 6, thereby showing the interest of the group in genetically controlling P.capsici.Thus, of the clones in the Guiana group that are more resistant to P.capsici than Scavina 6, some, which are also resistant to P.palmivora and/or Phytophthora megakarya, and also displaying some other notable qualities, could be incorporated into cocoa genetic improvement programmes in countries where P.capsici is rife on cacao trees. |
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CIRAD, UPR BSEF, BP 2572Yaoundé, Cameroon |
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Elsevier Ltd |
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Export Date: 12 November 2014; Coden: Crptd; Correspondence Address: Lachenaud, P.; CIRAD, UPR 106, BP 701, France |
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EcoFoG @ webmaster @ |
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565 |
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Sist, P.; Rutishauser, E.; Peña-Claros, M.; Shenkin, A.; Herault, B.; Blanc, L.; Baraloto, C.; Baya, F.; Benedet, F.; da Silva, K.E.; Descroix, L.; Ferreira, J.N.; Gourlet-Fleury, S.; Guedes, M.C.; Bin Harun, I.; Jalonen, R.; Kanashiro, M.; Krisnawati, H.; Kshatriya, M.; Lincoln, P.; Mazzei, L.; Medjibé, V.; Nasi, R.; d'Oliveira, M.V.N.; de Oliveira, L.C.; Picard, N.; Pietsch, S.; Pinard, M.; Priyadi, H.; Putz, F.E.; Rodney, K.; Rossi, V.; Roopsind, A.; Ruschel, A.R.; Shari, N.H.Z.; Rodrigues de Souza, C.; Susanty, F.H.; Sotta, E.D.; Toledo, M.; Vidal, E.; West, T.A.P.; Wortel, V.; Yamada, T. |
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The Tropical managed forests Observatory: A research network addressing the future of tropical logged forests |
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2015 |
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Applied Vegetation Science |
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Appl. Veg. Sci. |
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18 |
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1 |
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171-174 |
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Biodiversity; Carbon cycle; Climate change; Ecosystem resilience; Logging; Silviculture; Tropical forests; Tropical managed forests Observatory |
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While attention on logging in the tropics has been increasing, studies on the long-term effects of silviculture on forest dynamics and ecology remain scare and spatially limited. Indeed, most of our knowledge on tropical forests arises from studies carried out in undisturbed tropical forests. This bias is problematic given that logged and disturbed tropical forests are now covering a larger area than the so-called primary forests. A new network of permanent sample plots in logged forests, the Tropical managed Forests Observatory (TmFO), aims to fill this gap by providing unprecedented opportunities to examine long-term data on the resilience of logged tropical forests at regional and global scales. TmFO currently includes 24 experimental sites distributed across three tropical regions, with a total of 490 permanent plots and 921 ha of forest inventories. To improve our knowledge of the resilience of tropical logged forests, 20 research institutes are now collaborating on studies on the effects of logging on forest structure, productivity, biodiversity and carbon fluxes at large spatial and temporal scales. These studies are carried out in the Tropical managed Forests Observatory (TmFO), an international network including 24 sites and 490 permanent sample plots across South America, Africa and South East Asia. |
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Duke University's Nicholas School of the EnvironmentNorth Carolina, United States |
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Wiley-Blackwell |
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14022001 (Issn) |
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Export Date: 12 December 2014; Coden: Avscf; Correspondence Address: Sist, P.; Cirad, UR 105 TA/10CFrance |
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EcoFoG @ webmaster @ |
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571 |
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