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.

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.

In response to a request made by students in agricultural education (AE), a consortium involving AE, MNHN and CEFE was created in 2021, in order to study the complex and poorly-known relationship between livestock breeding and coprophagous beetles communities. Over the course of two years of collaboration, systems that not only answer the initial question, but also enrich educational approaches, improve scientific knowledge and question practices have been devised, discussed and tested with students and teachers in a dozen establishments. They are now intended to be deployed in agricultural schools throughout metropolitan France. Designed to answer the questions of AE learners, these systems allow future farmers to become familiar with the scientific approach and to participate in the constitution of a new knowledge, a key issue for agroecology development. Initiated early in their career, the approach should accompany future farmers in their practices and thus concern a large part of the society, while enriching research questions.

We advocate to study how adaptation of mosquito vectors to environmental modifications associated with global change impact their fitness and the life-history traits influencing vectorial capacity, in order to predict more accurately the epidemiological consequences of niche expansions and the spread of mosquito-borne pathogens. Such predictions are essential to adapt disease control programmes and avoid the emergence of vector-borne diseases. Toward this aim, we propose to adapt to the study of natural mosquito populations the multi-state/multi-event mark-recapture (MSMR) analytical approach, that has been instrumental to obtain unbiased field estimates of vertebrate populations demographic parameters. Individual capture histories will be obtained by 'marking' mosquitoes with genetic fingerprints, using environmental DNA collected non-invasively. We propose to verify whether the recent invasion of urban-polluted and coastal-brackish water habitats by populations of the Anopheles gambiae complex and Aedes aegypti, which are among the best vectors of malaria and dengue in the world, is adaptative, and to assess the cost of adaptation by comparing fitness trade-offs in reciprocally transplanted natural populations occurring in contrasting environments. To gain insights about the generality of the patterns observed, we propose to conduct these field and semi-field experiments using mosquito populations from four African countries and two environmental stressors, i.e. water pollution and salinity.

Adaptation plans have become increasingly popular across the globe. While some adaptations have beneficial outcomes, many have unintended consequences for vulnerability. This is particularly relevant in coastal zones where both marine and land-based adaptations have an impact and human pressures are greatest. We believe a better understanding of the underlying social-ecological processes driving adaptation in coastal areas, particularly the feedbacks between risk from biophysical change, cognitive processes, and adaptation, will reduce the incidence of maladaptations while increasing the frequency of win-win adaptations. Findings will directly inform and support adaptation decision making in coastal areas, add to current knowledge on vulnerability and adaptation, and facilitate learning and appreciation of feedbacks in adaptation responses. We use a model of “private proactive adaptation to climate change” to assess the interactions between: a) the actual risk posed by climate change; b) cognitive factors such as perceived risk and perceived adaptive capacity; c) adaptations; and d) situated learning when decisions makers participate in modelling processes. We assess the relationship between these drivers and adaptation plans in coastal areas at three scales: individual decision makers; local communities of practice; and regional planning authorities. Participatory modelling with decision makers will result in lasting impacts for enhanced coastal resilience. In each of three coastal regions: the Languedoc-Rousillon in France; Cornwall in the UK; and the Garden Route coast in South Africa, we will identify two to three examples where users, communities of practice, and regional authorities have developed adaptation plans and strategies resulting in the unintended transfer of vulnerability from one sector, scale or place to another. We will use available empirical data and models, participatory agent-based modeling, interpretative methods; and reflexive learning to catalyze and assess changes in the cognitive perceptions of decision makers who design adaptation plans.