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.

Eukaryotic organisms exhibit strikingly complex gene and genome architectures whose origin remains largely debated. In 2003, Michael Lynch proposed that this complexity emerged thanks to non-adaptive forces. Under this hypothesis, many genomic traits would be controlled by the balance between the emergence of slightly deleterious variants and their fixation rate, which ultimately depends on the effective population size (Ne). Although appealing because it is based on universal principles of population genetics, Lynch's theory has rarely been tested empirically. Here, we will compare the genome architecture of closely related species with contrasted Ne in five different groups of animals. We will first evaluate the influence of Ne on the evolution of genome size and on the dynamics of transposable elements. Then, we will test if Ne has an influence on the gene structure (number and size of introns) and transcription complexity (number and frequency of alternative transcripts). In parallel, we will use modeling and simulations to understand the reasons for a possible lack of applicability and to ultimately redefine or refine the contours of Lynch’s theory.

The ongoing global change is on the verge of triggering an unprecedented biodiversity crisis. This stimulated numerous studies about eco-evolutionary interactions conditioning the faunal response to environmental changes. As the past can be a key to the present, the present can be a key to the past. Revisiting past crises at the light of the concepts derived from studies on modern perturbations has the potential to provide an original view of past processes, and together to enlighten the dynamics that lead to modern biodiversity. By mobilizing multi-disciplinary expertises (paleobiology, ecology, evolution, developmental biology, evo-devo, paleoenvironments), the ECODEV project aims at renewing the understanding of an ancient period (the Late Devonian) characterized by one of the five major mass extinctions of Earth History. The project focuses on few model organisms (foraminifers, conodonts, cartilaginous and bony fishes), chosen for their abundance in sediments allowing the use of quantitative methods. (1) Three sections sampling all the Late Devonian period have been identified in France, Germany and Algeria. A detailed sampling will be performed during field trips and the fossil remains will be picked in order to deliver material for the other tasks. (2) Using geochemical proxies, environmental trends will be characterized and the trophic position of the groups of interest will be clarified. These analyses will be based on relevant well-known markers (oxygen isotopes for temperature; Rare Earth Elements for productivity). This task will also includes methodological developments. Benefiting from experimental data on fishes bred in controlled conditions, methods based on calcium isotopes will be developed to estimate temperatures as well as the trophic position of organisms. (3) The eco-evolutionary dynamics will be analyzed using geometric morphometrics. For each fossil group, these methods will deliver estimates of morphological diversity (disparity). This information will be interpreted in terms of occupation of the ecological space and resource exploitation, because the form of conodont and fish teeth is under obvious selective pressures related to nutrients, and form of foraminifers is related to subtract exploitation. Furthermore, evolutionary patterns will be documented. They constitute an important component of the adjustment of organisms to their environment. The interpretation of morphological variations in these ancient fossils will be supported by comparison with a modern model. Developments regarding multivariate data analyses will allow improvements in the exploitation of an exceptional data set including several parallel records (morphometrics of each group, geochemical proxies). (4) The project will be completed by an experimental approach on the lesser-spotted dogfish (Scyliorhinus canicula). Breeding in aquaria with different sea-water temperatures, and with diets of different consistencies and trophic positions (mackerel, soft and secondary consumer; shrimp, hard and primary consumer) will allow a calibration of geochemical developments, and an evaluation of the plastic sources of morphological variations. An exploratory study of fish teeth within and among populations will provide data about the relative importance of intra-individual (position along the jaw), intra-population and inter-population variations. These data based on modern material will be crucial to support the interpretations proposed in the fossil record. The original combination of quantitative morphometric analyses on several actors of a former ecosystem, of paleoenvironmental analyses in the same samples, of experimental data obtained on a modern model, has the potential to deliver a original view of the network of interactions between actors and with the environment of the former ecosystem. This is the key to understand the dynamics of construction of an ecosystem itself in evolution in this deep time.

Earth biodiversity is impacted by a wide range of environmental changes originating from dynamics at local(e.g. deforestation, urbanization) and regional (global climate changes) scales that have led to loss ofbiodiversity during the last decades. Biodiversity sustains ecosystem services (e.g. food security,epidemiological control) and its contribution in maintaining productive and resilient ecosystems is now widelysupported by empirical observations. Biodiversity, however, is not evenly distributed on Earth and someareas of exceptional richness facing severe anthropogenic perturbations have been identified as biodiversityhotspots. In Southeast Asia (SEA), several of the largest and most endangered hotspots have beenrecognized. The confusion that reigns over freshwater biodiversity in SEA, however, bridles conservationeffort and ecological climate change research.FRESHBIO aims at integrating human and life sciences with the objectives: (1) to break ground inbiodiversity monitoring by establishing new standards in biodiversity sciences, (2) to pioneer ecological andclimate change research in insular SEA through historical and monitoring approaches, (3) to explore manand biosphere relationship by assessing the impact of environmental changes on the biodiversity andcommunities at several spatial and temporal scales. With these objectives, FRESHBIO aims at: (1) framingbiodiversity research and monitoring through the development of automated DNA-based methods of speciesidentification and environmental DNA approaches, (2) assessing the ecological (community assembly anddynamics) and evolutionary (expansion vs. contraction) states of aquatic biodiversity in SEA insular hotspotsresulting from heterogeneous geological and biotic contexts, (3) assessing the impact of environmentalchanges on biodiversity through a mapping approach as well as identifying adaptive strategies andevaluating the resilience of local communities in front of biodiversity loss through a diachronic approach.FRESHBIO is proposed by a consortium of researchers from France, Germany, Philippines and Indonesiawith a long-standing interest on the ecology and evolution of insular SEA freshwater biotas as well as itsconservation and sustainable use. This project offers a unique opportunity to regionalize biodiversityresearch in insular SEA and helps break through the taxonomic impediment for large-scale assessments ofthe state of freshwater biodiversity. Compliant with the Access and Benefit Sharing principle of theConvention on Biological Diversity, FRESHBIO matches several of the national priorities of the participantssuch as the development of solutions for stopping biodiversity loss and concepts for sustainable usestrategies to ensure essential ecosystem services, the development of scientific networks to increase theacademic competitiveness of developing SEA partners and scientific innovation in a changing world.

The functional significance and the physiological mechanisms of sleep remain unsolved. A largely untested assumption is that sleep evolved to sustain immune defences and protect against diseases. The relationship between sleep and the immune system is of prime scientific and medical interests because a sharp decline in the average duration and quality of sleep has been documented over recent decades in all human populations. The relationship between sleep and the immune system have been, however, investigated almost exclusively under abnormal experimental conditions. Yet, understanding the functional significance of sleep variation within and between subjects requires studies in the natural ecological conditions in which sleep has evolved. Such observational and experimental studies have never been performed in large, natural populations of vertebrates. In this project, we propose to study the mechanistic and functional relationships between sleep and the immune system using long-term individual monitoring of nonhuman primates in combination with field experiments and laboratory analyses. In particular, we propose to identify i) the different factors causing sleep variation within and across individuals; ii) the mechanistic, physiological and immunological pathways that relate sleep to immunity and conversely; and iii) the short- and long-term consequences of both chronic and acute lack of sleep on animal physiology, behaviour and fitness. We propose to attain these three objectives in two populations of mandrills (Mandrillus sphinx) showing contrasted lifestyles and different constraints acting on individual sleep. In particular, we will perform a fine-grained description of sleep architecture and quality in the two studied populations. We will study how and why sleep naturally varies across individuals under normal vs. altered conditions (natural vs. captive populations) and how it changes when individuals face both parasite challenges (considering a large range of parasites) and experimental disruptions of their sleep. Additionally, we will study the physiological consequences of normal vs. altered and experimentally-disrupted sleep on cytokine production as well as on the production of stress hormones and cellular oxidative stress. Finally, sleep variation in normal vs. in altered conditions will be related to individual health and fitness thanks to long-term monitoring of the two populations.