104 Works

Data from: A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania

Nathalie Smitz, Olivia Jouvenet, Fredrick Ambwene Ligate, William-George Crosmary, Dennis Ikanda, Philippe Chardonnet, Alessandro Fusari, Kenny Meganck, François Gillet, Mario Melletti & Johan R. Michaux
The African lion (Panthera leo), listed as a vulnerable species on the IUCN Red List of Threatened Species (Appendix II of CITES), is mainly impacted by indiscriminate killing and prey base depletion. Additionally, habitat loss by land degradation and conversion has led to the isolation of some subpopulations, potentially decreasing gene flow and increasing inbreeding depression risks. Genetic drift resulting from weakened connectivity between strongholds can affect the genetic health of the species. In the...

Data from: A combinatorial analysis using observational data identifies species that govern ecosystem functioning

Benoît Jaillard, Philippe Deleporte, Michel Loreau & Cyrille Violle
Understanding the relationship between biodiversity and ecosystem functioning has so far resulted from two main approaches: the analysis of species' functional traits, and the analysis of species interaction networks. Here we propose a third approach, based on the association between combinations of species or of functional groups, which we term assembly motifs, and observed ecosystem functioning. Each assembly motif describes a biotic environment in which species interactions have particular effects on a given ecosystem function....

Data from: Fungal endophytes of Vanilla planifolia across Réunion Island: isolation, distribution and biotransformation.

Shahnoo Khoyratty, Joëlle Dupont, Sandrine Lacoste, Tony L. Palama, Young H. Choi, Hye K. Kim, Bertrand Payet, Michel Grisoni, Mireille Fouillaud, Robert Verpoorte & Hippolyte Kodja
Background The objective of the work was to characterize fungal endophytes from aerial parts of Vanilla planifolia. Also, to establish their biotransformation abilities of flavor-related metabolites. This was done in order to find a potential role of endophytes on vanilla flavors. Results Twenty three MOTUs were obtained, representing 6 fungal classes. Fungi from green pods were cultured on mature green pod based media for 30 days followed by 1H NMR and HPLC-DAD analysis. All fungi...

Data from: The determinants of tropical forest deciduousness: disentangling the effects of rainfall and geology in central Africa

Dakis-Yaoba Ouédraogo, Adeline Fayolle, Sylvie Gourlet-Fleury, Frédéric Mortier, Vincent Freycon, Nicolas Fauvet, Suzanne Rabaud, Guillaume Cornu, Fabrice Bénédet, Jean-François Gillet, Richard Oslisly, Jean-Louis Doucet, Philippe Lejeune & Charly Favier
Understanding the environmental determinants of forests deciduousness i.e. proportion of deciduous trees in a forest stand, is of great importance when predicting the impact of ongoing global climate change on forests. In this study, we examine (i) how forest deciduousness varies in relation to rainfall and geology, and (ii) whether the influence of geology on deciduousness could be related to differences in soil fertility and water content between geological substrates. The study was conducted in...

Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Daniel S. Karp, Rebecca Chaplin-Kramer, Timothy D. Meehan, Emily A. Martin, Fabrice DeClerck, Heather Grab, Claudio Gratton, Lauren Hunt, Ashley E. Larsen, Alejandra Martínez-Salinas, Megan E. O’Rourke, Adrien Rusch, Katja Poveda, Mattias Jonsson, Jay A. Rosenheim, Nancy A. Schellhorn, Teja Tscharntke, Stephen D. Wratten, Wei Zhang, Aaron L. Iverson, Lynn S. Adler, Matthias Albrecht, Audrey Alignier, Gina M. Angelella, Muhammad Zubair Anjum … & Yi Zou
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are...

Data from: Ploidy and domestication are associated with genome size variation in Palms

Bee F. Gunn, Luc Baudouin, Thierry Beulé, Pascal Ilbert, Christophe Duperray, Michael Crisp, Auguste Issali, Jean-Louis Konan & Alain Rival
PREMISE OF THE STUDY: The genome size of a species (C-value) is associated with growth, development and adaptation to environmental changes. Angiosperm C-values range 1200-fold and frequently vary within species, although little is known about the impacts of domestication on genome size. Genome size variation among related species of palms is of evolutionary significance because changes characterize clades and may be associated with polyploidy, transposon amplifications, deletions, or rearrangements. Further knowledge of genome size will...

Data from: Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield

Stéphanie Barthe, Giorgio Binelli, Bruno Hérault, Caroline Scotti-Saintagne, Daniel Sabatier & Ivan Scotti
How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on...

Data from: Taxonomic and functional composition of arthropod assemblages across contrasting Amazonian forests

P. A. Greg Lamarre, Bruno Hérault, Paul V. A. Fine, Vincent Vedel, Roland Lupoli, Italo Mesones, Christopher Baraloto & Greg P. A. Lamarre
Arthropods represent most of global biodiversity, with the highest diversity found in tropical rainforests. Nevertheless, we have a very incomplete understanding of how tropical arthropod communities are assembled. We conducted a comprehensive mass-sampling of arthropod communities within three major habitat types of lowland Amazonian rainforest, including terra firme clay, white-sand, and seasonally-flooded forests in Peru and French Guiana. We examined how taxonomic and functional composition (at the family level) differed across these habitat types in...

Data from: Understanding the recent colonization history of a plant pathogenic fungus using population genetic tools and Approximate Bayesian Computation

Benoit Barrès, Jean Carlier, Marc Seguin, Catherine Fenouillet, Christian Cilas & Viginie Ravigné
Understanding the processes by which new diseases are introduced in previously healthy areas is of major interest in elaborating prevention and management policies as well as in understanding the dynamics of pathogen diversity at large spatial scale. In this study, we aimed to decipher the dispersal processes that have led to the emergence of the plant pathogenic fungus Microcyclus ulei, which is responsible for the South American Leaf Blight (SALB) that has affected rubber trees...

Data from: Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations

Marie-Pierre Chapuis, Christophe Plantamp, Réjane Streiff, Laurence Blondin, Cyril Piou & M.-P. Chapuis
Unravelling variation among taxonomic orders regarding the rate of evolution in microsatellites is crucial for evolutionary biology and population genetics research. The mean mutation rate of microsatellites tends to be lower in arthropods than in vertebrates, but data are scarce and mostly concern accumulation of mutations in model species. Based on parent-offspring segregations and a hierarchical Bayesian model, the mean rate of mutation in the orthopteran insect Schistocerca gregaria was estimated at 2.1e-4 per generation...

Data from: Architectural differences associated to functional traits among 45 coexisting tree species in central Africa

Grace Jopaul Loubota Panzou, Gauthier Ligot, Sylvie Gourlet-Fleury, Jean-Louis Doucet, Eric Forni, Jean-Joël Loumeto & Adeline Fayolle
1. Architectural traits that determine the light captured in a given environment are an important aspect of the life-history strategies of tropical tree species. In this study, we examined how interspecific variation in architectural traits is related to the functional traits of 45 coexisting tree species in central Africa. 2. At the tree level, we measured tree diameter, total height and crown dimensions for an average of 30 trees per species (range 14–72, total 968...

Data from: Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish

Rhys A. Coleman, Bertrand Gauffre, Alexandra Pavlova, Luciano B. Beheregaray, Joanne Kearns, Jarod Lyon, Minami Sasaki, Raphael Leblois, Carla Sgro & Paul Sunnucks
Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fish, they...

Data from: Spatial heterogeneity in landscape structure influences dispersal and genetic structure: empirical evidence from a grasshopper in an agricultural landscape

Bertrand Gauffre, Sophie Mallez, Marie-Pierre Chapuis, Leblois Raphael, Isabelle Litrico, Sabrina Delaunay, Isabelle Badenhausser & Raphael Leblois
Dispersal may be strongly influenced by landscape and habitat characteristics that could either enhance or restrict movements of organisms. Therefore, spatial heterogeneity in landscape structure could influence gene flow and the spatial structure of populations. In the past decades, agricultural intensification has led to the reduction in grassland surfaces, their fragmentation and intensification. As these changes are not homogeneously distributed in landscapes, they have resulted in spatial heterogeneity with generally less intensified hedged farmland areas...

Data from: Demographic processes shaping genetic variation of the solitarious phase of the desert locust

Marie-Pierre Chapuis, Christophe Plantamp, Laurence Blondin, Christine Pagès, Jean-Michel Vassal & Michel Lecoq
Between plagues, the solitarious desert locust (Schistocerca gregaria) is generally thought to exist as small populations, which are particularly prone to extinction events in arid regions of Africa and Asia. Given the high genetic structuring observed in one geographical area (the Eritrean coast) by former authors, a metapopulation dynamics model involving repeated extinction and colonization events was favored. In this study, we assessed the validity of a demographic scenario involving temporary populations of the solitarious...

Benefits and costs of hosting facultative symbionts in plant-sucking insects: a meta-analysis

Sharon Zytynska, Karim Tighiouart & Enric Frago
This dataset contains data from a meta-analysis on the benefits and costs of hosting secondar symbionts in plant-sucking insects, as described in the paper: "Zytynska, S.E., Tighiouart, K. & Frago, E. (2021) Benefits and costs of hosting facultative symbionts in plant-sucking insects: A meta-analysis. Molecular Ecology https://doi.org/10.1111/mec.15897 " Many animals have evolved associations with symbiotic microbes that benefit the host through increased growth, lifespan, and survival. Some interactions are obligate (essential for survival) while others...

High tree diversity enhances light interception in tropical forests

Marina Melo Duarte, Caroline Isaac Ferreira Zuim, Taísi Bech Sorrini, Luís Eduardo Bernardini, Rafael De Andrade Moral, Joannes Guillemot, Catherine Potvin, Wagner Hugo Bonat, José Luiz Stape & Pedro Henrique Santin Brancalion
We used two forest plantation experiments, the Sardinilla site in Panama (containing monocultures, 2-, 3- and 5-species mixtures in the main plantation, established in 2001, and 6-, 9- and18-species mixtures in the high-diversity plantation, established in 2003), and the Anhembi site in Brazil (established in 2006, containing 20-, 58- and 114-species mixtures), to investigate the effects of forest tree richness on the amount and distribution (horizontal, vertical and temporal) of intercepted ligh (red:far-red ratio -...

Patterns of volatile diversity yield insights into the genetics and biochemistry of the date palm fruit volatilome

Jonathan Flowers, Khaled Hazzouri, Alain Lemansour, Tiago Capote, Muriel Gros-Balthazard, Sylvie Ferrand, Marc Lebrun, Khaled Amiri & Michael Purugganan
Volatile organic compounds are key components of the fruit metabolome that contribute to traits such as aroma and taste. Here we report on the diversity of 90 flavor-related fruit traits in date palms (Phoenix dactylifera L.) including 80 volatile organic compounds, which collectively represent the fruit volatilome, as well as 6 organic acids, and 4 sugars in tree-ripened fruits. We characterize these traits in 148 date palms representing 135 varieties using headspace solid-phase microextraction gas...

Publier un data paper

Laurence Dedieu
Cette fiche aborde les éléments suivants : - Qu’est-ce qu’un Data paper - Objectif et enjeu du Data paper - Structure et contenu du Data paper - Choisir la revue - Evaluer un Data paper

Rédiger un Plan de Gestion des Données

Laurence Dedieu
Un PGD est un document qui explicite, dans un projet ou une thèse, la manière dont sont obtenues et traitées les données tout au long de leur cycle de vie, de la collecte à l’archivage. C’est un document formalisé, assez court. L’enjeu n’est pas de décrire toutes les étapes mais de montrer que les données sont gérées selon des « bonnes pratiques » (de collecte, organisation, stockage, description, documentation, etc.), dans le respect d’un «...

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Michael Abrouk, Hanin Ibrahim Ahmed, Philippe Cubry, Denisa Šimoníková, Stéphane Cauet, Yveline Pailles, Jan Bettgenhaeuser, Liubov Gapa, Nora Scarcelli, Marie Couderc, Leila Zekraoui, Nagarajan Kathiresan, Jana Čížková, Eva Hřibová, Jaroslav Doležel, Sandrine Arribat, Hélène Bergès, Jan Wieringa, Mathieu Gueye, Ndjido Kane, Christian Leclerc, Sandrine Causse, Sylvie Vancoppenolle, Claire Billot, Thomas Wicker … & Simon Krattinger
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we established high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure,...

Data from: Comparison of the genetic determinism of two key phenological traits, flowering and maturity dates, in three Prunus species: peach, apricot and sweet cherry

Patrick Lambert, David Ruiz, Luca Dondini, Eudald Illa, Jean-Marc Audergon, Stefano Tartarini, Philippe Letourmy, Elisabeth Dirlewanger, José Quéro-Garcia, Loïck Le Dantec, Bénédicte Quilot-Turion & Pere Arus
The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five progenies from three Prunus species, peach, apricot and sweet cherry, during three to eight years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs...

Data from: Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Faisal Almathen, Pauline Charruau, Elmira Mohandesan, Joram M. Mwacharo, Pablo Orozco-TerWengel, Daniel Pitt, Abdussamad M. Abdussamad, Margarethe Uerpmann, Hans-Peter Uerpmann, Bea De Cupere, Peter Magee, Majed A. Alnaqeeb, Bashir Salim, Abdul Raziq, Tadelle Dessie, Omer M. Abdelhadi, Mohammad H. Banabazi, Marzook Al-Eknah, Chris Walzer, Bernard Faye, Michael Hofreiter, Joris Peters, Olivier Hanotte & Pamela A. Burger
Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and...

Data from: Extra molting and selection on nymphal growth in the desert locust

Benjamin Pélissié, Cyril Piou, Hélène Jourdan-Pineau, Christine Pagès, Laurence Blondin & Marie-Pierre Chapuis
In insects, extra-molting has been viewed as a compensatory mechanism for nymphal growth that contributes to optimize body weight for successful reproduction. However, little is known on the capacity of extra-molting to evolve in natural populations, which limits our understanding of how selection acts on nymphal growth. We used a multi-generational pedigree, individual monitoring and quantitative genetics models to investigate the evolution of extra-molting and its impact on nymphal growth in a solitarious population of...

Data from: Population sizes and dispersal pattern of tsetse flies: rolling on the river?

Jeremy Bouyer, Thomas Balenghien, Sophie Ravel, Laurence Vial, Sophie Thevenon, Philippe Solano & Thierry De Meeus
The West African trypanosomoses are mostly transmitted by riverine species of tsetse fly . In this study, we estimate the dispersal and population size of tsetse populations located along the Mouhoun River in Burkina Faso where tsetse habitats are experiencing increasing fragmentation caused by human encroachment. Dispersal estimated through direct (mark and recapture) and indirect (genetic isolation by distance) methods appeared consistent with one another. In these fragmented landscapes, tsetse flies displayed localised, small sub-populations...

Data from: Assessing the distribution of disease-bearing rodents in human-modified tropical landscapes

Serge Morand, Frédéric Bordes, Kim Blasdell, Shai Pilosof, Jean-François Cornu, Kittipong Chaisiri, Yannick Chaval, Jean-François Cosson, Julien Claude, Tristan Feyfant, Vincent Herbreteau, Stéphane Dupuy & Annelise Tran
1. We tested how habitat structure and fragmentation affect the spatial distribution of common murine rodents inhabiting human-dominated landscapes in southeast Asia. The spatial distribution patterns observed for each rodent species were then used to assess how changes in habitat structure may potentially affect the risk of several major rodent-borne diseases. 2. For this analysis, we used an extensive geo-referenced database containing details of rodents trapped from seven sites in Thailand, Cambodia and Lao PDR....

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  • Centre de Coopération Internationale en Recherche Agronomique pour le Développement
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  • French National Centre for Scientific Research
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  • French National Institute for Agricultural Research
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