EcoFoG Papers -- Query Results

Tysklind, N., Etienne, M. - P., Scotti-Saintagne, C., Tinaut, A., Casalis, M., Troispoux, V., et al. (2020). Microgeographic local adaptation and ecotype distributions: The role of selective processes on early life-history traits in sympatric, ecologically divergent Symphonia populations. Ecology and Evolution, 10(19), 10735–10753. Abstract: Trees are characterized by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually, only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely on variations in adaptations to microgeographic heterogeneity? and do these processes matter at all in determining tree species distribution and abundance?. We have studied these questions with the Neotropical Symphonia tree species. In the Guiana shield, Symphonia are represented by at least two sympatric taxa or ecotypes, Symphonia globulifera found almost exclusively in bottomlands, and a yet undescribed more generalist taxon/ecotype, Symphonia sp1. A reciprocal transplantation experiment (510 seeds, 16 conditions) was set up and followed over the course of 6 years to evaluate the survival and performance of individuals from different ecotypes and provenances. Germination, survival, growth, and herbivory showed signs of local adaptation, with some combinations of ecotypes and provenances growing faster and surviving better in their own habitat or provenance region. S. globulifera was strongly penalized when planted outside its home habitat but showed the fastest growth rates when planted in its home habitat, suggesting it is a specialist of a high-risk high-gain strategy. Conversely, S. sp1 behaved as a generalist, performing well in a variety of environments. The differential performance of seeds and seedlings in the different habitats matches the known distribution of both ecotypes, indicating that environmental filtering at the very early stages can be a key determinant of tree species distributions, even at the microgeographic level and among very closely related taxa. Furthermore, such differential performance also contributes to explain, in part, the maintenance of the different Symphonia ecotypes living in intimate sympatry despite occasional gene flow. © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd Keywords: determinants of plant community diversity and structure; evolutionary ecology; landscape ecology; local adaptation; Neotropical forest; plant development and life-history traits; reciprocal transplantation experiments; Symphonia http://php.ecofog.gf/refbase/show.php?record=951
Binelli, G., Montaigne, W., Sabatier, D., Scotti-Saintagne, C., & Scotti, I. (2020). Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus. Ecology and Evolution, 10(11), 4726–4738. Abstract: Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the “true” picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology—although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence. © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Keywords: allopatric divergence; Amazon; Guiana Shield; interspecific gene flow; Myristicaceae; secondary contact; Virola http://php.ecofog.gf/refbase/show.php?record=963
Pastorello, G., Trotta, C., Canfora, E., Chu, H., Christianson, D., Cheah, Y. - W., et al. (2020). The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data. Sci Data, 7(1), 225. Abstract: The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible. Keywords: article; breathing; ecophysiology; ecosystem; Eddy covariance; licence; metadata; photosynthesis; pipeline; remote sensing; time series analysis; uncertainty http://php.ecofog.gf/refbase/show.php?record=958
Laybros, A., Aubry-Kientz, M., Féret, J. - B., Bedeau, C., Brunaux, O., Derroire, G., et al. (2020). Quantitative airborne inventories in dense tropical forest using imaging spectroscopy. Remote Sens., 12(10), 1577. Abstract: Tropical forests have exceptional floristic diversity, but their characterization remains incomplete, in part due to the resource intensity of in-situ assessments. Remote sensing technologies can provide valuable, cost-effective, large-scale insights. This study investigates the combined use of airborne LiDAR and imaging spectroscopy to map tree species at landscape scale in French Guiana. Binary classifiers were developed for each of 20 species using linear discriminant analysis (LDA), regularized discriminant analysis (RDA) and logistic regression (LR). Complementing visible and near infrared (VNIR) spectral bands with short wave infrared (SWIR) bands improved the mean average classification accuracy of the target species from 56.1% to 79.6%. Increasing the number of non-focal species decreased the success rate of target species identification. Classification performance was not significantly affected by impurity rates (confusion between assigned classes) in the non-focal class (up to 5% of bias), provided that an adequate criterion was used for adjusting threshold probability assignment. A limited number of crowns (30 crowns) in each species class was sufficient to retrieve correct labels effectively. Overall canopy area of target species was strongly correlated to their basal area over 118 ha at 1.5 ha resolution, indicating that operational application of the method is a realistic prospect (R2 = 0.75 for six major commercial tree species). © 2020 by the authors. Keywords: Hyperspectral; LiDAR; Species diversity; Tropical forest; Cost effectiveness; Discriminant analysis; Infrared devices; Infrared radiation; Logistic regression; Remote sensing; Tropics; Classification accuracy; Classification performance; Linear discriminant analysis; Operational applications; Regularized discriminant analysis; Remote sensing technology; Short wave infrared bands; Visible and near infrared; Forestry http://php.ecofog.gf/refbase/show.php?record=969
Aili, S. R., Touchard, A., Hayward, R., Robinson, S. D., Pineda, S. S., Lalagüe, H., et al. (2020). An integrated proteomic and transcriptomic analysis reveals the venom complexity of the bullet ant Paraponera clavata. Toxins, 12(5). Abstract: A critical hurdle in ant venom proteomic investigations is the lack of databases to comprehensively and specifically identify the sequence and function of venom proteins and peptides. To resolve this, we used venom gland transcriptomics to generate a sequence database that was used to assign the tandem mass spectrometry (MS) fragmentation spectra of venom peptides and proteins to specific transcripts. This was performed alongside a shotgun liquid chromatography-mass spectrometry (LC-MS/MS) analysis of the venom to confirm that these assigned transcripts were expressed as proteins. Through the combined transcriptomic and proteomic investigation of Paraponera clavata venom, we identified four times the number of proteins previously identified using 2D-PAGE alone. In addition to this, by mining the transcriptomic data, we identified several novel peptide sequences for future pharmacological investigations, some of which conform with inhibitor cysteine knot motifs. These types of peptides have the potential to be developed into pharmaceutical or bioinsecticide peptides. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. Keywords: DRG neurons; Hyaluronidase; Neurotoxins; Paraponeritoxin; Phospholipases; Rp-Hplc; alpha latrotoxin; ant venom; arginine kinase; cathepsin; contig; defensin 2; hyaluronidase; icarapin; metalloproteinase; neurotoxin; novel toxin like protein; phospholipase; phospholipase A2; poneratoxin; proteome; serine proteinase; transcriptome; unclassified drug; amino acid sequence; ant; Article; liquid chromatography-mass spectrometry; neurotoxicity; nonhuman; Paraponera clavata; protein expression; proteomics; sequence database; tandem mass spectrometry; transcriptomics; venom gland http://php.ecofog.gf/refbase/show.php?record=972
Longo, M., Saatchi, S., Keller, M., Bowman, K., Ferraz, A., Moorcroft, P. R., et al. (2020). Impacts of Degradation on Water, Energy, and Carbon Cycling of the Amazon Tropical Forests. J. Geophys. Res. Biogeosci., 125(8), e2020JG005677. Abstract: Selective logging, fragmentation, and understory fires directly degrade forest structure and composition. However, studies addressing the effects of forest degradation on carbon, water, and energy cycles are scarce. Here, we integrate field observations and high-resolution remote sensing from airborne lidar to provide realistic initial conditions to the Ecosystem Demography Model (ED-2.2) and investigate how disturbances from forest degradation affect gross primary production (GPP), evapotranspiration (ET), and sensible heat flux (H). We used forest structural information retrieved from airborne lidar samples (13,500 ha) and calibrated with 817 inventory plots (0.25 ha) across precipitation and degradation gradients in the eastern Amazon as initial conditions to ED-2.2 model. Our results show that the magnitude and seasonality of fluxes were modulated by changes in forest structure caused by degradation. During the dry season and under typical conditions, severely degraded forests (biomass loss ≥66%) experienced water stress with declines in ET (up to 34%) and GPP (up to 35%) and increases of H (up to 43%) and daily mean ground temperatures (up to 6.5°C) relative to intact forests. In contrast, the relative impact of forest degradation on energy, water, and carbon cycles markedly diminishes under extreme, multiyear droughts, as a consequence of severe stress experienced by intact forests. Our results highlight that the water and energy cycles in the Amazon are driven by not only climate and deforestation but also the past disturbance and changes of forest structure from degradation, suggesting a much broader influence of human land use activities on the tropical ecosystems. ©2020. The Authors. Keywords: Amazon; drought; ecosystem modeling; evapotranspiration; forest degradation; remote sensing; carbon cycle; deforestation; dry season; evapotranspiration; hydrological cycle; logging (timber); net primary production; remote sensing; sensible heat flux; tropical forest; understory; water stress; Amazon River http://php.ecofog.gf/refbase/show.php?record=957
Do, N. A., Dias, D., Zhang, Z., Huang, X., Nguyen, T. T., Pham, V. V., et al. (2020). Study on the behavior of squared and sub-rectangular tunnels using the Hyperstatic Reaction Method. Transp. Geotech., 22(100321). Keywords: Finite element method; Lining; Squared shape; Sub-rectangular shape; Tunnel; efficiency measurement; finite element method; numerical model; transportation development; transportation planning; tunnel design; tunnel lining http://php.ecofog.gf/refbase/show.php?record=915

Tysklind, N., Etienne, M. - P., Scotti-Saintagne, C., Tinaut, A., Casalis, M., Troispoux, V., et al. (2020). Microgeographic local adaptation and ecotype distributions: The role of selective processes on early life-history traits in sympatric, ecologically divergent Symphonia populations. Ecology and Evolution, 10(19), 10735–10753.

Abstract: Trees are characterized by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually, only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely on variations in adaptations to microgeographic heterogeneity? and do these processes matter at all in determining tree species distribution and abundance?. We have studied these questions with the Neotropical Symphonia tree species. In the Guiana shield, Symphonia are represented by at least two sympatric taxa or ecotypes, Symphonia globulifera found almost exclusively in bottomlands, and a yet undescribed more generalist taxon/ecotype, Symphonia sp1. A reciprocal transplantation experiment (510 seeds, 16 conditions) was set up and followed over the course of 6 years to evaluate the survival and performance of individuals from different ecotypes and provenances. Germination, survival, growth, and herbivory showed signs of local adaptation, with some combinations of ecotypes and provenances growing faster and surviving better in their own habitat or provenance region. S. globulifera was strongly penalized when planted outside its home habitat but showed the fastest growth rates when planted in its home habitat, suggesting it is a specialist of a high-risk high-gain strategy. Conversely, S. sp1 behaved as a generalist, performing well in a variety of environments. The differential performance of seeds and seedlings in the different habitats matches the known distribution of both ecotypes, indicating that environmental filtering at the very early stages can be a key determinant of tree species distributions, even at the microgeographic level and among very closely related taxa. Furthermore, such differential performance also contributes to explain, in part, the maintenance of the different Symphonia ecotypes living in intimate sympatry despite occasional gene flow. © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd

Keywords: determinants of plant community diversity and structure; evolutionary ecology; landscape ecology; local adaptation; Neotropical forest; plant development and life-history traits; reciprocal transplantation experiments; Symphonia

http://php.ecofog.gf/refbase/show.php?record=951

Binelli, G., Montaigne, W., Sabatier, D., Scotti-Saintagne, C., & Scotti, I. (2020). Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus. Ecology and Evolution, 10(11), 4726–4738.

Abstract: Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the “true” picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology—although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence. © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

Keywords: allopatric divergence; Amazon; Guiana Shield; interspecific gene flow; Myristicaceae; secondary contact; Virola

http://php.ecofog.gf/refbase/show.php?record=963

Pastorello, G., Trotta, C., Canfora, E., Chu, H., Christianson, D., Cheah, Y. - W., et al. (2020). The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data. Sci Data, 7(1), 225.

Laybros, A., Aubry-Kientz, M., Féret, J. - B., Bedeau, C., Brunaux, O., Derroire, G., et al. (2020). Quantitative airborne inventories in dense tropical forest using imaging spectroscopy. Remote Sens., 12(10), 1577.

Abstract: Tropical forests have exceptional floristic diversity, but their characterization remains incomplete, in part due to the resource intensity of in-situ assessments. Remote sensing technologies can provide valuable, cost-effective, large-scale insights. This study investigates the combined use of airborne LiDAR and imaging spectroscopy to map tree species at landscape scale in French Guiana. Binary classifiers were developed for each of 20 species using linear discriminant analysis (LDA), regularized discriminant analysis (RDA) and logistic regression (LR). Complementing visible and near infrared (VNIR) spectral bands with short wave infrared (SWIR) bands improved the mean average classification accuracy of the target species from 56.1% to 79.6%. Increasing the number of non-focal species decreased the success rate of target species identification. Classification performance was not significantly affected by impurity rates (confusion between assigned classes) in the non-focal class (up to 5% of bias), provided that an adequate criterion was used for adjusting threshold probability assignment. A limited number of crowns (30 crowns) in each species class was sufficient to retrieve correct labels effectively. Overall canopy area of target species was strongly correlated to their basal area over 118 ha at 1.5 ha resolution, indicating that operational application of the method is a realistic prospect (R2 = 0.75 for six major commercial tree species). © 2020 by the authors.

Keywords: Hyperspectral; LiDAR; Species diversity; Tropical forest; Cost effectiveness; Discriminant analysis; Infrared devices; Infrared radiation; Logistic regression; Remote sensing; Tropics; Classification accuracy; Classification performance; Linear discriminant analysis; Operational applications; Regularized discriminant analysis; Remote sensing technology; Short wave infrared bands; Visible and near infrared; Forestry

http://php.ecofog.gf/refbase/show.php?record=969

Aili, S. R., Touchard, A., Hayward, R., Robinson, S. D., Pineda, S. S., Lalagüe, H., et al. (2020). An integrated proteomic and transcriptomic analysis reveals the venom complexity of the bullet ant Paraponera clavata. Toxins, 12(5).

Longo, M., Saatchi, S., Keller, M., Bowman, K., Ferraz, A., Moorcroft, P. R., et al. (2020). Impacts of Degradation on Water, Energy, and Carbon Cycling of the Amazon Tropical Forests. J. Geophys. Res. Biogeosci., 125(8), e2020JG005677.

Abstract: Selective logging, fragmentation, and understory fires directly degrade forest structure and composition. However, studies addressing the effects of forest degradation on carbon, water, and energy cycles are scarce. Here, we integrate field observations and high-resolution remote sensing from airborne lidar to provide realistic initial conditions to the Ecosystem Demography Model (ED-2.2) and investigate how disturbances from forest degradation affect gross primary production (GPP), evapotranspiration (ET), and sensible heat flux (H). We used forest structural information retrieved from airborne lidar samples (13,500 ha) and calibrated with 817 inventory plots (0.25 ha) across precipitation and degradation gradients in the eastern Amazon as initial conditions to ED-2.2 model. Our results show that the magnitude and seasonality of fluxes were modulated by changes in forest structure caused by degradation. During the dry season and under typical conditions, severely degraded forests (biomass loss ≥66%) experienced water stress with declines in ET (up to 34%) and GPP (up to 35%) and increases of H (up to 43%) and daily mean ground temperatures (up to 6.5°C) relative to intact forests. In contrast, the relative impact of forest degradation on energy, water, and carbon cycles markedly diminishes under extreme, multiyear droughts, as a consequence of severe stress experienced by intact forests. Our results highlight that the water and energy cycles in the Amazon are driven by not only climate and deforestation but also the past disturbance and changes of forest structure from degradation, suggesting a much broader influence of human land use activities on the tropical ecosystems. ©2020. The Authors.

Keywords: Amazon; drought; ecosystem modeling; evapotranspiration; forest degradation; remote sensing; carbon cycle; deforestation; dry season; evapotranspiration; hydrological cycle; logging (timber); net primary production; remote sensing; sensible heat flux; tropical forest; understory; water stress; Amazon River

http://php.ecofog.gf/refbase/show.php?record=957

Do, N. A., Dias, D., Zhang, Z., Huang, X., Nguyen, T. T., Pham, V. V., et al. (2020). Study on the behavior of squared and sub-rectangular tunnels using the Hyperstatic Reaction Method. Transp. Geotech., 22(100321).