65 Works

Data from: Divergent evolutionary morphology of the axial skeleton as a potential key innovation in modern cetaceans

Amandine Gillet, Bruno Frederich & Eric Parmentier
Cetaceans represent the most diverse clade of extant marine tetrapods. Although restructuring of oceans could have contributed to their diversity, other factors might also be involved. Similar to ichthyosaurs and sharks, variation of morphological traits could have promoted the colonization of new ecological niches and supported their diversification. By combining morphological data describing the axial skeleton of 73 cetacean species with phylogenetic comparative methods, we demonstrate that the vertebral morphology of cetaceans is associated to...

Data from: Seed and pollen dispersal distances in two African legume timber trees and their reproductive potential under selective logging

Olivier J. Hardy, Boris Delaide, Hélène Hainaut, Jean-François Gillet, Pauline Gillet, Esra Kaymak, Nina Vankerckhove, Jérôme Duminil & Jean-Louis Doucet
The natural regeneration of tree species depends on seed and pollen dispersal. To assess if limited dispersal could be critical for the sustainability of selective logging practices, we performed parentage analyses in two Central African legume canopy species displaying contrasted floral and fruit traits: Distemonanthus benthamianus and Erythrophleum suaveolens. We also developed new tools linking forward dispersal kernels with backward migration rates to better characterize long-distance dispersal. Much longer pollen dispersal in D. benthamianus (mean...

Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

Nathalie Smitz, Pim Van Hooft, Rasmus Heller, Daniel Cornélis, Philippe Chardonnet, Robert Kraus, Ben J. Greyling, Richard Crooijmans, Martien Groenen, Johan Michaux & Ben Greyling
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African...

Data from: Phenotype classification of zebrafish embryos by supervised learning

Nathalie Jeanray, Raphaël Marée, Benoist Pruvot, Olivier Stern, Pierre Geurts, Louis Wehenkel & Marc Muller
Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances on embryo survival and development are generally evaluated manually through microscopic observation by an expert and documented by several typical photographs. Here, we present a methodology to automatically classify brightfield images of wildtype zebrafish embryos according to their defects by using an image analysis approach based on...

Data from: Phylotranscriptomic consolidation of the jawed vertebrate timetree

Iker Irisarri, Denis Baurain, Henner Brinkmann, Frédéric Delsuc, Jean-Yves Sire, Alexander Kupfer, Jörn Petersen, Michael Jarek, Axel Meyer, Miguel Vences & Hervé Philippe
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on “standards” for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find...

Data from: Body shape convergence driven by small size optimum in marine angelfishes

Bruno Frédérich, Francesco Santini, Nicolai Konow, Joseph Schnitzler, David Lecchini & Michael E. Alfaro
Convergent evolution of small body size occurs across many vertebrate clades and may reflect an evolutionary response to shared selective pressures. However it remains unclear if other aspects of phenotype undergo convergent evolution in miniaturized lineages. Here we present a comparative analysis of body size and shape evolution in marine angelfishes (Pomacanthidae), a reef fish family characterized by repeated transitions to small body size. We ask if lineages that evolve small sizes show convergent evolution...

Data from: Bayesian analysis of hybridization and introgression between the endangered european mink (Mustela lutreola) and the polecat (Mustela putorius)

Maria Teresa Cabria, Johan R Michaux, Benjamín J Gómez-Moliner, Dimitry Skumatov, Tiit Maran, Pascal Fournier, Javier López De Luzuriaga & Rafael Zardoya
Human-mediated global change will probably increase the rates of natural hybridization and genetic introgression between closely related species, and this will have major implications for conservation of the taxa involved. In this study, we analyse both mitochondrial and nuclear data to characterize ongoing hybridization and genetic introgression between two sympatric sister species of mustelids, the endangered European mink (Mustela lutreola) and the more abundant polecat (M. putorius). A total of 317 European mink, 114 polecats...

Data from: Globally, functional traits are weak predictors of juvenile tree growth, and we do not know why

C. E. Timothy Paine, Lucy Amissah, Harald Auge, Christopher Baraloto, Martin Baruffol, Nils Bourland, Helge Bruelheide, Kasso Daïnou, Roland C. De Gouvenain, Jean-Louis Doucet, Susan Doust, Paul V. A. Fine, Claire Fortunel, Josephine Haase, Karen D. Holl, Hervé Jactel, Xuefei Li, Kaoru Kitajima, Julia Koricheva, Cristina Martínez-Garza, Christian Messier, Alain Paquette, Christopher Philipson, Daniel Piotto, Lourens Poorter … & Andy Hector
1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates. 2. If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global...

Data from: Persistence of the effect of frugivore identity on post-dispersal seed fate: consequences for the assessment of functional redundancy

Ana Paula Lugon, Marion Boutefeu, Emilie Bovy, Fernando Z. Vaz-De-Mello, Marie-Claude Huynen, Mauro Galetti & Laurence Culot
Large frugivores play an important role as seed dispersers and their extinction may affect plant regeneration. The consequences of such extinctions depend on the likelihood of other species being functionally redundant and on how post-dispersal events are affected. We assess the functional redundancy of two seed dispersers of the Atlantic Forest, the muriqui (Brachyteles arachnoides) and the tapir (Tapirus terrestris) through the comparison of their seed dispersal quality, taking into account post-dispersal events. We compare...

Data from: The ‘male escape hypothesis’: sex-biased metamorphosis in response to climatic drivers in a facultatively paedomorphic amphibian

Anthony G.E. Mathiron, Jean-Paul Lena, Sarah Baouch, Mathieu Denoël & Anthony G. E. Mathiron
Paedomorphosis is a major evolutionary process that bypasses metamorphosis and allows reproduction in larvae. In newts and salamanders, it can be facultative with paedomorphs retaining gills and metamorphs dispersing. The evolution of these developmental processes is thought to have been driven by the costs and benefits of inhabiting aquatic versus terrestrial habitats. In this context, we aimed at testing the hypothesis that climatic drivers affect phenotypic transition and the difference across sexes because sex-ratio is...

Data from: Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales: Jungermanniopsida), including two reinstated and five new species

Matt A. M. Renner, Nicolas Devos, Jairo Patiño, Elizabeth A. Brown, Andrew Orme, Michael Elgy, Trevor Wilson, Lindsey J. Gray, Matt J. Von Konrat, Lindsey Gray, Matt Renner, Elizabeth Brown & Matt Von Konrat
Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph....

Data from: Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees

Federica Lucati, Manon Poignet, Alexandre Miró, Audrey Trochet, Fabien Aubret, Laurent Barthe, Romain Bertrand, Teresa Buchaca, Olivier Calvez, Jenny Caner, Elodie Darnet, Mathieu Denoël, Olivier Guillaume, Hugo Le Chevalier, Albert Martínez-Silvestre, Marc Mossoll-Torres, David O’Brien, Víctor Osorio, Gilles Pottier, Murielle Richard, Ibor Sabás, Jérémie Souchet, Jan Tomàs & Marc Ventura
Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species’ present-day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present-day gene flow dynamics in determining the genetic diversity and structure of the newt Calotriton asper (Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a...

Tree diversity is key for promoting the diversity and abundance of forest‐associated taxa in Europe

Eric Allan, Evy Ampoorter, Luc Barbaro, Hervé Jactel, Lander Baeten, Johanna Boberg, Monique Carnol, Bastien Castagneyrol, Yohan Charbonnier, Seid Muhie Dawud, Marc Deconchat, Pallieter De Smedt, Hans De Wandeler, Virginie Guyot, Stephan Hättenschwiler, François‐Xavier Joly, Julia Koricheva, Harriet Milligan, Bart Muys, Diem Nguyen, Sophia Ratcliffe, Karsten Raulund‐Rasmussen, Michael Scherer‐Lorenzen, Fons Plas, J. Van Keer … & Lars Vesterdal
Plant diversity is an important driver of diversity at other trophic levels, suggesting that cascading extinctions could reduce overall biodiversity. Most evidence for positive effects of plant diversity comes from grasslands. Despite the fact that forests are hotspots of biodiversity, the importance of tree diversity, in particular its relative importance compared to other management related factors, in affecting forest‐associated taxa is not well known. To address this, we used data from 183 plots, located in...

Data from: Maintenance of genetic and morphological identity in two sibling Syrrhopodon species (Calymperaceae, Bryopsida) despite extensive introgression

Marta R. Pereira, Alice Ledent, Patrick Mardulyn, Charles E. Zartman & Alain Vanderpoorten
Bryophytes are a group of land plants wherein the role of hybridization has long been challenged. Using Genotyping by Sequencing to circumvent the lack of molecular variation at selected loci previously used for phylogeny and morphology, we determine the level of genetic and morphological divergence and reproductive isolation between the sibling Syrrhopodon annotinus and S. simmondsii (Calymperaceae, Bryopsida) that occur in sympatry but in different habitats in lowland Amazonian rainforests. A clear morphological differentiation and...

Highlighting convergent evolution in morphological traits in response to climatic gradient in African tropical tree species: the case of genus Guibourtia Benn

Felicien Tosso, Jean-Louis Doucet, Kasso Daïnou, Adeline Fayolle, Alain Hambuckers, Charles Doumenge, Honoré Agbazahou, Piet Stoffelen & Olivier Hardy
Adaptive evolution is a major driver of organism diversification but the links between phenotypic traits and environmental niche remains little documented in tropical trees. Moreover, trait-niche relationships are complex because a correlation between the traits and environmental niches displayed by a sample of species may result from (1) convergent evolution if different environmental conditions have selected different sets of traits, and/or (2) phylogenetic inertia if niche and morphological differences between species are simply function of...

Data from: Testing the divergent adaptation of two congeneric tree species on a rainfall gradient using eco-physio-morphological traits

Anaïs-Pasiphaé Gorel, Kathy Steppe, Hans Beeckman, Niels J.F. De Baerdemaeker, Jean-Louis Doucet, Gauthier Ligot, Kasso Daïnou & Adeline Fayolle.
In tropical Africa, evidence of widely distributed genera transcending biomes or habitat boundaries has been reported. The evolutionary processes that allowed these lineages to disperse and adapt into new environments are far from being resolved. To better understand these processes, we propose an integrated approach, based on the eco-physio-morphological traits of two sister species with adjacent distributions along a rainfall gradient. We used wood anatomical traits, plant hydraulics (vulnerability to cavitation, wood volumetric water content...

Unprecedented biting performance in herbivorous fish: how the complex biting system of Pomacentridae circumvents performance trade-offs

Damien Olivier, Sam Van Wassenbergh, Eric Parmentier & Bruno Frédérich
It is well accepted that the complexity of functional systems may mitigate performance trade-offs. However, data supporting this theory is hard to find because it needs to be based on a functional system with different complexity levels in closely-related species. The Pomacentridae (damselfishes) provide an excellent opportunity to test the hypothesis because most of the species have two mouth-closing systems: the first using the adductor mandibulae, as in all teleost fishes, and a second one...

Volatiles of bacteria associated with parasitoid habitats elicit distinct olfactory responses in an aphid parasitoid and its hyperparasitoid

Tim Goelen, Islam S. Sobhy, Christophe Vanderaa, Jetske G. De Boer, Frank Delvigne, Frédéric Francis, Felix Wäckers, Hans Rediers, Kevin J. Verstrepen, Tom Wenseleers, Hans Jacquemyn & Bart Lievens
1. To locate mating partners and essential resources such as food, oviposition sites and shelter, insects rely to a large extent on chemical cues. While most research has focused on cues derived from plants and insects, there is mounting evidence that indicates that microorganisms emit volatile compounds that may play an important role in insect behaviour. 2. In this study, we assessed how volatile compounds emitted by phylogenetically diverse bacteria affected the olfactory response of...

Genomic footprints of recovery in the European bison

Tom Druet, Kamil Oleński, Laurence Flori, Amandine Bertrand, Wanda Olech, Malgorzata Tokarska, Stanislaw Kaminski & Mathieu Gautier
After extinction in the wild in the beginning of the twentieth century, the European bison has been successfully recovered in two distinct genetic lines from only twelve and seven captive founders. We here aimed at characterizing the levels of realized inbreeding in these two restored lines to provide empirical insights into the genomic footprints left by population recovery from a small number of founders. To that end, we genotyped 183 European bison born over the...

Data from: Partitioning the relative contribution of one-phase and two-phase seed dispersal when evaluating seed dispersal effectiveness

Laurence Culot, Marie-Claude Huynen & Eckhard W. Heymann
Seed dispersal effectiveness (SDE) is a conceptual framework that aims at quantifying the contribution of seed dispersal vectors to plant fitness. While it is well recognized that diplochorous dispersal systems, characterized by two successive dispersal steps performed by two different vectors (Phase I = primary seed dispersal and Phase II = secondary seed dispersal) are common in temperate and tropical regions, little attention has been given to distinguishing the relative contribution of one-phase and two-phase...

Data from: From animal tracks to fine-scale movement modes: a straightforward approach for identifying multiple, spatial movement patterns

Kevin Morelle, Nils Bunnefeld, Philippe Lejeune & Steve A. Oswald
1. Thanks to developments in animal tracking technology, detailed data on the movement tracks of individual animals are now attainable for many species. However, straightforward methods to decompose individual tracks into high-resolution, spatial modes are lacking but are essential to understand what an animal is doing. 2. We developed an analytical approach that combines separately-validated methods into a straightforward tool for converting animal GPS tracks to short-range movement modes. Our three-step analytical process comprises: (1)...

Data from: Minimally invasive estimation of ventricular dead space volume through use of Frank-Starling curves

Shaun Davidson, Chris Pretty, Antoine Pironet, Thomas Desaive, Nathalie Janssen, Bernard Lambermont, Philippe Morimont & J. Geoffrey Chase
This paper develops a means of more easily and less invasively estimating ventricular dead space volume (Vd), an important, but difficult to measure physiological parameter. Vd represents a subject and condition dependent portion of measured ventricular volume that is not actively participating in ventricular function. It is employed in models based on the time varying elastance concept, which see widespread use in haemodynamic studies, and may have direct diagnostic use. The proposed method involves linear...

Data from: Similar levels of trophic and functional diversity within damselfish assemblages across Indo–Pacific coral reefs

Laura Gajdzik, Eric Parmentier, Loïc N. Michel, Nicolas Sturaro, Keryea Soong, Gilles Lepoint & Bruno Frédérich
1. Understanding the forces that influence the dynamics of communities is a key challenge to undertake in changing environments. Despite recent advances in coral reef community ecology, a more comprehensive knowledge about processes (niche related–traits and phylogenies) driving the composition of reef fish community is needed. 2. Here, we conducted a quantitative comparison of these processes in damselfish assemblages that belong to three distinct Indo–Pacific coral reefs differing in taxonomic composition, morphology and degree of...

Data from: Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

Cindy F. Verdu, Erwan Guichoux, Samuel Quevauvillers, Olivier De Thier, Yec'han Laizet, Adline Delcamp, Frédéric Gévaudant, Arnaud Monty, Annabel J. Porté, Philippe Lejeune, Ludivine Lassois & Stéphanie Mariette
The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from...

Data from: How bees deter elephants: beehive trials with forest elephants (Loxodonta africana cyclotis) in Gabon

Steeve Ngama, Lisa Korte, Jérôme Bindelle, Cédric Vermeulen & John R. Poulsen
In Gabon, like elsewhere in Africa, crops are often sources of conflict between humans and wildlife. Wildlife damage to crops can drastically reduce income, amplifying poverty and creating a negative perception of wild animal conservation among rural people. In this context, crop-raiding animals like elephants quickly become “problem animals”. To deter elephants from raiding crops beehives have been successfully employed in East Africa; however, this method has not yet been tested in Central Africa. We...

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Resource Types

  • Dataset


  • University of Liège
  • Université Libre de Bruxelles
  • French National Institute for Agricultural Research
  • French National Centre for Scientific Research
  • Centre de Coopération Internationale en Recherche Agronomique pour le Développement
  • Royal Museum for Central Africa
  • Ghent University
  • Duke University
  • University of California Los Angeles
  • Wageningen University & Research