A key challenge of 21st century biology, arguably, is to merge concepts and findings from ecology and evolution into a predictive science. These two ‘sister disciplines’ have seen much progress during the last century, but an integrated, empirically validated, predictive framework has yet to emerge. There is, to our knowledge, no predictive theory that has been shown to make sense of the wealth of empirical observations across species, ecosystems and environments. Evolutionary Rescue (ER) is an emerging and somewhat central example of such processes where eco-evolutionary thinking is required, and where critical applied issues are at stake. ER occurs when a population, initially declining because of exposure to an environment outside of its ecological niche, avoids extinction via genetic adaptation restoring population growth. This phenomenon underlies a range of biological contexts of fundamental and applied importance: range expansions/contractions, host shifts in pathogens, and the emergence of resistance to chemical treatment in various agronomic and medical contexts. The development of general models of ER is a typical example where an eco-evolutionary framework is required. Their empirical test is also a challenge, as it requires fine-scale studies of demographic and evolutionary dynamics, at high replication, under well-controlled or at least well-quantified stresses. Better management strategies of resistance emergence is a critical demand for health and agronomy. Such strategies would benefit from an empirically established and general framework to understand and predict ER, in more or less complex situations. This is the aim of this project. To capture the dependence of mutational parameters on stress levels for different demographic rates, we will use Fisher’s geometrical model. We will assume that these rates depend on some underlying multivariate phenotype, with a given optimum per environment and rate considered. We will assume that, among other effects, increasing stress levels (e.g. antibiotic concentration) increasingly shift this optimum along a given direction, for a given stress and the rate considered (e.g. birth vs. death rate). We will predict adaptation trajectories and resulting stochastic demographic dynamics in this landscape, to compute the probability of ER vs. extinction, in a given pattern of stress (level, combinations, time dynamics and spatial pattern). The coordinators have already successfully applied this approach to the case of a single component (growth rate) under an abrupt change. Various extensions will be considered: abrupt stress with multiple components, combinations of stresses (synergism/antagonism), arbitrarily changing stress over time, coupling with ecological dynamics for a biotic stress (predation, epidemiology), source-sink connected by migration, gradual change in stress level over space. We will test our predictions quantitatively on in vitro experiments in Escherichia coli (in an original high-throughput experimental system). Various stresses will be explored: copper ions (as used in agronomy), antibiotics (single or in combinations), predation by a unicellular eukaryote or infection by one or several lytic phage species (phagotherapy). Some predictions will also be tested in the field and in natura on a virus – plant pathosystem near Avignon. A collaborative website will be developed where authors can contribute their own ER data, to expand the tests and parameter estimates across species and stresses. Associated online toolboxes will be produced to facilitate the use and test of the models and a summer school will be organized at the end of the project. This is a collaboration between an evolutionary biologist (PI) and a mathematician (coPI), and their respective colleagues, forming a very multidisciplinary consortium with various skills (theoretical evolution/ecology, statistics, mathematics, virology, microbial experimental evolution).

Biodiversity loss in hotspots of biodiversity is, among other socio-ecological factors, key to understand, prevent and react to future pandemics. However, despite this knowledge, the current COVID-19 crisis highlights the limitations of the implementation of One Health approaches. A main limitation is the lack of context-adapted solutions that stakeholders (national authorities but also local communities, NGOs and private companies) could easily implement on the field. To overcome this, the MARBLES partners will build on past international projects to co-construct innovations with all stakeholders of biodiversity hotspots to reduce the risk of infectious disease emergence through biodiversity conservation and disease surveillance strategies. The activities of the project will be implemented in Europe and three tropical biodiversity hotspots in Southeast Asia, West Africa and Central America and will have the following expected impacts: • the results of the MARBLES project will lead to a better understanding of the mechanisms underlying the impact of biodiversity on the risk of infectious disease emergence • Stakeholder’s engagement tools developed during the MARBLES project will facilitate the design of context-adapted biodiversity conservation and restoration strategies that reduce zoonotic risk • the surveillance strategies and pathogen detection tools developed during the MARBLES project will improve the capacities to detect emergences and stop future epidemics before they can turn into pandemics The consortium will constitute a strong multi-actor group of partners with a history of successful cooperation including academics from biomedical, environmental and social sciences, private companies, NGOs, local and international stakeholders who bring together the wide range of disciplines and expertise required to reach all the expected outcomes of the HORIZON-CL6-2021-BIODIV-01-11 call. Overall, the implementation of the MARBLES project in various ecological, climatic and cultural settings will allow the consortium members to develop generic innovations that could subsequently be adapted through to a wide range of socio-ecological settings, contributing to the understanding, prevention and early detection of zoonotic emerging threats globally. The embedment of the MARBLES project in the Prezode initiative will help to scale up the project innovations and disseminate cutting-edge socio-economic environmental strategies.

Depredation by toothed whales of Patagonian toothfish on demersal longline and tuna and swordfish on pelagic longlines is a growing problem internationally and the main problem exposed the French longline fisheries operated from Reunion Island. Pelagic and demersal longline fishery operated from Réunion Island is the first French fishery in terms of economic value and the second merchant economic sector of Réunion Island (100 M d'€/yr). These fisheries are highly affected by this depredation with an estimated financial loss of € 65 million over the 2003-2013 period. The observed depredation levels raise both economic and conservation issues. Indeed the artificial supply of food helps in creating an imbalance between these populations of cetaceans and their natural resources. Longlining is one of the fishing methods with the lowest environmental effect. The objectives of OrcaDepred are firstly to better understand the depredation behaviour of and ecology of cetacean species involved to offer fishing companies operational and technological solutions to depredation. Technological approaches tested to this day, namely the use of pots, acoustic repellents are ineffective. Under the OrcaDepred four Work Packages (WP) will be implemented to study and solve the depredation issue. - WP1 aims at better understanding the natural feeding and interaction behaviours with the fishery cetaceans interacting with the lines, and in the case of pelagic longlines identify the cetacean species involves. For this two dimensions tracking movements (tracks and dives) of these cetaceans will be studied using i) a new generation of satellite tags processing on-board the pressure and acceleration data and ii) by passive acoustic monitoring using hydrophones deployed along pelagic longline or a dedicated acoustic vertical array to the demersal fishery. The interactions of cetaceans with the lines will be studied using an experimental line on which the hooks are equipped with accelerometers to assess when fish are caught and depredated. - WP2 is devoted to assessments of the bio-economic consequences of depredation through an ecological economic for sustainable management of these fisheries taking into-account depredation. Finally, ecosystem modelling based on trophic links between species will be carried out to assess the ecological consequences of fishing-depredation at the ecosystem level. - WP3 will consider whether changes in levels of interaction between cetaceans and ships are related to fishing practice differences between captains and/or vessel characteristics, with a special focus on acoustic noise generated. These analyses are essential to guide the fishing companies in their strategic choices: training their fishing captains and/or conducting technical changes on their vessels. - WP4 will implement a technological approach to remove depredation. In partnership with industry, new prototypes of fish protection devices on the lines and not harmful to cetaceans and possibly limiting the levels of accessory catch such as skate on demersal long line will be tested and operational systems will be patented. OrcaDepred federates the complete French scientific community currently involved in addressing the longline depredation issue. Other fisheries at both national and international levels should benefit directly from the OrcaDepred as this problem is expending worldwide. Orcadepred outcomes will lead to mitigation solutions and should generate a strong national and international audience.

Anticipating emerging infectious diseases and mitigating their impacts are the major challenges of Human, Veterinary and Plant Pathology. Surveillance for the detection of plant diseases and the subsequent response to limit their effects mobilize significant human and economic resources in Europe and elsewhere. Current plant disease surveillance plans of national and international organizations target known pathogens in the context of agriculture or commercial exchange or are based on symptom expression in the field. These surveillance plans do not monitor dissemination of plant pathogens by the natural “highways” of air and surface water movement and they do not involve tracking potential but-not-yet-described pathogens before they have caused a disease outbreak. Air and surface waters can move plant pathogens across distances of meters to hundreds and even thousands of kilometers and there are numerous examples of plant disease outbreaks due to these means of dissemination. Furthermore, the natural movements of air and water have the particularity of not only disseminating known pathogens of crops but also of bringing microorganisms from a diversity of habitats into contact with agricultural production fields. These habitats include ecosystems without agriculture, where the pathogenic potential of indigenous microorganisms is unknown and has generally been disregarded by plant pathology. Therefore, a plan for surveillance of aerial and water-borne dissemination of pathogens would be complementary to existing disease surveillance measures that involve importation restrictions of plant tissues and monitoring of disease symptoms in the field. It would markedly enhance the effectiveness of current surveillance by providing a means to monitor for unknown, potentially new pathogens traveling on natural highways in addition to known pathogens disseminated within the context of agriculture and commerce. In this project we will bring together competence in biology, math and economics to leverage recent developments concerning the ecology of plant pathogens in natural environments, network analyses, epidemiological modeling, and land use mapping and simulation to develop a framework for surveillance of dissemination of plant pathogens via air and surface water movements. The project will involve partners who have worked together for several years to develop the tools and resources to build this framework. We will focus on plant pathogens for which we have confirmed their presence in habitats outside of agriculture and in particular in waterways and the atmosphere: Pseudomonas syringae, Pectobacterium spp. and Dickeya spp. We will focus our analysis on the Durance river basin in Southern France. We have worked at multiple field sites in this basin for over a decade and know its hydrology and meteorology well. We have also established large culture collections of the model bacteria from this basin in preparation for this study. Importantly, this basin is also in the PACA (Provence Alpes Côtes d’Azur) region, one of the only regions in Europe where fine-scale land use data are available. These data include over 900 digital cadastral maps, the associated fiscal data on land and private property, information on land use regulation and on the nature of farmland including crop type at the field level. The partners of this project are involved in the management of a geomatic platform for the analyses of these and other spatial data. This context puts us into the unique position of being able to develop a framework for surveillance of aerial and surface water dissemination of plant pathogens with the most modern tools and concepts and the full interdisciplinarity needed for this development. It also facilitates our ability to set up relationships with stewards of plant disease surveillance and policy makers to foster understanding of our work, transfer of technology and development of policy recommendations.

With the shift towards a reduced reliance on external inputs in agriculture, identifying management options that enhance the provision of ecosystem services has become a critical issue. Pest control resulting from the activity of naturally present predators and parasitoids is frequently cited as an important service that could reduce pesticide use as targeted by the French 2018 Ecophyto governmental action. However, the link between management options, pest control level and ultimately crop yield is poorly understood. The PEERLESS project aims to identify alternative management strategies that enhance the crop protection service provided by functional biodiversity and ultimately to optimize agricultural systems, at local and landscape scales, for economic viability and sustainability. PEERLESS brings together six partners organisations with extensive expertise in agronomy, spatial ecology, ecology of interactions and public economy. The project combines: (i) an empirical assessment of naturally occurring crop protection from weed and insects pests in annual (wheat-oilseed rape rotations) and perennial (apple orchards) systems across a broad range of landscape and agronomic situations; (ii) ecological engineering with an assessment of alternative plant protection system to improve crop protection at the local scale; (iii) an in-depth study of the structure of trophic networks; and, (iv) population dynamics of key pests and their regulators in case study areas. These components will support the parametrisation of spatially-explicit, predictive models to (v) test the effect of landscape patterns of alternative local and landscape management strategies on pesticide use, pest control, crop yield and farmer income and (vi) identify landscape scale viable management strategies to control insect and weed pests.