175 Works

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: Neighborhood effects determine plant-herbivore interactions below ground

Wei Huang, Elias Zwimpfer, Maxime R. Hervé, Zoe Bont & Matthias Erb
1. Plant neighbors can strongly influence the interactions between herbivores and focal plants, for instance by providing food of different quality (consumptive effects) or by changing the behavior and metabolism of the herbivore and the focal plant without being consumed (non-consumptive effects). Determining the species-specific contributions of consumptive and non-consumptive effects is important to understand the ecophysiological mechanisms which underlie neighborhood effects. 2. We quantified the impact of nine different grassland plant species on the...

Data from: Finding the best management policy to eradicate invasive species from spatial ecological networks with simultaneous actions

Sam Nicol, Régis Sabbadin, Nathalie Peyrard & Iadine Chades
1. Spatial management of invasive species is more likely to be successful when multiple locations are treated simultaneously. However, selecting the best locations to act is difficult due to the many options available at any time. 2. We design a near-optimal policy for applying multiple actions simultaneously for faster invasive species control within a network. Our method uses a recent optimisation tool, the Graph-based Markov decision process (GMDP). Since the policy can be difficult to...

Data from: How to quantify a distance-dependent landscape effect on a biological response

Paul Miguet, Lenore Fahrig & Claire Lavigne
To quantify the effect of the surrounding landscape context on a biological response at a site, most studies measure landscape variables within discs centred on this biological response (threshold-based method). This implicitly assumes that the effect of a unit area of the landscape is consistent up to a threshold distance beyond which it drops to zero. However, it seems more likely that the landscape effect declines with increasing distance from the biological response point. Here...

Data from: Outlier loci highlight the direction of introgression in oaks

Erwan Guichoux, Pauline Garnier-Gere, Lélia Lagache, Tiange Lang, Christophe Boury & Rémy J. Petit
Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Q. petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with...

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
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: The population biology of fungal invasions

Pierre Gladieux, Alice Feurtey, Michael E. Hood, Alodie Snirc, Joanne Clavel, Cyril Dutech, Melanie Roy & Tatiana Giraud
Fungal invasions are increasingly recognized as a significant component of global changes, threatening ecosystem health and damaging food production. Invasive fungi also provide excellent models to evaluate the generality of results based on other eukaryotes. We first consider here the reasons why fungal invasions have long been overlooked: they tend to be inconspicuous, and inappropriate methods have been used for species recognition. We then review the information available on the patterns and mechanisms of fungal...

Data from: Facilitation promotes invasions in plant-associated microbial communities

Mei Li, Zhong Wei, Jianing Wang, Alexandre Jousset, Ville-Petri Friman, Yangchun Xu, Qirong Shen & Thomas Pommier
While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant–pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise...

Data from: High genetic variation in resting stage production in a metapopulation: is there evidence for local adaptation?

Anne Carole Roulin, Mahendra Mariadassou, Matthew D. Hall, Jean-Claude Walser, Christoph Haag & Dieter Ebert
Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy,...

Data from: Fitness cost due to herbicide resistance may trigger genetic background evolution

Henri Darmency, Yosra Menchari, Valérie Le Corre & Christophe Délye
This paper investigates the possible existence of mechanisms counterbalancing the negative pleiotropic effects on development and reproduction that are conferred by alleles responsible for herbicide resistance in the weed Alopecurus myosuroides. We considered three herbicide-resistant, mutant acetyl-CoA carboxylase (ACCase) alleles: Leu1781, Asn2041 and Gly2078 found in eight resistant populations. Of these, Gly2078 is the only allele with a known fitness cost. We compared plants homozygous for wild-type ACCase alleles that were siblings of plants carrying...

Data from: Low reproductive isolation and highly variable levels of gene flow reveal limited progress toward speciation between European river and brook lampreys

Quentin Rougemont, Arnaud Gaigher, Emilien Lasne, Jessica Côte, Maïra Coke, Anne-Laure Besnard, Sophie Launey & Guillaume Evanno
Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here we used a combination of mating trials, experimental crosses and population genetics analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000...

Data from: Linking niche theory to ecological impacts of successful invaders: insights from resource fluctuation-specialist herbivore interactions

Cindy Gidoin, Lionel Roques & Thomas Boivin
1. Theories of species coexistence and invasion ecology are fundamentally connected and provide a common theoretical framework for studying the mechanisms underlying successful invasions and their ecological impacts. Temporal fluctuations in resource availability and differences in life-history traits between invasive and resident species are considered as likely drivers of the dynamics of invaded communities. Current critical issues in invasion ecology thus relate to the extent to which such mechanisms influence coexistence between invasive and resident...

Data from: Plasticity in leaf litter traits partly mitigates the impact of thinning on forest floor carbon cycling

Ludovic Henneron, Matthieu Chauvat, Frédéric Archaux, Marthe Akpa-Vinceslas, Fabrice Bureau, Yann Dumas, Francois Ningre, Claudine Richter, Philippe Balandier & Michael Aubert
1. Reducing stand density by thinning intensification has been emphasized as an efficient strategy of forest adaptation to climate change as it improves stand resistance to drought. Yet, it is still unclear how it could affect litter C cycling processes. Recent evidence indicates that the plasticity of an oak tree species can lead to a decline in its leaf litter quality and decomposability following thinning. The consequences for litter decomposition and forest floor C storage...

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: Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics

Amy J. Osborne, John Pearson, Sandra S. Negro, B. Louise Chilvers, Martin A. Kennedy & Neil J. Gemmell
The effect of MHC polymorphism on individual fitness variation in the wild remains equivocal; however, much evidence suggests that heterozygote advantage is a major determinant. To understand the contribution of MHC polymorphism to individual disease resistance or susceptibility in natural populations, we investigated two MHC class II B loci, DQB and DRB, in the New Zealand sea lion (NZSL, Phocarctos hookeri). The NZSL is a threatened species which is unusually susceptible to death by bacterial...

Data from: Within-range translocations and their consequences in European larch

Stefanie Wagner, Sascha Liepelt, Sophie Gerber & Rémy J. Petit
In contrast to biological invasions, translocations of individuals within a species range are understudied, due to difficulties in systematically detecting them. This results in limited knowledge about the corresponding processes and uncertainties regarding the status of extant populations. European larch, a forest tree whose fragmented native distribution is restricted to the Alps and to other Central European mountains, has been massively planted for at least 300 years. Here we focus on the genetic characterization of...

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: 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: 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: The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies

Marine Pratlong, Anne Haguenauer, Olivier Chabrol, Christophe Klopp, Pierre Pontarotti & Didier Aurelle
The question of species survival and evolution in heterogeneous environments has long been a subject for study. Indeed, it is often difficult to identify the molecular basis of adaptation to contrasted environments, and nongenetic effects increase the difficulty to disentangle fixed effects, such as genetic adaptation, from variable effects, such as individual phenotypic plasticity, in adaptation. Nevertheless, this question is also of great importance for understanding the evolution of species in a context of climate...

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...

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  • French National Institute for Agricultural Research
  • French National Centre for Scientific Research
  • University of Bordeaux
  • Centre de Coopération Internationale en Recherche Agronomique pour le Développement
  • Montpellier SupAgro
  • University of Montpellier
  • University of Liège
  • Ecologie des Forêts Méditerranéennes
  • University of Toulouse
  • University of Lausanne