CNRS Ecosystems, Biodiversity, and Evolution Laboratory

Rennes, France

CNRS Ecosystems, Biodiversity, and Evolution Laboratory

Rennes, France
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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.

Bringel F.,University of Strasbourg | Couee I.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
Frontiers in Microbiology | Year: 2015

The phyllosphere, which lato sensu consists of the aerial parts of plants, and therefore primarily, of the set of photosynthetic leaves, is one of the most prevalent microbial habitats on earth. Phyllosphere microbiota are related to original and specific processes at the interface between plants, microorganisms and the atmosphere. Recent -omics studies have opened fascinating opportunities for characterizing the spatio-temporal structure of phyllosphere microbial communities in relation with structural, functional, and ecological properties of host plants, and with physico-chemical properties of the environment, such as climate dynamics and trace gas composition of the surrounding atmosphere. This review will analyze recent advances, especially those resulting from environmental genomics, and how this novel knowledge has revealed the extent of the ecosystemic impact of the phyllosphere at the interface between plants and atmosphere. Highlights: • The phyllosphere is one of the most prevalent microbial habitats on earth. • Phyllosphere microbiota colonize extreme, stressful, and changing environments. • Plants, phyllosphere microbiota and the atmosphere present a dynamic continuum. • Phyllosphere microbiota interact with the dynamics of volatile organic compounds and atmospheric trace gasses. © 2015 Bringel and Couée.

Colinet H.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Sinclair B.J.,University of Western Ontario | Vernon P.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Renault D.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
Annual Review of Entomology | Year: 2015

All climate change scenarios predict an increase in both global temperature means and the magnitude of seasonal and diel temperature variation. The nonlinear relationship between temperature and biological processes means that fluctuating temperatures lead to physiological, life history, and ecological consequences for ectothermic insects that diverge from those predicted from constant temperatures. Fluctuating temperatures that remain within permissive temperature ranges generally improve performance. By contrast, those which extend to stressful temperatures may have either positive impacts, allowing repair of damage accrued during exposure to thermal extremes, or negative impacts from cumulative damage during successive exposures. We discuss the mechanisms underlying these differing effects. Fluctuating temperatures could be used to enhance or weaken insects in applied rearing programs, and any prediction of insect performance in the field-including models of climate change or population performance-must account for the effect of fluctuating temperatures. © 2015 by Annual Reviews. All rights reserved.

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.

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.

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.

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.

Paillisson J.-M.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Marion L.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
Ecological Engineering | Year: 2011

The importance of water level fluctuations (WLF) and a suite of linked factors in lake management has been the focus of active research in the past decades. The interest of WLF as a method to limit excessive macrophyte development is addressed in this paper. For this, we assessed the response of three common nymphaeid species (Nymphaea alba, Nuphar lutea and Nymphoides peltata) in terms of biomass to slight changes in water regime (<50cm) in a large shallow eutrophic lake in the frame of a long-term study (1995-2007). The modelled response of the plants to several descriptors of WLF (water level (WL) and duration of exposure to high water levels (D) in the course of various plant life cycle stages) varied between species. Significant negative correlations (r2 ranging from 58.1 to 75.4%) were found between changes in N. alba biomass (until 50%) and high water regimes occurring in all life stages of the plant. Such relationships were also observed for N. lutea, but to a lesser degree, and variations in N. peltata biomass were poorly explained by WLF. Support for the importance of the period in the life cycle of the plant in which high water regimes occur is provided to explain the successful limitation in plant biomass, despite the known tolerance of nymphaeids to large WLF. Results also reflect the importance of lake size, and the supposed factors associated with WLF, in the management of dense macrophyte-covered aquatic ecosystems. Additional research on this issue is needed to generate more widespread application of WLF under different environmental conditions (trophic state, morphology and size of lakes). © 2010 Elsevier B.V.

Chelaifa H.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Monnier A.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Ainouche M.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
New Phytologist | Year: 2010

•Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaptation of newly formed allopolyploid species. In spite of the significant progress made in recent years, few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions.•We used Agilent rice oligomicroarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classic example of recent allopolyploid speciation: S. anglica formed during the 19th century following genome duplication of the hybrid S. × townsendii.•Our data indicate important, but different, effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance was attenuated following genome duplication in S. anglica, but this species exhibits an increased number of transgressively overexpressed genes.•These results reflect the decoupled effects of the 'genomic shock' following hybridization and genome redundancy on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).

Guiller A.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Madec L.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory
BMC Evolutionary Biology | Year: 2010

Background. Despite its key location between the rest of the continent and Europe, research on the phylogeography of north African species remains very limited compared to European and North American taxa. The Mediterranean land mollusc Cornu aspersum (= Helix aspersa) is part of the few species widely sampled in north Africa for biogeographical analysis. It then provides an excellent biological model to understand phylogeographical patterns across the Mediterranean basin, and to evaluate hypotheses of population differentiation. We investigated here the phylogeography of this land snail to reassess the evolutionary scenario we previously considered for explaining its scattered distribution in the western Mediterranean, and to help to resolve the question of the direction of its range expansion (from north Africa to Europe or vice versa). By analysing simultaneously individuals from 73 sites sampled in its putative native range, the present work provides the first broad-scale screening of mitochondrial variation (cyt b and 16S rRNA genes) of C. aspersum. Results. Phylogeographical structure mirrored previous patterns inferred from anatomy and nuclear data, since all haplotypes could be ascribed to a B (West) or a C (East) lineage. Alternative migration models tested confirmed that C. aspersum most likely spread from north Africa to Europe. In addition to Kabylia in Algeria, which would have been successively a centre of dispersal and a zone of secondary contacts, we identified an area in Galicia where genetically distinct west and east type populations would have regained contact. Conclusions. Vicariant and dispersal processes are reviewed and discussed in the light of signatures left in the geographical distribution of the genetic variation. In referring to Mediterranean taxa which show similar phylogeographical patterns, we proposed a parsimonious scenario to account for the "east-west" genetic splitting and the northward expansion of the western (B) clade which roughly involves (i) the dispersal of ancestral (eastern) types through Oligocene terranes in the Western Mediterranean (ii) the Tell Atlas orogenesis as gene flow barrier between future west and east populations, (iii) the impact of recurrent climatic fluctuations from mid-Pliocene to the last ice age, (iv) the loss of the eastern lineage during Pleistocene northwards expansion phases. © 2010 Guiller and Madec; licensee BioMed Central Ltd.

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