The California coast is a worldwide biodiversity hotspot with a long and rich history of prehistoric and colonial migration, contacts and peopling processes. However, little is still known about the role that these processes played in the configuration of Californian landscapes over time. MeSCAL is designed to fill in this gap in current research by examining the role that past cultural interactions and human mobility played in the configuration of Southern California (SoCal) landscapes during the last 4000 years. Main goals are to analyse the spatial distribution of land-uses and plants following migratory and colonial processes, and to assess their impact into native terrestrial and aquatic ecosystems, particularly in terms of floristic richness, landscape structure, and impact on native flora, wetlands and soilscapes. This ambitious interdisciplinary project proposes a novel approach based on the coupling of 1) high temporal resolution multi-proxy palaeoenvironmental analyses –i.e. pollen, non-pollen palynomorphs (NPP), fire history analysis, diatoms, sedimentology, geochemistry- in continental wetlands and marine records, respectively providing local and regional information on vegetation and land-use changes and their impact in terrestrial and aquatic ecosystems; 2) calibration of fossil palaeoenvironmental datasets with modern pollen and NPPs analogues of vegetation and land-uses; 3) archaeobotanical analyses furnishing direct information on past consumption and use of plants in relation to migratory and colonial processes; and 4) coupling of paleoenvironmental results with archaeo-historical and ethnographic datasets to gauge landscape changes following prehistoric and colonial settling. Selected study areas are located in coastal (San Diego city and Santa Barbara region) and nearby backcountry (San Emigdio Hills, Kern County) areas. This transect of records will allow us to track differences in landscape changes following colonial settling between coastal areas under direct colonial control and hinterland areas exposed to a lesser colonial influence that may have served as refuge for native populations and landscapes. MeSCAL will contribute to a better understanding of the long-term shaping of SoCal Mediterranean landscape heritages, identities and cultures, and will provide Californian societies and land-management agencies with important historical and cultural information on their landscapes and wetlands that can help promote culturally conscious and sustainable landscape management tools and mitigate current degradation and over-exploitation of SoCal landscapes and wetlands. It will also provide local SoCal Native tribes with historical information on their ancestral landscapes and traditional land-uses that will enrich their cultural identities and help to protect their landscape heritage and traditional lifeways. MeSCAL will surely be a springboard for the candidate’s young career as it will 1) broaden her competences as project manager; 2) help her build an international network of palaeoenvionmentalists and archaeologists working on a ground breaking research topic; 3) foster her visibility at the national and the international spheres; and 4) consolidate her scientific independence.

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.

Organisms have always been confronted with changes in environmental conditions, either in space or time. However, the number and rate of anthropogenic alterations impose so intense selective pressures that biodiversity is irreversibly impacted. As well, biodiversity monitoring shows that extinction rate due to global change continues to increase. Plasticity and adaptability are key eco-evolutionary processes that could mitigate biodiversity loss in the face of environmental changes. However, few studies have determined how the combined effects of anthropogenic stressors affect the immediate and evolutionary response of organisms. POLLUCLIM aims at experimentally studying a freshwater organism’s response to the combined effects of climate warming and pollution. Using laboratory microcosms of a ciliate, I will first determine the plastic response to warmer and/or polluted environments (4 different pollutants) of a panel of genotypes. I will then study the probability of evolutionary rescue to these stressors, and determine if exposure to a stressful environment influences the evolutionary response to another stressful environment. Finally, I will relate adaptive patterns to genetic backgrounds and mutagenesis effects of stressors. At the end, the project should improve our understanding of tolerance and adaptability patterns to multiple anthropogenic stressors, with access to the underlying molecular mechanisms.

At the current warming rate, many organisms should go extinct if they are not able to disperse or adapt locally, which often involves plastic responses. In ectotherms, warming influences plastic life history traits with an acceleration of early life production at the expense of longevity and senescence. This may be due to trade-offs involving warming-induced oxidative stress and telomere shortening. Although pace-of-life acceleration may provide short-term benefits, it also increases sensitivity to limited resources, extreme climate events and unusual nighttime thermal conditions. Thus, in an increasingly warmer climate, ectotherms could reach critical physiological thresholds that would precipitate their decline. To date, physiological mechanisms and ecological consequences of this pace-of-life acceleration are poorly characterized. Here, we will combine experimental, observational and analytical approaches to unlock critical gaps in our understanding of thermal plasticity of life history. We will focus on a bimodal reproductive lizard (Zootoca vivipara), which offers a unique context to analyze how evolutionary transition between oviparity and viviparity influenced pace-of-life acceleration. Using long-term data sets and surveys across climatic gradients, we will document patterns of pace-of-life acceleration in response to climate warming in the two reproductive modes, focusing on vulnerable populations of the warm margin. In addition, we will perform outdoor and laboratory experiments to identify physiological tipping points in the context of day-night asymmetry of warming and extreme climate events. Given their major potential role in this thermal plasticity, non-energetic trade-offs will be quantified using longitudinal and cross-sectional assays of oxidative stress and telomere length dynamics. Altogether, this project will highlight patterns, mechanisms, and consequences on population viability of pace-of-life acceleration in response to climate warming.

Nitrogen protoxide (N2O) is a powerful greenhouse gas (GHG), with an impact 300 times higher than carbon dioxide, contributing significantly to global warming. Microbial processes (nitrification or denitrification) in soils or water contribute significantly to the production of N2O. To date, the contribution of wastewater management is still controversial as N2O emissions were poorly measured in wastewater treatment plants. Recent campaigns demonstrated however that the values assumed by the IPPC are much lower than reality. Moreover intensification of nitrogen removal in wastewater treatment and innovation for minimizing energy consumption can potentially increase the N2O emissions if nitrification and denitrification are insufficiently controlled with appropriate tools. This project aims to quantify, model and reduce N2O emissions from wastewater treatment facilities. The ambition of the project is to evaluate solutions in intensive processes receiving domestic wastewater which are used for nutrient removal. The project is divided in different tasks: (1) monitoring of full scale systems during long term campaigns, (2) tracking the main microbial pathways by innovative techniques (isotopes signature and NO:N2O ratio), (3) validation of a multiple pathway model for simulation and evaluation of mitigation strategies, (4) demonstration of innovative sensors and control tools for energy reduction and N2O mitigation. N2OTRACK will provide representative and objective information on direct greenhouse gas emissions from depollution systems. The contribution of these systems to the national anthropogenic N2O emissions will be estimated. Special effort will be deployed on biofilters at full scale, systems poorly characterized so far. The aim is also to provide an N2O modelling framework validated by lab-scale data with isotopic signature measurements and calibrated by full scale campaigns. Finally innovative control tools based on well-known and new sensors will be developed for both activated sludge processes and biofilters. The project involves six partners: three academic laboratories (LISBP-INSA, IEES-UPMC, RBPE-ECOBIO), one applied research institute (IRSTEA), a large WWTP facility (SIAAP-Paris) and a private company SME (BIOTRADE).