Gene flow has long been considered to take place within species only but we now realize that it often occurs between species as well. We still don’t know, however, how much gene flow effectively affects the genome of hybridizing species in the late stage of speciation. Such hybridization may be a source of adaptive genetic variation via the transfer of adaptations from the genome of one species to another, a phenomenon called “adaptive introgression”. While there are a few known prominent examples, its overall importance for adaptation is still largely unknown. In this project, we address the following main questions: i) how much of the genome is affected by introgression and ii) what proportion of introgression is adaptive? We have selected the Iberian wall lizard species complex because they have accumulated substantial genomic divergence; in spite of strong barriers to gene flow, nuclear and mitochondrial introgression still occurs; a transcriptome from our model and a reference genome from a close relative are available and we know their distribution, ecology and climatic niches. Last, we already have over 1000 tissue samples so sampling will be limited to additional locations specifically targeted for this project. To achieve this, we will use whole-genome sequencing to quantify the proportion of the genome affected by admixture. We will then quantify which proportion of introgressed genome is better explained by positive selection. To do so, instead of trying to pinpoint which genes have been experienced adaptive introgression, we will develop a theoretical study using simulations to establish the neutral variance in admixture rates among loci then estimate which proportion of admixture events cannot be explained by neutral processes (see Task 4). To overcome some of the limits of purely genomic approaches, we also propose an ecological test of the adaptation hypothesis based on candidate genes for climatic adaptation (mitochondrial DNA and the nuclear genes of the OXPHOS chain) in populations living in contrasted climatic conditions (Task 5). We will sample several pairs of populations within each species, each pair being composed of one population located in highly suitable climatic areas and the other in areas where climatic conditions resemble the climatic niche of a hybridizing (donor) species. Finding more loci that have been subjected to introgression in areas that resemble more the climatic conditions of the “donor” species would support the role of adaptive introgression. Tasks 1 & 2 We will model the current realized climatic niche in all lineages. We will then sample populations in locations (2 per species) of high climatic suitability for the focal species and in the heart of their distribution and in locations (2 per species) where climatic suitability is higher for the other species that hybridizes with the focal species. Task 3 We will obtain WGS data from 3 individuals in each sampled population (6 per species, 6 species). Task 4 We will establish by simulation the neutral variance in introgression levels between nuclear loci in the absence of selection. This should give us the limits of the variation that can be reached between loci in terms of introgression level in absence of selection and allow developing methodological tools to identify loci that have been subject to adaptive introgression. Task 5 We will identify introgressed genomic regions using already published methods then apply results from task 4 to test our idea that the proportion of loci affected by adaptive introgression (the proportion of high-frequency introgressed alleles that cannot be explained by neutral processes) is higher in areas where climatic conditions are closer to the climatic niche of the species which “gave” its genes through introgression, both for the whole genome data and for the OXPHOS genes and mtDNA.

A global increase in the demand for wood products has been observed worldwide during the last decades. This trend is expected to continue in the future as a consequence of population growth. Additionally, the need for wood is augmented by the increasing substitution of fossil energy by wood biomass-based energy to mitigate greenhouse gas emissions. This demand will not be satisfied by natural and naturally regenerated forests: they are threatened by high deforestation rates and forest degradation mainly in the tropics and the costs of wood mobilization in the temperate zones is a concern. Forest plantations (FP) are therefore expected to provide a large part of the global wood supply. Their ability to meet wood demand is limited by competing land uses. Higher stand yields must be obtained on soils that may not necessarily support such intensification especially as nitrogen (N) and phosphorus (P) exportations by biomass removal are generally not offset by fertilization. Therefore, FP sustainability is currently a major concern, particularly with regard to serious long-term N and P deficits. Innovative FP management schemes, and attractive to the stakeholders must be then deployed. The Intens&Fix project will deal with the ecological intensification of FP through the association of N2-fixing species (NFS) with the goal to increase stand production as, in particular, a result of better N and P availability in the soil. These systems hould combine positive environmental impacts while ensuring social-economical improvement of livelihood for smallholders or performances for commercial companies. The project will develop an experimental approach on various and complementary FP with associated NFS, both in France (Juglans sp. and Alnus cordata or herbaceous NFS in Languedoc, Populus sp + Robinia pseudoacacia. in North-Est of France) and in the Tropics (mixed-species plantations of Eucalyptus grandis and Acacia mangium in Brazil and Congo). An integrated biophysical model will be developed for the simulation of mixed species in FP. Outputs of virtual experiments performed with the biophysical model will feed a plantation-level model allowing to assess the economical feasibility and to test decision rules for the management of FP with NFS. Crossing models outputs and a survey of stakeholders’ innovation process concerning the use of NFS will entitle us to assess the potential development of these systems. The approach will be multidisciplinary and involve scientists working in ecophysiology, biogeochemistry, soil science, microbiology, silviculture, socio-economics, and modelling. This project will contribute to the production of innovative results i.e. refined methodological techniques for estimation of N transfer, documentation of mechanisms of competition/ facilitation for N and P bioavailability, model coupling water, N and C functioning adapted to mixed-species forests and practices (species, density…) to manage NFS in FP, and socio-economical assessment of these new management schemes. The results will be valorised through publications in high level scientific journals, as well as in R/D journals and participation to international conferences. More generally the involvement of a top resource partner in farm forestry and agroforestry, the participative approach deployed, and the strong partnership developed with producer organisations in France, Brazil and Congo will warrant a large and efficient dissemination of the Intens&Fix results. From an operational view point, the Intens&Fix project will provide tools of ecological intensification to significantly improve FP management with specific targets in eucalyptus plantations in Congo and Brazil (several millions ha), Very Short Rotation Coppices, and high value timber in agroforestry systems (potential of several millions ha in Europe).

Animal bodies house trillions of bacteria, which can influence host behavior in ways that have far-reaching implications for host ecology and evolution. Recent studies have revealed surprising roles for bacteria in shaping behaviors across many animal taxa. But questions remain and recent perspective papers have thus emphasized the need of studying the interaction between non-pathogenic bacteria and host behavior. In many species, individuals preferentially mate with MHC (Major Histocompatibility Complex) unrelated partners which they discriminate using odor cues. The mechanism by which MHC genes influence odor is still unclear, but one hypothesis suggests that MHC genes may influence body odor indirectly by shaping bacterial communities in scent integument. Bacteria are well-known to produce odorants, but whether they shape the odor cues signaling MHC genotype remains unknown. The main objective of the BactOdo project is to inquire whether bacteria in scent integument may be responsible for the production of MHC-related odors in birds. We will adopt a step by step empirical and experimental approach, bringing together the fields of genetic, behavioral, microbial and chemical ecology. We will use a bird model, the blue petrel Halobaena caerulea nesting on Kerguelen Archipelago. The blue petrel is particularly well adapted for such a project as it preferentially mates with MHC unrelated partners, its musky odor carries information on genetic relatedness and it possesses a very well developed olfactory sense. The BactOdo project will be organized around 4 scientific tasks, plus a coordination task and a communication task. More specifically, we will determine (1) whether microbial communities in feathers and preen gland correlate with body odor and MHC traits. Then we will determine whether an experimental change in bacterial community disrupts (2) the MHC signal in odors and (3) the perception by mice of odor similarity between related birds. Finally we will determine (4) whether social relationships between pair mates make their bacterial community more similar and therefore reduce the MHC signal in odor. Our interdisciplinary BactOdo project aims therefore at filling a knowledge gap within one of the most attractive field of research in evolutionary ecology in the past decade, i.e., the role of odor cues in MHC-related mate choice. This very innovative work will include cutting edge ultra-deep sequencing methods, and fells into efforts being made worldwide to describe the factors associated with variations in host-associated microbiota (Human Microbiome Project, Earth Microbiome Project). This project will be carried out at the "Centre d’Ecologie Fonctionelle et Evolutive" (CEFE, UMR 5175), Montpellier, in the Behavioural Ecology group, which has decade-long experience on olfactory communication in petrels and fieldwork at Kerguelen Archipelago. In addition, the CEFE hosts several research groups on chemistry and microbiology and the candidate will be associated to a network of scientists from complementary backgrounds, creating a supremely appropriate environment for research in this area.