28 Works

Data from: Sylleptic branching in winter-headed apple (Malus × domestica) trees: accession-dependent responses and their relationships with other tree architectural characteristics

Stijn Vanderzande, Niek Hias, Daniel Edge-Garza, Evelyne Costes, Mark W. Davey & Johan Keulemans
Well-feathered apple trees are essential for commercial orchards to optimize yields. However, most cultivars do not form these sylleptic branches readily in commercial nurseries due to high apical dominance. Several treatments exist to promote their formation in the nurseries, one of which is heading. However, not all cultivars are expected to react similarly to these treatments. We studied the branching response of 155 genotypes following heading and its relation to other architectural traits as a...

Data from: Grape moth density in Bordeaux vineyards depends on local habitat management despite effects of landscape heterogeneity on their biological control

Adrien Rusch, Lionel Delbac & Denis Thiéry
1. Biological control of crop pests is a major ecosystem service affected by several variables acting at multiple spatial scales. Among these variables, heterogeneity at the habitat and landscape scales are known key drivers of trophic interactions and pest density in agroecosystems. However, studies that try to disentangle their relative effects in perennial cropping systems are scarce and nothing is known about their impacts on insect pest density and pesticide applications. 2. We examined the...

Data from: Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA

Lucie Zinger, Jérôme Chave, Eric Coissac, Amaia Iribar, Eliane Louisanna, Sophie Manzi, Vincent Schilling, Heidy Schimann, Guilhem Sommeria-Klein & Pierre Taberlet
DNA metabarcoding on soil samples is increasingly used for large-scale and multi-taxa biodiversity studies. However, DNA extraction may be a major bottleneck for such wide uses. It should be cost/time effective and allow dealing with large sample volumes so as to maximise the representativeness of both micro- and macro-organisms diversity. Here, we compared the performances of a fast and cheap extracellular DNA extraction protocol with a total DNA extraction method in retrieving bacterial, eukaryotic and...

Data from: Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

Quentin Rougemont, Pierre-Alexandre Gagnaire, Charles Perrier, Clémence Genthon, Anne-Laure Besnard, Sophie Launey & Guillaume Evanno
Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns...

Data from: Genetic diversity and population structure in South African, French and Argentinian Angora Goats from genome-wide SNP data

Carina Visser, Simon F. Lashmar, Este Van Marle Koster, Mario A. Poli, Daniel Allain & Este Van Marle-Köster
The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity...

Data from: Spatial scale and intraspecific trait variability mediate assembly rules in alpine grasslands

Loïc Chalmandrier, Tamara Münkemüller, Marie-Pascale Colace, Julien Renaud, Serge Aubert, Bradley Z. Carlson, Jean Christophe Clement, Nicolas Legay, Gilles Pellet, Amélie Saillard, Sebastien Lavergne & Wilfried Thuiller
Assembly of grassland communities has long been scrutinized through the lens of functional diversity. Studies generally point to an overwhelming influence of climate on observed patterns of functional diversity, despite experimental evidence demonstrating the importance of biotic interactions. We postulate that this is because most observational studies neglect both scale dependencies of assembly processes and phenotypic variation between individuals. Here, we test for changes in the importance of abiotic filtering and biotic interactions along a...

Data from: The Red Queen lives: epistasis between linked resistance loci

César M. J. A. Metzger, Pepijn Luijckx, Gilberto Bento, Mahendra Mariadassou & Dieter Ebert
A popular theory explaining the maintenance of genetic recombination (sex) is the Red Queen Theory. This theory revolves around the idea that time-lagged negative frequency-dependent selection by parasites favors rare host genotypes generated through recombination. Although the Red Queen has been studied for decades, one of its key assumptions has remained unsupported. The signature host-parasite specificity underlying the Red Queen, where infection depends on a match between host and parasite genotypes, relies on epistasis between...

Data from: Shifts and linkages of functional diversity between above- and below-ground compartments along a flooding gradient

Corentin Abgrall, Matthieu Chauvat, Estelle Langlois, Mickaël Hedde, David Mouillot, Sandrine Salmon, Bruna Winck & Estelle Forey
Trait-based approaches have the potential to reveal general and predictive relationships between organisms and ecosystem functioning. However, the mechanisms underlying the functional structure of communities are still unclear. Within terrestrial ecosystems, several studies have shown that many ecological processes are controlled by the interacting above- and below-ground compartments. However, few studies have used traits to reveal the functional relationships between plants and soil fauna. Mostly, research combining plants and soil fauna solely used the traits...

Data from: Adaptation of a plant pathogen to partial host resistance: selection for greater aggressiveness in grapevine downy mildew

Chloé E. L. Delmas, Frédéric Fabre, Jérôme Jolivet, Isabelle D. Mazet, Sylvie Richart Cervera, Laurent Delière & François Delmotte
An understanding of the evolution of pathogen quantitative traits in response to host selective pressures is essential for the development of durable management strategies for resistant crops. However, we still lack experimental data on the effects of partial host resistance on multiple phenotypic traits (aggressiveness) and evolutionary strategies in pathogens. We performed a cross-inoculation experiment with four grapevine hosts and 103 isolates of grapevine downy mildew (Plasmopara viticola) sampled from susceptible and partially resistant grapevine...

Data from: Contemporary variations of immune responsiveness during range expansion of two invasive rodents in Senegal

Christophe Diagne, Emmanuelle Gilot-Fromont, Stéphane Cornet, Laëtitia Husse, Souleymane Doucouré, Ambroise Dalecky, Khalilou Bâ, Mamadou Kane, Youssoupha Niang, Mamoudou Diallo, Aliou Sow, Odile Fossati-Gaschignard, Sylvain Piry, Emmaneulle Artige, Mbacké Sembène, Carine Brouat, Nathalie Charbonnel & Emmanuelle Artige
Biological invasions provide unique opportunities for studying life history trait changes over contemporary time scales. As spatial spread may be related to changes in parasite communities, several hypotheses (such as the evolution of increased competitive ability (EICA) or EICA-refined hypotheses) suggest immune changes in invasive species along invasion gradients. Although native hosts may be subject to similar changes in parasite selection pressures, their immune responses have been rarely investigated in invasion contexts. In this study,...

Data from: New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance

Stéphane Decroocq, Amandine Cornille, David Tricon, Sevda Babayeva, Aurélie Chague, Jean-Philippe Eyquard, Raul Karychev, Svetlana Dolgikh, Tatiana Kostritsyna, Shuo Liu, Weisheng Liu, Wenjuan Geng, Kang Liao, Bayram Asma, Zeynal Akparov, Tatiana Giraud, Veronique Decroocq & Bayram M. Asma
Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from...

Data from: Fungal disease incidence along tree diversity gradients depends on latitude in European forests

Diem Nguyen, Bastien Castagneyrol, Helge Bruelheide, Filippo Bussotti, Virginie Guyot, Hervé Jactel, Bogdan Jaroszewicz, Fernando Valladares, Jan Stenlid & Johanna Boberg
European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree species diversity in different forest types across Europe. We measured...

Data from: Exotic invasive plants increase productivity, abundance of ammonia-oxidizing bacteria, and nitrogen availability in intermountain grasslands

Morgan Luce McLeod, Cory C. Cleveland, Ylva Lekberg, John L. Maron, Laurent Philippot, David Bru & Ragan M. Callaway
1. Exotic plant invasion is often associated with dramatic increases in above-ground net primary productivity and soil nitrogen. However, most evidence for these increases comes from correlative studies of single species, leaving open the question of whether invasive plants drive these processes and if they are consistent among invaders. 2. We combined field surveys and measurements within experimental plantings to examine how plant productivity, soil nitrogen, and the abundance of ammonia-oxidizing bacteria (AOB) change in...

Data from: Genome scan reveals selection acting on genes linked to stress response in wild pearl millet

Cécile Berthouly-Salazar, Anne-Céline Thuillet, Bénédicte Rhoné, Cédric Mariac, Issaka Salia Ousseini, Marie Couderc, Maud I. Tenaillon & Yves Vigouroux
Uncovering genomic regions involved in adaption is a major goal in evolutionary biology. High-throughput sequencing now makes it possible to tackle this challenge in nonmodel species. Yet, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. The aim of this study was to identify climate adaptations in wild pearl millet populations, Cenchrus americanus ssp....

Data from: Patterns of MHC-dependent mate selection in humans and non-human primates: a meta-analysis

Jamie Winternitz, Jessica Abbate, Elise Huchard, Jan Havlíček & Laszlo Z. Garamszegi
Genes of the major histocompatibility complex (MHC) in vertebrates are integral for effective adaptive immune response and are associated with sexual selection. Evidence from a range of vertebrates supports MHC-based preference for diverse and dissimilar mating partners, but evidence from human mate choice studies has been disparate and controversial. Methodologies and sampling peculiarities specific to human studies make it difficult to know whether wide discrepancies in results among human populations are real or artefact. To...

Data from: Familiarity to a feed additive modulates its effects on brain responses in reward and memory regions in the pig model

David Val-Laillet, Paul Meurice & Caroline Clouard
Brain responses to feed flavors with or without a feed additive (FA) were investigated in piglets familiarized or not with this FA. Sixteen piglets were allocated to 2 dietary treatments from weaning until d 37: the naive group (NAI) received a standard control feed and the familiarized group (FAM) received the same feed added with a FA mainly made of orange extracts. Animals were subjected to a feed transition at d 16 post-weaning, and to...

Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution

Akito Y. Kawahara, David Plotkin, Issei Ohshima, Carlos Lopez-Vaamonde, Peter R. Houlihan, Jesse W. Breinholt, Atsushi Kawakita, Lei Xiao, Jerome C. Regier, Donald R. Davis, Tosio Kumata, Jay-Cheon Sohn, Jurate De Prins, Charles Mitter & JAE-CHEON SOHN
Gracillariidae are one of the most diverse families of internally feeding insects, and many species are economically important. Study of this family has been hampered by lack of a robust and comprehensive phylogeny. In the present paper, we sequenced up to 22 genes in 96 gracillariid species, representing all previously recognized subfamilies and genus groups, plus 20 outgroups representing other families and superfamilies. Following objective identification and removal of two rogue taxa, two datasets were...

Data from: Trait-matching and mass effect determine the functional response of herbivore communities to land use intensification

Gaëtane Le Provost, Nicolas Gross, Luca Börger, Hélène Deraison, Marilyn Roncoroni & Isabelle Badenhausser
1. Trait-based approaches represent a promising way to understand how trophic interactions shape animal communities. The approach relies on the identification of the traits that mediate the linkages between adjacent trophic levels, i.e. “trait-matching”. Yet, how trait-matching explains the abundance and diversity of animal communities has been barely explored. This question may be particularly critical in the context of land use intensification, currently threatening biodiversity and associated ecosystem services. 2. We collected a large dataset...

Data from: Signatures of local adaptation in candidate genes of oaks (Quercus spp.) in respect to present and future climatic conditions

Christian Rellstab, Stefan Zoller, Lorenz Walthert, Isabelle Lesur, Andrea R. Pluess, René Graf, Catherine Bodénès, Christoph Sperisen, Antoine Kremer & Felix Gugerli
Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested if >3'500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show...

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: Local human pressures influence gene flow in a hybridizing Daphnia species complex

Benjamin Alric, Markus Möst, Isabelle Domaizon, Cecile Pignol, Piet Spaak & Marie-Elodie Perga
Anthropogenic environmental changes are considered critical drivers of the genetic structure of populations and communities through, for example, the facilitation of introgressive hybridization between syntopic species. However, the mechanisms by which environmental perturbations trigger changes in the genetic structure of populations and communities, such as the processes that determine the directionality of hybridization and patterns of mitochondrial introgression over many generations, remain largely unexplored. In this study, the changes in genetic structure of hybridizing members...

Data from: Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea

Ludovic Henneron, Michaël Aubert, Fréderic Archaux, Fabrice Bureau, Yann Dumas, François Ningre, Claudine Richter, Philippe Balandier & Matthieu Chauvat
Plant–soil interactions are increasingly recognized to play a major role in terrestrial ecosystems functioning. However, few studies to date have focused on slow dynamic ecosystems such as forests. As they are vertically stratified by multiple vegetation strata, canopy tree removal by thinning operations could alter forest plant community through tree canopy opening. Very little is known about cascading effects on soil biodiversity. We conducted a large-scale, multi-site assessment of collembolan assemblage response to long-term canopy...

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: Unusually limited pollen dispersal and connectivity of Pedunculate oak (Quercus robur) refugial populations at the species' southern range margin

Eva Moracho, Gerardo Moreno, Arndt Hampe & Pedro Jordano
Low-latitudinal range margins of temperate and boreal plant species typically consist of scattered populations that persist locally in microrefugia. It remains poorly understood how their refugial habitats affect patterns of gene flow and connectivity, key components for their long-term viability and evolution. We examine landscape-scale patterns of historical and contemporary gene flow in refugial populations of the widespread European forest tree Pedunculate oak (Quercus robur) at the species' southwestern range margin. We sampled all adult...

Data from: Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift

Cécile Gracianne, Pierre-Loup Jan, Sylvain Fournet, Eric Olivier, Jean-François Arnaud, Catherine Porte, Sylvie Bardou-Valette, Marie-Christine Denis, Eric Petit & Eric J. Petit
Studying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the...

Registration Year

  • 2016
    28

Resource Types

  • Dataset
    28

Affiliations

  • French National Institute for Agricultural Research
    28
  • French National Centre for Scientific Research
    8
  • University of Bordeaux
    5
  • University of Lyon System
    2
  • Swedish University of Agricultural Sciences
    2
  • Montpellier SupAgro
    2
  • University of Maryland, College Park
    2
  • University of Savoy
    2
  • Estación Biológica de Doñana
    1
  • Azerbaijan National Academy of Sciences
    1