303 Works

Additional file 1 of Joint modeling strategy for using electronic medical records data to build machine learning models: an example of intracerebral hemorrhage

Jianxiang Tang, Xiaoyu Wang, Hongli Wan, Chunying Lin, Zilun Shao, Yang Chang, Hexuan Wang, Yi Wu, Tao Zhang & Yu Du
Additional file 1. Additional file showed the performance with 95% CI of all 84 combinations of joint modeling strategy.

3D Ecoli nucleoid stained with SYBR-Gold

Simona Streckaite, Dmitrij Frolov, Jevgenij Chmeliov, Andrius Gelzinis, Cristian Ilioaia, Sylvie Rimsky, Rienk van Grondelle, Leonas Valkunas, Andrew Gall & Bruno Robert
Movie S1 shows volumetric 3D reconstruction of the E. coli bacterial chromatin stained with SYBR® Gold—a rotation around y axis. The sample was scanned with 40 nm x & y steps, and 200 nm z steps, λexc = 488 nm, emission collected at 505–545 nm window. 3D reconstruction was obtained from 12 planes.

Host-plant adaptation as a driver of incipient speciation in the fall armyworm (Spodoptera frugiperda)

Estelle Fiteni, Karine Durand, Sylvie Gimenez, Robert L. Meagher, Fabrice Legeai, Gael J. Kergoat, Nicolas Nègre, Emmanuelle d’Alençon & Kiwoong Nam
Abstract Background Divergent selection on host-plants is one of the main evolutionary forces driving ecological speciation in phytophagous insects. The ecological speciation might be challenging in the presence of gene flow and assortative mating because the direction of divergence is not necessarily the same between ecological selection (through host-plant adaptation) and assortative mating. The fall armyworm (FAW), a major lepidopteran pest species, is composed of two sympatric strains, corn and rice strains, named after two...

Data from: Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes

Marlène Chiarello, Jean-Christophe Auguet, Nicholas Graham, Thomas Claverie, Elliott Sucré, Corinne Bouvier, Fabien Rieuvilleneuve, Claudia Restrepo-Ortiz, Yvan Bettarel, Sébastien Villéger & Thierry Bouvier
Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However the diversity of such microbiomes is mostly described in a few coral species, and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the...

Data from: Wolbachia increases susceptibility to Plasmodium infection in a natural system

Flore Zélé, Antoine Nicot, Arnaud Berthomieu, Mylène Weill, Olivier Duron, Ana Rivero & F. Zele
Current views about the impact of Wolbachia on Plasmodium infections are almost entirely based on data regarding artificially transfected mosquitoes. This work has shown that Wolbachia reduces the intensity of Plasmodium infections in mosquitoes, raising the exciting possibility of using Wolbachia to control or limit the spread of malaria. Whether natural Wolbachia infections have the same parasite-inhibiting properties is not yet clear. Wolbachia–mosquito combinations with a long evolutionary history are, however, key for understanding what...

Data from: Accelerated evolutionary rate of housekeeping genes in tunicates

Georgia Tsagkogeorga, Xavier Turon, Nicolas Galtier, Emmanuel J. P. Douzery & Frédéric Delsuc
Phylogenomics has recently revealed that tunicates represent the sister-group of vertebrates in the newly defined clade Olfactores. However, phylogenomic and comparative genomic studies have also suggested that tunicates are characterized by an elevated rate of molecular evolution and a high degree of genomic divergence. Despite the recurrent interest in the group, the picture of tunicate peculiar evolutionary dynamics is still fragmentary, as it mainly lies in studies focusing on only a few model species. In...

Data from: Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

Ylenia Chiari, Vincent Cahais, Nicolas Galtier & Frédéric Delsuc
BACKGROUND: The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have...

Data from: Rapid evolutionary responses of life history traits to different experimentally-induced pollution in Caenorhabditis elegans

Morgan Dutilleul, Jean-Marc Bonzom, Catherine Lecomte, Benoit Goussen, Fabrice Daian, Simon Galas & Denis Réale
Background Anthropogenic disturbances can lead to intense selection pressures on traits and very rapid evolutionary changes. Evolutionary responses to environmental changes, in turn, reflect changes in the genetic structure of the traits, accompanied by a reduction of evolutionary potential of the populations under selection. Assessing the effects of pollutants on the evolutionary responses and on the genetic structure of populations is thus important to understanding the mechanisms that entail specialization to novel environmental conditions or...

Data from: Gene-dosage effects on fitness in recent adaptive duplications: ace-1 in the mosquito Culex pipiens

Pierrick Labbé, Pascal Milesi, André Yébakima, Nicole Pasteur, Mylène Weill & Thomas Lenormand
Gene duplications have long been advocated to contribute to the evolution of new functions. The role of selection in their early spread is more controversial. Unless duplications are favored for a direct benefit of increased expression, they are likely detrimental. In this paper, we investigated the case of duplications favored because they combine already functionally divergent alleles. Their gene-dosage/fitness relations are poorly known, because selection may operate on both overall expression and duplicates relative dosage....

Data from: Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Pierre-Jean G. Malé, Léa Bardon, Guillaume Besnard, Eric Coissac, Frédéric Delsuc, Julien Engel, Emeline Lhuillier, Caroline Scotti-Saintagne, Alexandra Tinaut & Jérôme Chave
Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid...

Data from: Patterns of selection on Plasmodium falciparum erythrocyte binding antigens after the colonisation of the New World

Erhan Yalcindag, Virginie Rougeron, Eric Elguero, Céline Arnathau, Patrick Durand, Sylvain Brisse, Laure Diancourt, Agnes Aubouy, Pierre Becquart, Umberto D'Alessandro, Didier Fontenille, Dionicia Gamboa, Amanda Maestre, Didier Ménard, Lise Musset, Oscar Noya, Vincent Veron, Albina Wide, Bernard Carme, Eric Legrand, Christine Chevillon, Francisco J. Ayala, François Renaud & Franck Prugnolle
Pathogens, which have recently colonized a new host species or new populations of the same host, are interesting models for understanding how populations may evolve in response to novel environments. During its colonization of South America from Africa Plasmodium falciparum, the main agent of malaria, has been exposed to new conditions in distinctive new human populations (Amerindian and populations of mixed origins), that likely exerted new selective pressures on the parasite's genome. Among the genes...

Data from: Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit

Miguel Carneiro, Stuart J. E. Baird, Sandra Afonso, Esther Ramirez, Pedro Tarroso, Henrique Teotonio, Rafael Villafuerte, Michael W. Nachman & Nuno Ferrand
Maintenance of genetic distinction in the face of gene flow is an important aspect of the speciation process. Here, we provide a detailed spatial and genetic characterization of a hybrid zone between two subspecies of the European rabbit. We examined patterns of allele frequency change for 22 markers located on the autosomes, X-chromosome, Y-chromosome, and mtDNA in 1078 individuals sampled across the hybrid zone. While some loci revealed extremely wide clines (w>=300 km) relative to...

Data from: Root community traits along a land use gradient: evidence of a community-level economics spectrum

Iván Prieto, Catherine Roumet, Remi Cardinael, Christian Dupraz, Christophe Jourdan, John H. Kim, Jean Luc Maeght, Zhun Mao, Alain Pierret, Noelia Portillo, Olivier Roupsard, Chantanousone Thammahacksa & Alexia Stokes
1. There is a fundamental trade-off between leaf traits associated with either resource acquisition or resource conservation. This gradient of trait variation, called the economics spectrum also applies to fine roots but whether it is consistent for coarse roots or at the plant community level remains untested. 2. We measured a set of morphological and chemical root traits at a community level (functional parameters; FP) in 20 plant communities located along land-use intensity gradients and...

Data from: Density- and trait-mediated effects of a parasite and a predator in a tri-trophic food web

Aabir Banerji, Alison B. Duncan, Joanne S. Griffin, Stuart Humphries, Owen L. Petchey & Oliver Kaltz
1. Despite growing interest in ecological consequences of parasitism in food webs, relatively little is known about effects of parasites on long-term population dynamics of non-host species or about whether such effects are density- or trait- mediated. 2. We studied a tri-trophic food chain comprised of: (i) a bacterial basal resource (Serratia fonticola), (ii) an intermediate consumer (Paramecium caudatum), (iii) a top predator (Didinium nasutum), and (iv) a parasite of the intermediate consumer (Holospora undulata)....

Data from: Quantifying the effects of migration and mutation on adaptation and demography in spatially heterogeneous environments

Florence Débarre, Ophélie Ronce & Sylvain Gandon
How do mutation and gene flow influence population persistence, niche expansion, and local adaptation in spatially heterogeneous environments? In this article, we analyse a demographic and evolutionary model of adaptation to an environment containing two habitats in equal frequencies, and we bridge the gap between different theoretical frameworks. Qualitatively, our model yields four qualitative types of outcomes: (i) global extinction of the population (ii) adaptation to one habitat only, but also adaptation to both habitats...

Data from: Contrasting patterns of genome-wide polymorphism in the native and invasive range of the marine mollusk Crepidula fornicata

Florentine Riquet, Claire Daguin-Thiébaut, Marion Ballenghien, Nicolas Bierne & Frederique Viard
Selection processes are believed to be an important evolutionary driver behind the successful establishment of non-indigenous species, however evidence is still scarce. Genome-scans have often identified loci with atypical patterns of genetic differentiation (i.e. outliers) indicative of selection processes. Using microsatellite- and AFLP-based genome-scans, we looked for evidence of post-introduction selection in the mollusk Crepidula fornicata, native from the northwestern Atlantic and introduced in the northeastern Atlantic and northeastern Pacific during the 19th and 20th...

Data from: An integrative framework of coexistence mechanisms in competitive metacommunities

Bertrand Fournier, Nicolas Mouquet, Mathew A. Leibold & Dominique Gravel
Species distribution in a metacommunity varies according to their traits, the distribution of environmental conditions and connectivity among localities. These ingredients contribute to coexistence across spatial scales via species sorting, patch dynamics, mass effects and neutral dynamics. These mechanisms however seldom act in isolation and the impact of landscape configuration on their relative importance remains poorly understood. We present a new model of metacommunity dynamics that simultaneously considers these four possible mechanisms over spatially explicit...

Data from: Rare species contribute disproportionately to the functional structure of species assemblages

Rafael P. Leitão, Jansen Zuanon, Sebastien Villeger, Stephen E. Williams, Christopher Baraloto, Claire Fortunel, Fernando P. Mendonça & David Mouillot
There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to go extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare and the rate of species extinction can be high. Here we investigated the consequences of local and...

Data from: Local inter-species introgression is the main cause of extreme levels of intra-specific differentiation in mussels

Christelle Fraïsse, Khalid Belkhir, John J. Welch & Nicolas Bierne
Structured populations, and replicated zones of contact between species, are an ideal opportunity to study regions of the genome with unusual levels of differentiation; and these can illuminate the genomic architecture of species isolation, and the spread of adaptive alleles across species ranges. Here, we investigated the effects of gene flow on divergence and adaptation in the Mytilus complex of species, including replicated parental populations in quite distant geographical locations. We used target enrichment sequencing...

Data from: Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts

Anna-Lisa Coi, Frederic Bigey, Sandrine Mallet, Souhir Marsit, Giacomo Zara, Pierre Gladieux, Virginie Galeote, Marilena Budroni, Sylvie Dequin, Jean-Luc Legras & A. L. Coi
The molecular and evolutionary processes underlying fungal domestication remain largely unknown despite the importance of fungi to bioindustry and for comparative adaptation genomics in eukaryotes. Wine fermentation and biological aging are performed by strains of S. cerevisiae with, respectively, pelagic fermentative growth on glucose, and biofilm aerobic growth utilizing ethanol. Here, we use environmental samples of wine and flor yeasts to investigate the genomic basis of yeast adaptation to contrasted anthropogenic environments. Phylogenetic inference and...

Data from: Vegetation recovery in tidal marshes reveals critical slowing down under increased inundation

Jim Van Belzen, Johan Van De Koppel, Matthew L. Kirwan, Daphne Van Der Wal, Peter M. J. Herman, Vasilis Dakos, Sonia Kéfi, Marten Scheffer, Glenn R. Guntenspergen & Tjeerd J. Bouma
A declining rate of recovery following disturbance has been proposed as an important early warning for impending tipping points in complex systems. Despite extensive theoretical and laboratory studies, this ‘critical slowing down’ remains largely untested in the complex settings of real-world ecosystems. Here, we provide both observational and experimental support of critical slowing down along natural stress gradients in tidal marsh ecosystems. Time series of aerial images of European marsh development reveal a consistent lengthening...

Data from: Impact of disease on the survival of three commercially fished species

John M. Hoenig, Maya L. Groner, Matthew W. Smith, Wolfgang K. Vogelbein, David M. Taylor, , John T. Swenarton, David T. Gauthier, Philip Sadler, Mark A. Matsche, Ashley N. Haines, Hamish J. Small, Roger Pradel, Rémi Choquet & Jeffrey D. Shields
Recent increases in emergent infectious diseases have raised concerns about the population stability of some marine species. The complexity and expense of studying diseases in marine systems often dictate that conservation and management decisions are made without quantitative data on population-level impacts of disease. Mark-recapture is a powerful, underutilized, tool for calculating impacts of disease on population size and structure, even in the absence of etiological information. We applied logistic regression models to mark-recapture data...

Data from: The ace-1 locus is amplified in all resistant Anopheles gambiae mosquitoes: fitness consequences of homogeneous and heterogeneous duplications.

Benoît S. Assogba, Pascal Milesi, Luc S. Djogbénou, Arnaud Berthomieu, Patrick Makoundou, Lamine S. Baba-Moussa, Anna-Sophie Fiston-Lavier, Khalid Belkir, Pierrick Labbé, Mylène Weill & Khalid Belkhir
Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides’ target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies. We used an integrative approach, from genome to phenotype...

Data from: Frugivory-related traits promote speciation of tropical palms

Renske E. Onstein, William J. Baker, Thomas L. P. Couvreur, Søren Faurby, Jens-Christian Svenning & W. Daniel Kissling
Animal-mediated seed dispersal by frugivorous birds and mammals is central to the ecology and functioning of ecosystems, but whether and how frugivory-related traits have affected plant speciation remains little explored. Fruit size is directly linked to plant dispersal capacity and therefore influences gene flow and genetic divergence of plant populations. Using a global species-level phylogeny with comprehensive data on fruit sizes and plant species distributions, we test whether fruit size has affected speciation rates of...

Data from: Pollination along an elevational gradient mediated both by floral scent and pollinator compatibility in the fig and fig‐wasp mutualism

Daniel Souto-Vilarós, Magali Proffit, Bruno Buatois, Michal Rindos, Mentap Sisol, Thomas Kuyaiva, Jan Michalek, Clive T. Darwell, Martine Hossaert-Mckey, George D. Weiblen, Vojtech Novotny, Simon T. Segar & Brus Isua
In the fig (Moraceae) and fig‐wasp (Agaonidae) mutualism, scent is believed to be of primary importance in pollinator attraction and maintenance of species specificity. Scent divergence between closely related Ficus species seems sufficient in promoting reproductive isolation through pollinator behaviour, starting the process of speciation. We investigated volatile organic compound (VOC) variation from figs in several Ficus species endemic to Papua New Guinea. Sister species of section Papuacyse and subspecies of Ficus trichocerasa substitute each...

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