255 Works

Pedigree-free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer

Laura Gervais, Aidan.J Mark Hewison, Nicolas Morellet, Maria Bernard, Joël Merlet, Bruno Cargnelutti, Yannick Chaval, Benoit Pujol & Erwan QUEMERE
Assessing the evolutionary potential of animal populations in the wild is crucial to understanding how they may respond to selection mediated by rapid environmental change (e.g. habitat loss and fragmentation). A growing number of studies have investigated the adaptive role of behaviour, but assessments of its genetic basis in a natural setting remain scarce. We combined intensive biologging technology with genome-wide data and a pedigree-free quantitative genetic approach to quantify repeatability, heritability and evolvability for...

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...

Opposite latitudinal patterns for bird and arthropod predation revealed in the experiments with differently colored artificial prey

Elena Zvereva, Bastien Castagneyrol, Tatiana Cornelissen, Anders Forsman, Juan Antonio Hernández-Agüero, Tero Klemola, Lucas Paolucci, Vicente Polo, Norma Salinas, K. Jurie Theron, Guorui Xu, Vitali Zverev & Mikhail Kozlov
The strength of biotic interactions is generally thought to increase towards the equator, but support for this hypothesis is contradictory. We explored whether predator attacks on artificial prey of eight different colours vary among climates and whether this variation affects the detection of latitudinal patterns in predation. The data set provides number of damage marks on each of 1320 plasticine caterpillars of eight different colours, which were attached to branches of woody plants and exposed...

From refugia to contact: pine processionary moth hybrid zone in a complex biogeographic setting

Kahraman İpekdal, Christian Burban, Laure Sauné, Andrea Battisti & Carole Kerdelhué
Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyse their co-occurrence and hybridisation patterns in this biogeographical context. We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between...

Data from: Leaf drought tolerance cannot be inferred from classic leaf traits in a tropical rainforest

Isabelle Maréchaux, Laurent Saint-André, Megan K. Bartlett, Lawren Sack & Jérôme Chave
Plants are enormously diverse in their traits and ecological adaptation, even within given ecosystems, such as tropical rainforests. Accounting for this diversity in vegetation models poses serious challenges. Global plant functional trait databases have highlighted general trait correlations across species that have considerably advanced this research program. However, it remains unclear whether trait correlations found globally hold within communities, and whether they extend to drought tolerance traits. For 134 individual plants spanning a range of...

Data from: Fear of the dark? contrasting impacts of humans vs lynx on diel activity of roe deer across Europe

Nadège C. Bonnot, Ophélie Couriot, Anne Berger, Francesca Cagnacci, Simone Ciuti, Johannes De Groeve, Benedikt Gehr, Marco Heurich, Petter Kjellander, Max Kröschel, Nicolas Morellet, Leif Sönnichsen & A.J. Mark Hewison
Humans, as super predators, can have strong effects on wildlife behaviour, including profound modifications of diel activity patterns. Subsequent to the return of large carnivores to human-modified ecosystems, many prey species have adjusted their spatial behaviour to the contrasting landscapes of fear generated by both their natural predators and anthropogenic pressures. The effects of predation risk on temporal shifts in diel activity of prey, however, remain largely unexplored in human-dominated landscapes. We investigated the influence...

Data from: Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

Olivier Lepais, Laura Taillebois, Stephen Sabatino, Aurélie Manicki, Françoise Daverat & David José Nachon
Hybridization dynamics between co-occurring species in environments where human-mediated changes take place is important to quantify for furthering our understanding of human impacts on species evolution and for informing management. The allis shad Alosa alosa (Linnaeus, 1758) and twaite shad Alosa fallax (Lacépède, 1803), two clupeids sister species, have been severely impacted by human activities across Europe. The shrinkage of A. alosa distribution range along with the decline of the remaining populations’ abundance threaten its...

Data from: Assessing the effects of quantitative host resistance on the life-history traits of sporulating parasites with growing lesions

Melen Leclerc, Julie Clément, Didier Andrivon & Frédéric Hamelin
Assessing life-history traits of parasites on resistant hosts is crucial in evolutionary ecology. In the particular case of sporulating pathogens with growing lesions, phenotyping is difficult because one needs to disentangle properly pathogen spread from sporulation. By considering Phytophthora infestans on potato, we use mathematical modelling to tackle this issue and refine the assessment pathogen response to quantitative host resistance. We elaborate a parsimonious leaf-scale model by convolving a lesion growth model and a sporulation...

Data from: New resources for genetic studies in Populus nigra: genome wide SNP discovery and development of a 12k Infinium array

P. Faivre Rampant, G. Zaina, V. Jorge, S. Giacomello, V. Segura, S. Scalabrin, V. Guérin, E. De Paoli, C. Aluome, M. Viger, F. Cattonaro, A. Payne, P. PaulStephenRaj, MC. Le Paslier, A. Berard, M. R. Allwright, M. Villar, G. Taylor, C. Bastien, M. Morgante, P. Faivre-Rampant & M. C. Le Paslier
Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1,878,727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions; 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over...

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, P. Gladieux, A. L. Coi, G. Zara, M. Budroni, F. Bigey, S. Mallet, S. Marsit, V. Galeote, S. Dequin & J. L. Legras
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: Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex

Julie Jaquiéry, Solenn Stoeckel, Pierre Nouhaud, Lucie Mieuzet, Frédérique Mahéo, Fabrice Legeai, Nina Bernard, Antoine Bonvoisin, Renaud Vitalis & Jean-Christophe Simon
A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result in adaptive population differentiation and reproductive isolation and affect differentially the level of genetic divergence along the genome. Genome-wide scan of large sets of individuals from multiple populations is a powerful approach to identify loci or genomic regions under ecologically divergent selection. Here, we focused on the pea aphid, a species complex of...

Data from: Modeling spatial expansion of invasive alien species: relative contributions of environmental and anthropogenic factors to the spreading of the harlequin ladybird in France

Sophie Veran, Sylvain Piry, Vincent Ternois, Christine N. Meynard, Benoit Facon & Arnaud Estoup
Species distribution models (SDM) have often been used to predict the potential ranges of introduced species and prioritize management strategies. However, this approach assumes equilibrium between occurrences and environmental gradients, an assumption which is violated during the invasion process, where many suitable sites are empty because the species has not yet reached them. Here we considered the invasive ladybird Harmonia axyridis as a case study to show the benefits of using a dynamic colonization–extinction model...

Data from: Varroa destructor changes cuticular hydrocarbons to mimic its new host.

Zachary Y. Huang, Yves Le Conte, Jean-Philippe Christidès, Zhi Jiang Zeng, Maurice Roux, Anne-Genevieve Bagnères, Z. Y. Huang, Y. Le Conte & Z. J. Zeng
Varroa destructor (Vd) is a honeybee ectoparasite. Its original host is the Asian honeybee, Apis cerana, but it has also become a severe, global threat to the European honeybee, Apis mellifera. Previous studies have shown that Varroa can mimic a host's cuticular hydrocarbons (HC), enabling the parasite to escape the hygienic behaviour of the host honeybees. By transferring mites between the two honeybee species, we further demonstrate that Vd is able to mimic the cuticular...

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: Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks

Camille Lepoittevin, Catherine Bodénès, Emilie Chancerel, Laure Villate, Tiange Lang, Isabelle Lesur, Christophe Boury, François Ehrenmann, Diana Zelenika, Anne Boland, Céline Besse, Pauline Garnier-Géré, Christophe Plomion & Antoine Kremer
An Illumina Infinium SNP genotyping array was constructed for European white oaks. Six individuals of Quercus petraea and Q. robur were considered for SNP discovery using both previously obtained Sanger sequences across 676 gene regions (1371 in vitro SNPs) and Roche 454 technology sequences from 5112 contigs (6542 putative in silico SNPs). The 7913 SNPs were genotyped across the six parental individuals, full-sib progenies (one within each species and two interspecific crosses between Q. petraea...

Data from: Impact of past climatic changes and resource availability on the population demography of three food-specialist bees

Simon Dellicour, Denis Michez, Jean-Yves Rasplus & Patrick Mardulyn
Past climate change is known to have strongly impacted current patterns of genetic variation of animals and plants in Europe. However, ecological factors also have the potential to influence demographic history, and thus patterns of genetic variation. In this study, we investigated the impact of past climate, and also the potential impact of host plant species abundance, on intraspecific genetic variation in three co-distributed and related specialized solitary bees of the genus Melitta with very...

Data from: Combining GWAS and RNA-seq approaches for detection of the causal mutation for hereditary junctional epidermolysis bullosa in sheep

Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Julio Benavides, Valentín Perez, Gwenola Tosser-Klopp, Christophe Klopp, Stephen J. Keennel & Juan José Arranz
In this study, we demonstrate the use of a genome-wide association mapping together with RNA-seq in a reduced number of samples, as an efficient approach to detect the causal mutation for a Mendelian disease. Junctional epidermolysis bullosa is a recessive genodermatosis that manifests with neonatal mechanical fragility of the skin, blistering confined to the lamina lucida of the basement membrane and severe alteration of the hemidesmosomal junctions. In Spanish Churra sheep, junctional epidermolysis bullosa (JEB)...

Data from: Adaptive admixture in the West African bovine hybrid zone: insight from the Borgou population

Laurence Flori, Sophie Thevenon, Guiguigbaza-Kossigan Dayo, Marcel Sénou, Souleymane Sylla, David Berthier, Katayou Moazami-Goudarzi, Mathieu Gautier & Katayoun Moazami-Goudarzi
Understanding the adaptive response to environmental fluctuations represents a central issue in evolutionary biology. Population admixture between divergent ancestries has often been considered as an efficient short-term adaptation strategy. Cattle populations from the West African Bos taurus x Bos indicus hybrid zone represent a valuable resource to characterize the effect of such adaptive admixture at the genome level. We here provide a detailed assessment of the global and local genome ancestries of the Borgou breed,...

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: Development of SNP genotyping arrays in two shellfish species

Sylvie Lapègue, Estelle Harrang, Serge Heurtebise, Emilie Flahauw, Cécile Donnadieu, Philippe Gayral, Marion Ballenghien, Lucie Genestout, Laetitia Barbotte, Rachid Mahla, Pierrick Haffray, Christophe Klopp, P. Gayral, M. Ballenghien, C. Donnadieu, C. Klopp & P. Haffray
Use of SNPs has been favored due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two...

Data from: Estimation of the dispersal of a major pest of maize by cline analysis of a temporary contact zone between two invasive outbreaks

Gérald Bermond, Aurélie Blin, Elodie Vercken, Virginie Ravigné, Adrien Rieux, Sophie Mallez, Thibaut Morel-Journel, Thomas Guilllemaud & Thomas Guillemaud
Dispersal is a key factor in invasion, and in the persistence and evolution of species. Despite the importance of estimates of dispersal distance, dispersal measurement remains a real methodological challenge. In this study, we characterized dispersal by exploiting a specific case of biological invasion, in which multiple introductions in disconnected areas lead to secondary contact between two differentiated expanding outbreaks. By applying cline theory to this ecological setting, we estimated σ, the standard deviation of...

Data from: Divergent evolutionary processes associated with colonization of offshore islands

Natália Martínková, Ross Barnett, Thomas Cucchi, Rahel Struchen, Marine Pascal, Michel Pascal, Martin C. Fischer, Thomas Higham, Selina Brace, Simon Y. W. Ho, Jean-Pierre Quéré, Paul O'Higgins, Laurent Excoffier, Gerald Heckel, A. Rus Hoelzel, Keith M. Dobney, Jeremy B. Searle & A. Rus Hoelzel
Oceanic islands have been a test ground for evolutionary theory, but here, we focus on the possibilities for evolutionary study created by offshore islands. These can be colonized through various means and by a wide range of species, including those with low dispersal capabilities. We use morphology, modern and ancient sequences of cytochrome b (cytb) and microsatellite genotypes to examine colonization history and evolutionary change associated with occupation of the Orkney archipelago by the common...

Data from: Ecological determinants of mating system within and between three Fagus sylvatica populations along an elevational gradient

Julie Gauzere, Etienne K. Klein & Sylvie Oddou-Muratorio
Studies addressing the variation of mating system between plant populations rarely account for the variability of these parameters between individuals within populations, although this variability is often non-negligible. Here, we propose a new direct method based on paternity analyses (Mixed Effect Mating Model) to estimate individual migration (mi) and selfing rates (si) together with the pollen dispersal kernel. Using this method and the KINDIST approach, we investigated the variation of mating system parameters within and...

Data from: Effects of two grass species on the composition of soil fungal communities

Bello Mouhamadou, Jeremy Puissant, Emanuelle Personeni, Marie Desclos-Theveniau, Eva M. Kastl, Michael Schloter, Lucie Zinger, Julien Roy, Sandra Lavorel, Roberto A. Geremia, E. Personeni, M. Desclos-Theveniau, B. Mouhamadou, J. Puissant, L. Zinger, J. Roy, R. A. Geremia & S. Lavorel
Many studies have shown effects of plants species on fungal communities, but these are often confounded with soil effects. Thus, the specific role of plant species in structuring rhizospheric and soil fungal communities is poorly described. Our study used microcosms in which plants were grown under artificial conditions to bridge this gap. Two perennial grasses dominating subalpine grasslands, Festuca paniculata and Dactylis glomerata, were grown at two levels of fertilization on standard soil. Fungal communities...

Data from: Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity

Najwa Taib, Jean-François Mangot, Isabelle Domaizon, Gisèle Bronner & Didier Debroas
Recent advances in next-generation sequencing (NGS) technologies spur progress in determining the microbial diversity in various ecosystems by highlighting, for example, the rare biosphere. Currently, high-throughput pyrotag sequencing of PCR-amplified SSU rRNA gene regions is mainly used to characterize bacterial and archaeal communities, and rarely to characterize protist communities. In addition, although taxonomic assessment through phylogeny is considered as the most robust approach, similarity and probabilistic approaches remain the most commonly used for taxonomic affiliation....

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