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Salmon A.,Iowa State University | Ainouche M.L.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
Molecular Ecology | Year: 2010

Most plant species are recent or ancient polyploids (displaying at least one round of genome duplication in their history). Cultivated species (e.g. wheat, cotton, canola, sugarcane, coffee) and invasive species are often relatively recent polyploids, and frequently of hybrid origin (i.e. allopolyploids). Despite the genetic bottleneck occurring during the allopolyploid speciation process, the formation of such species from two divergent lineages leads to fixed heterozygosity decisive to their success. New phenotypes and new niche occupation are usually associated with this mode of speciation, as a result of both genomic rearrangements and gene expression changes of different magnitudes depending on the different polyploid species investigated. These gene expression changes affecting newly formed polyploid species may result from various, interconnected mechanisms, including (i) functional interactions between the homoeologous copies and between their products, that are reunited in the same nucleus and cell; (ii) the fate of duplicated copies, selective pressure on one of the parental copy being released which could lead to gene loss, pseudogenization, or alternatively, to subfunctionalization or neofunctionalization; and (iii) epigenetic landscape changes that in turn affect gene expression. As one of the interrelated processes leading to epigenetic regulation of gene expression, the DNA methylation status of newly formed species appears to be consistently affected following both hybridization and genome doubling. In this issue, Verhoeven et al. have investigated the fate of DNA methylation patterns that could affect naturally occurring new asexual triploid lineages of dandelions. As a result of such a ploidy level change, the authors demonstrate stably transmitted DNA methylation changes leading to unique DNA methylation patterns in each newly formed lineage. Most studies published to date on plant DNA methylation polymorphism were performed using restriction enzymes sensitive to methylation. Recently, new high-throughput methods were made available, thanks to the development of 'next-generation sequencing' techniques. The combination of these methods offers powerful and promising tools to investigate epigenetic variation in both model and non-model systems. © 2010 Blackwell Publishing Ltd. Source

Pierre J.-S.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
Oikos | Year: 2011

In the so-called 'patch problem', at any given moment, the forager must decide whether to leave the current patch or to remain there and continue foraging. Optimal foraging theory and subsequent theoretical works have identified theoretical optimal policies governing this decision. In a stochastic environment, the Bayesian framework has proved to be effective. A set of mechanistic proximal mechanisms explaining how parasitoid wasps may take decisions has been proposed. These mechanisms are based in on changes in the degree of motivation to continue foraging during a particular foraging episode. Using a simple, straightforward model, we show here that the psychological mechanism proposed mimics precisely the theoretical Bayesian solution, provided that motivation displays exponential decay, rather than the linear pattern of decay initially assumed. Changes in motivation thus function as a sort of analogue computer, and may be seen as more than purely heuristic rules of thumb. This link between psychological processes and ultimate optimisation places foraging theory in the domain of neuroeconomics. © 2011 The Authors. Source

Sirot E.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
Animal Behaviour | Year: 2010

Flight initiation distance (FID), the distance at which an animal begins to flee from an approaching intruder, is commonly used to estimate the impact of human activities on wildlife. It reflects the level of risk tolerated by the animals. However, animals frequently approached by nonthreatening humans may progressively learn that there will be no adverse consequence for them, and thus perceive a reduced level of risk. I used an optimality model to study how this habituation process and risk allocation strategies could interact to determine FID. First, I computed the optimal FID for a foraging animal confronted with a single kind of threat. In this situation, the model predicts that FID should increase with the level of risk perceived during each encounter, and decrease when encounters become more frequent. Next, I used the model to explore what could happen after the arrival of nonthreatening humans in the environment, assuming that, initially, only predators were present. I studied how these environmental modifications could progressively affect the expectations of the forager, and its FIDs towards predators and humans. The model predicts that risk allocation strategies may either facilitate or impede habituation to nonlethal disturbance, with conflicting effects on the FIDs. Depending on the initial predation regime, the disturbance conditions created by humans and the number of predators that remain after human arrival, the animal may either progressively accept the presence of nonthreatening humans or retain a high level of sensitivity towards both predators and humans. © 2010 The Association for the Study of Animal Behaviour. Source

Sirot E.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
Proceedings of the Royal Society B: Biological Sciences | Year: 2012

Game-theoretical models have been highly influential in behavioural ecology. However, these models generally assume that animals choose their action before observing the behaviour of their opponents while, in many natural situations, individuals in fact continuously react to the actions of others. A negotiation process then takes place and this may fundamentally influence the individual attitudes and the tendency to cooperate. Here, I use the classical model system of vigilance behaviour to demonstrate the consequences of such behavioural negotiation among selfish individuals, by predicting patterns of vigilance in a pair of animals foraging under threat of predation. I show that the game played by the animals and the resulting vigilance strategies take radically different forms, according to the way predation risk is shared in the pair. In particular, if predators choose their target at random, the prey respond by displaying moderate vigilance and taking turns scanning. By contrast, if the individual that takes flight later in an attack endures a higher risk of being targeted, vigilance increases and there is always at least one sentinel in the pair. Finally, when lagging behind its companion in fleeing from an attacker becomes extremely risky, vigilance decreases again and the animals scan simultaneously. © 2012 The Royal Society. Source

Ernoult A.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Alard D.,French National Institute for Agricultural Research
Landscape Ecology | Year: 2011

Understanding the determinants of hedgerow plant diversity in agricultural landscapes remains a difficult task, because the potential drivers affect the complete range of biodiversity components (alpha to gamma diversity). We surveyed herbaceous plant communities (of a height ≪1.5 m) in 84 hedgerows in the Seine river floodplain of France. Two types of potential drivers for species richness, accounting for landscape mosaic and hedgerow network, were recorded at both hedgerow and site scale. The distribution of species richness through the components of alpha hedgerow diversity (i.e. the average diversity within a habitat) and gamma hedgerow diversity (i.e. the total diversity across habitats) were assessed using additive partitioning methods, while the relationship between species diversity and its potential landscape drivers at both scales was modeled using Generalized Additive Models. Our results indicated that gamma hedgerow diversity is explained by the heterogeneity of the landscape structure, which is correlated with the mosaic of agricultural land use. At this scale, intrinsic properties of the configuration of the hedgerow networks have a weak influence on species richness. Alpha hedgerow diversity is also explained by landscape variables, accounting for both the configuration of agricultural mosaics and hedgerow networks, but to a lesser extent. Time lags for species responses are shown at both scales, and for the two types of drivers. Extinction or colonization debt may be indicated at both scales, while the remnant effects of former practices may also be responsible for such patterns at a local scale. We suggest that hedgerow management should take the specific parameters of both scales into account. At a local scale, management actions should aim to decrease the influence of adjacent land use when the impact is negative, through the implementation of extended buffer zones, while at the landscape and farm scales, agri-environmental schemes should be dedicated to the conservation of specific agricultural land uses. © Springer Science+Business Media B.V. 2011. Source

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