Dinoflagellates are one of the most widespread and abundant unicellular eukaryotes in aquatic ecosystems, in which they play key roles in carbon cycling. Their ecological success can be related to the extraordinary diversity of their roles, interactions, but also trophic modes, as they can be strictly photosynthetic, strictly heterotrophic, or perform both (mixotrophy) depending on external conditions. Dinoflagellates also exhibit remarkable molecular features including Gb-sized nuclear genomes, permanently condensed chromosomes, and a 10- fold lower ratio of protein to DNA than other eukaryotes. Genomic and transcriptomic studies from the last decade based on cultivated lineages confirmed their remarkable sequence divergence and complexity, revealing millions of « dark » proteins (i.e. they do not share significant similarity to any known sequences). Are these dark proteins lineage-specific? Are dark proteins and genomic novelty linked to organismal traits (e.g., trophic modes, life style, toxicity)? Are dark proteins abundant in the ecosystems? Do they show biogeographical structure and are they particularly expressed in certain niches? DIVEDINO will study the functional diversity of dinoflagellates, in order to link their hyper diversification (e.g., high molecular evolutionary rates, high gene copy numbers, large dark proteomes) to their evolution and ecology. Existing datasets will be gathered and complemented with new transcriptomes obtained from under-represented lineages. The objectives will be:1) Exploring to an unprecedented scale functional diversity using comparative omics, phylogenomics and structure prediction; 2) Linking functional diversity to organismal traits; 3) Investigating how functional diversity and genomic novelty correlate to biotic/abiotic factors in the marine ecosystems. DIVEDINO will constitute the most extensive eco-evolutionary study of these highly divergent lineage, shedding light on the origins of genomic and functional diversity.

Species with limited dispersal can overcome the challenges of climate change by changing their phenotype (phenotypic plasticity) or by adapting at the genetic level (adaptive evolution). Predicting the long-term ability of a species to adapt to climate is challenging, because most of the relevant traits are influenced by many genes. Quantitative genetics is able to provide short-term predictions without the knowledge of these genes, but for longer-term predictions, we require more information regarding the genetic architecture of the traits. The ORACLE project will tackle this issue by developing a framework to predict adaptation on the longer run and apply it on a well-studied common lizard (Zootoca vivipara) population, in order to predict its response to changes in its thermal environment cause by climate change. Thermal environment is a key aspect of the environment for ectotherms such as the common lizard, and the evolutionary potential of reptiles to changes in the thermal environment is scarcely known. I will (i) characterise the link between the phenotype and thermal environment, through natural selection, phenotypic plasticity and their interaction; (ii) characterise the genetic and phenotypic variances of the traits, as well as covariances between traits; and (iii) use whole-genome sequencing to characterise the genetic architecture of the traits. These inferences on key evolutionary features of the traits and their relationship with the thermal environment will then be used to (iv) predict the long-term evolution of traits and its impact on population dynamics, regarding long-term projections on the thermal environment of the population. By bridging the gap between quantitative genetics and population genomics, this project will deepen our knowledge about the accuracy of the predictive approaches typical from each field, but also provide new, hybrid tools to predict long-term evolution. I expect this approach to be applicable, to a large extent, to a wide range of species, where genomic analysis is possible. Being an umbrella species of concern, the results on the evolutionary potential of the common lizard also have a value for conservation.

The POPPY project aims to determine the origin and early diffusion of the opium poppy (Papaver somniferum L.). Opium poppy could be the sole plant domesticated during the Neolithic period in Europe, at least from the middle of the sixth millennium. The main objectives of the project are to 1) identify the geographical origin(s) of poppy including the location(s) of its wild progenitor(s) and of its domestication, 2) define a chrono-cultural framework for its early domestication process and dispersal from Prehistory to the end of the Iron Age (6000-50 cal BC). The POPPY project is based on archaeological material, as well as sampling of modern and historical biodiversity kept in seed banks and herbaria. It implements multidisciplinary analyses – archaeobotany, dating techniques, genomics, geometric morphometrics (GMM), spatial analyses – to elucidate the role of the opium poppy in Europe’s natural and cultural heritage. The project (42 months) is structured around three complementary tasks. Task 1 will build a database that integrate an exhaustive review of archaeological records to reveal the trajectories and the chrono-cultural framework of poppy dispersal from the Early Neolithic (6000 cal BC) to the end of the Iron Age (50 cal BC). Based on an already validated methodology carried out in the frame of previous one-year project (Fondation Fyssen, 2018), this task will also produce a new series of radiocarbon dating directly performed on poppy remains at key sites located in Europe (from the Balkans to the British Isles), North Africa (Maghreb and Egypt) and the Near-East. It will confirm and track precisely the early dispersal of the plant. These results will be integrated and compared to the general radiocarbon framework provided by other materials (cereals, bones, wood, artefacts) on sites inventoried in the archaeological database. Task 2 will consist in a co-analysis of the genetic and morphometric diversity (regional and varietal) of a common set of modern poppy and herbarium samples. The use of molecular markers such as SNPs in modern and sub-modern (herbaria) landraces of Papaver spp. will identify its wild progenitor(s) as well as trace the genetic markers of the early geographical dispersal of the plant. The genetic characterisation of the herbaria samples considered as reservoirs of ancient DNA (aDNA) constitute a pioneer research in prevision of future application on archaeological material. The GMM will allow to analyse the morphometric diversity within and among the modern samples and, more especially, to distinguish wild and cultivated subspecies based on the size/shape differences of their seeds and on the number of cells on their testa (seed coat). The methodology has been tested and validated on a small set of poppy seeds in the frame of the AgriChange project (SNSF, 2018-2021). The production of this solid modern reference database will open the way to future application of GMM on archaeological material to track the start of opium poppy cultivation. Task 3 will propose an interdisciplinary interpretation of the spatial analysis of the archaeobotanical database (Task 1) and the genetic/GMM database (Task 2) through inclusive visual restitutions, and taking into account multi-source variables with the Geographic Information System (GIS) tool. By testing the interdisciplinary integrative potential and the analytical geostatistical possibilities offered by the GIS tools,Task 3 could give solid bases for a future modelling of the opium poppy’s history. The POPPY project will initiate new and long-term collaborations with junior and senior researchers in France and in Europe. It will pave the way for systemic and cross-cultural approaches to the history of opium poppy. A significant attention will be made throughout the POPPY project duration and beyond to disseminate an up-to-date knowledge about opium poppy and the research methodologies.

This project will bridge gaps between micro and macro evolution by ascertaining the evolutionary feedbacks between trait and species diversification, focusing on closely-related species living in sympatry. Sympatric species often differ in suites of traits involved in niche partitioning: how do ecological interactions induce the sequential evolution of series of traits? In turn, how does phenotypic divergence open up new niches and fuel sympatric speciation? The project focuses on the neo-tropical butterfly genus Morpho where multiple behavioural and morphological traits strikingly differ between sympatric species living in the canopy vs. understorey. Studying trait variations within and among these closely-related species living in sympatry allows reconstructing the evolutionary steps leading to the divergence in suites of traits linked to niche specialization. Within the understorey clade, striking parallel geographic variations are observed among sympatric species, resulting in repeated local convergences in iridescent blue wing patterns, that may be driven by mimicry among these fast-flying, conspicuous butterflies. Such evasive mimicry may induce costly reproductive interferences, favouring segregation of circadian activities between species and thus contributing to the speciation process. The project relies on the original combination of both up-to-date and field-based approaches: (1) cutting-edge phenotypic characterisation of complex traits (eg. iridescence, flight) (2) empirical estimations of selective forces with wild butterflies (3) machine learning-based population genomics applied to demographic inferences (4) and mathematical modelling of density-dependent processes with stochasticity. These innovative approaches will shed light on unrevealed ecological interactions between species, impacting diversification of traits and species, therefore bringing major scientific breakthrough and attracting society attention on biodiversity loss in Amazonia.

Emergence and evolution of ancient agroecosystems in Greater Iran: Biodiversity, impact and legacy In the framework of an international research project entitled KHARMAN (‘harvest’ in Persian) we will aim at reconstructing past human-plant and animal interactions in the area of Greater Iran. Our approach is based on archaeozoological and achaeobotanical research applied in a diachronic perspective from the Late Pleistocene until modern times. Three themes are concerned: reconstruction of wild and domesticated biodiversity; understanding how agroecosystems adapted to environmental and climatic conditions; evaluation of the impact of agropastoral activities on the environment. The French bio-archaeological community, namely archaeozoologists and archaoebotanists, has stood out during the last decades as one of the main partners of national archaeologies in Iran and adjacent countries. This status has been achieved by long term efforts and a continuous presence in the field during the last two decades and expressed by 1) a wide communication with the Iranian and adjacent areas scholars and institutions of various fields of research (archaeology, botany, zoology, environmental studies, ethnography, history); 2) a continuous expertise of bio-archaeological material; 3) the creation of an archaeozoological laboratory and the training of Iranian and French students. Besides maintaining the leading role of French scholars in this domain, we wish to associate our colleagues in an ambitious program combining scientific research, expertise and higher education. The detailed proposition submitted here aims at preparing, together with European and Asian colleagues, a large-scale scientific project that can be submitted, within two or three years, to an international funding scheme (ERC, ANR or others). Such a funding scheme will allow us to gather the leading scientific community, establish common research strategies and consolidate already obtained data by the creation of a bio-archaeological database of the Iranian domain and adjacent areas. The precise actions that are to be undertaken during the next 24 months will thus be 1) the constitution of the scientific network through our existing or blooming collaborations in Europe and in Asia in order to define the outlines and the agenda for the future collaborative research, 2) The constitution of the database as a fundamental action and as start-up project 3) The technical preparation of future research.