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.

In the continuity of the approach implemented in previous works (ANR COOLTREES 2018-2021), the aim of TIR4sTREEt is firstly to carry out a new measurement campaign to acquire thermal infrared (TIR), meteorological, eco-physiological as well as geometric data, at different seasons, around street trees. The acquisition will be enriched by measurements from an innovative aerial robotic system, never deployed for this kind of topic. The second objective is to develop a methodology for merging the 3D geometry of an urban scene with the measured surface temperatures. The fusion of 3D and thermal infrared data at the scale of a street will then be used to validate estimations produced by microclimatic models. Finally, no study has yet investigated the impact of interspecific variability of trees and their environment on the urban microclimate. This project aims to fill this gap by carrying out measurements at the scale of three streets and on three tree species in the city of Strasbourg.

Considering the forecasted world demographic growth and the global changes in climate, it is becoming a major challenge for human society to provide sufficient amounts of high nutritional and sensory quality food. The TomEpiSet project aims to uncover new means and strategies to overcome poor fruit setting and the resulting low yield under elevated temperature using tomato as reference species. Screen tomato germoplasm and available auxin related and epigenetic mutants to select lines that successfully initiate fruit setting without need for pollination, normal or high yield with maintenance of fruit quality under heat stress conditions. The main novelty of the project is to unravel of the epigenetic components of the fruit set process and parthenocarpy in relation to auxin signaling. Genome-wide transcriptomic profiling combined to chromatin immuno-precipitation and DNA methylation studies will generate extensive multidimensional expression maps of epigenetic marks and auxin signaling factors allowing uncovering new components of the fruit set process. These new candidate genes will be analyzed with reverse genetics approaches using transgenic lines mis-expressing these genes to generate loss-of-function mutants by CRISPR/cas9 - RNAi approaches or overexpression plants. Then, the mutant plants will be analyzed at the physiological level for their capacity to produce normal or higher fruit yields in conditions of elevated ambient temperatures. An attempt to setup a new approach for breading using epigenetic information will be developed in the frame of the project. Programmable epigenetic marks based on the CRISPR/Cas9 gene regulation system, consisting of the nuclease-null dCas9 protein fused to the catalytic core histone or DNA modifiers will be in generated to guide for specific epigenetic modifications to candidate genes identified by an integrated approach combining RNA-Seq, ChIP-Seq and BS-Seq approaches. Validated epi-mutants will be phenotyped regarding their ability to display normal or higher fruit yield under elevated temperatures without loss of fruit quality. A major goal of our project will be the integration of all data sets coming from different high throughput approaches. TomEpiSet will take advantage of the tomato transcriptomic platform called TomExpress (http://gbf.toulouse.inra.fr/tomexpress) which has been developed by P1, allows processing and analyzing the data in standardized and unified ways for the whole project. Elucidating the mechanisms underpinning fruit set by integrating epigenetic mechanisms and auxin signaling will represent a major breakthrough in our understanding of reproductive biology and will open the way to the design of new strategies towards improving crop yield, particularly in adverse environmental condition leading to poor flower fertilization. TomEpiSet will highly contribute to enrich the content of high education courses at the national and international level through an Erasmus+ Capacity Building in the Field of Higher Education ‘MABIOVA’ (creation of a Master degree in plant Biotechnology field) project coordinated by P1 and through different partners of the project regarding their involvement in teaching activities at the high education level. The use of our data for tomato breeding will be in the scope of the valorization procedures and we shall use the Partners’ national and international network of contacts, for such perspectives.

Winegrape production is one of the most economically important agrosystems in Europe. Grapevine has a large breadth of genetic diversity at the rootstock, variety, and clone levels. Unfortunately, very little of this diversity is currently utilized and its potential role in abiotic stress response has not been properly quantified. This leaves growers with the open-question of which is the best tool(s) to adapt their vineyards to specific environmental challenges (e.g. heatwaves, drought, waterlogging, etc). At the scientific level, it is essential to understand the genetic plasticity of rootstocks, varieties and clones (and their interactions) to further adapt and improve the current planting material and to preserve the genetic diversity of grape varieties used across Europe. Standards for physiological traits need to be defined, and the influence of the diverse genetic backgrounds to the value and flexibility of these traits under different environmental conditions needs to be understood. With this in mind, project DiverGrape has been designed including partners from four European countries with varying environmental and vineyard conditions. The partnership will exchange pre-doctoral and postdoc researchers using a standardized methodological approach based on both eco-physiology and metabolomics tools to quantify the contribution to environmental response of: i) clonal variation within given local varieties, ii) rootstock material for a given variety and ii) the interaction between rootstock and scion. Taking advantage of existing vineyards with a variety of genetic material located in different European viticulture areas, the partnership will quantify how environment drives grapevine plasticity to specific climates. The results obtained through project DiverGrape will provide grape growers with the knowledge to optimize the existing grapevine genetic diversity in order to adapt their vineyards to more extreme climate situations.

In this project we will study how self-fertilization evolves and its evolutionary consequences in hermaphroditic animals . A strong limitation of the theory of mating system evolution is that it has been tested quasi exclusively in flowering plants. This poses problems of generality (to what extent do the arguments made depend on specificities of this group ?) and feasibility (most plants are not easily amenable to multi-generation experiments such as experimental evolution). For these two reasons it is urgent to develop animal models. We will here focus on a group of freshwater snails (basommatophorans) with highly diverse mating systems, presenting a suite of advantages making them ideal to address hitherto unsolved questions. We will focus on evolutionary transitions between outcrossing and selfing, how and when they occur, and their consequences. In particular we will test the long-standing hypothesis that selfing is an evolutionary dead-end in two ways. First we will characterize the number and unidirectionality of transitions in the phylogeny; second, we will empirically test the key steps of the most plausible scenario describing how an outcrossing species can become a preferential selfer (but not the reverse). The main components of this scenario are (i) constraints on mate or pollen availability resulting in a selection for selfing as a reproductive insurance. (ii) the existence of an intermediate state of preferential outcrossing with delayed, optional selfng when mates are lacking. (iii) the purging of inbreeding depression, resulting in runaway selection for selfing and even less inbreeding depression. (iv) the lack of adaptive potential in selfers, resulting in high extinction rates. All these aspects will be tested experimentally by looking at experimental evolution under elevated contraints on mating (frequent lack of mates), by measuring response to artificial and natural selection in pairs of outcrossing/selfing species living in the same environment, and by comparing their ability to colonize empty sites, estimated from metapopulation studies in the field This project is very ambitious in terms of (i) gathering molecular polymorphism data from many hitherto unstudied species, (ii) the number of size of experiments, and (iii) the requirement for long-term field data. It brings together a highly qualified consortium with previous experience of common work and complementary skills. Among the expected breakthroughs of this project will be the first experimental-evolution study of mating system evolution; and the first unbiased estimates of the frequency of mixed-mating in animals, and why it seems to be lower than in plants. All this will serve our ambition to establish animals, and especially basommatophoran snails, as essential models for mating system theory.