Since the middle of the 20th century, insecticides have been massively used to control the vectors of infectious diseases and thus limit their impact on public health. This drastic modification of their environment has selected different adaptations in these vectors, collectively referred to as insecticide resistance. The genomic architecture of these adaptations can be very diverse, ranging from simple nucleotide substitutions to large-scale mutations such as gene duplication. The effects of these different mutations on the vectors phenotype and fitness can differ and are difficult to anticipate, particularly in an environment that is itself variable. Using interdisciplinary approaches, the ArchR project aims 1) to understand how these different genomic architectures impact the phenotype of their carriers, and to measure the evolutionary dynamics of multi-copy alleles under various intensities of insecticidal pressure in natura, 2) to study how variations in environmental conditions and the architecture of these adaptive mutations influence the dynamics of genome polymorphism, via the natural selection of resistance alleles and the demographic effects of insecticide treatments, and 3) to measure the effect of mutations on vectorial competence and mosquito metabolism, in order to anticipate their impact on public health. To achieve these objectives, the ArchR project will rely on the wide diversity of resistance alleles with copy number variations found in the Culex pipiens mosquito, and on a unique collection of natural population samples collected over 30 years, combined with quantitative data on insecticide treatment variations. The ArchR project will also rely on a recognized international consortium, which has worked or is already working together on other projects, and which combines the complementary skills (population genetics, genomics and bioinformatics, molecular biology, vector competence and experimental infections, computer modeling, ...) and resources and infrastructure (insectariums level 2 and 3, molecular platforms and computer platforms) necessary to carry out this project. During this project, two PhD and several Master students will also be trained in high-level research with the different partners of this consortium. The ArchR project will thus allow crucial developments for fundamental research in evolutionary biology: early evolution of duplications, impacts of adaptive dynamics on genome evolution, impact of environmental variations on genome polymorphism and population adaptability, evolutionary trade-offs between adaptation and transmission. By linking the treatment practices with their demographic impacts and the dynamics of resistance alleles in natural populations, and by assessing the impact of resistance alleles on mosquito vectorial capacity, it will also provide useful information for professionals in charge of vector control or crop protection, and help design sustainable control strategies.

Hydrothermal vents are ephemeral habitats inhabited by a highly specialized fauna. If connectivity between vent sites is relatively well understood along continuous oceanic ridges, it is a lot less clear for back-arc basins of the western Pacific, despite the increasing threat of deep-sea mining in this specific area. The motion of plates in the West Pacific initiated about 25 Mya has led to species complexes by vicariance, with the progressive opening of the present-day basins spanning over 2-10 My. Since their opening, larval dispersal modeling predicts episodic and unidirectional exchanges between basins. Here, we want to understand the factors that control hydrothermal vent biodiversity between and within basins and in particular the role of connectivity on the resilience of communities. This will allow us to further address with genomic tools the question of the temporal and spatial dynamics of BAB fauna in order to assess its vulnerability to the ongoing anthropogenic pressures. We formed a research consortium to tackle this societal issue with an integrative approach based on the samples that will be collected during an upcoming research cruise on 5 back-arc west Pacific basins. The project is sub-divided into 5 tasks, including the coordination task. The first scientific task will be dedicated to inventory communities using morphological, barcode, and metabarcode approaches and assess geochemical diversity of the vent habitat. Faunal datasets will be used to examine biogeographic patterns within and between basins using co-occurrence networks and to define more precisely the role of geography and fluid chemistry in the partition of the vent biodiversity. The second task aims at estimating levels of gene flow between and within basins for about 10 species (vent-endemic and peripheral) using high-throughput population genomic approach (RAD) and to date vicariant events over the geodynamic history of basins. This task intends to use new and promising population genomics methods (JAFS, distance inference methods based on introgression queue/allelic clines) to disentangle past and present-day connectivity at the appropriate spatial scale. The third task will focus on larval biology and reproduction dynamics of the vent fauna thanks to the sample collection and the use of in situ automatic larval samplers. The origin of recently-recruited individuals will also be determined by elemental fingerprinting of larval shells for species which possess developing embryos in capsules. Finally, information gathered in the 3 tasks will be used to refine a demo-genetic model for exploring scenarios of population connectivity in the face of anthropic perturbations. This knowledge is paramount for the proper management of this peculiar fauna, potentially threatened by the increasing mining effort to exploit metal sulfide deposits in the area.

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.

Tropical forests are currently experiencing huge pressures from global changes. If tropical deforestation has been rightly the focus of much attention these last decades, forest degradation and its consequences in the tropics has been much less studied and quantified. Yet, forest degradation is pervasive throughout the tropics and leads to a significant loss of ecosystem services. Hence, a major issue is the reversibility of degradation. In many cases, natural successional processes are expected to bring back the system to a state similar to the initial one. However, in some cases, the system may have trespassed a threshold and lost its ability to follow such a classical successional pathway; it may remain in a so-called blocked succession or in an alternative degraded stable state. The Marantaceae forests from Central Africa likely correspond to such stable degraded systems. They cover very large areas in Central Africa and have a very low density of trees with a dense understory composed of giant herbs. The few studies on Marantaceae forests suggest that their large patches (up to 2000 km2) are likely to have originated from old disturbances (>1000 years ago) and have been maintained over long periods through positive feedback mechanisms, e.g. inhibition of tree regeneration by giant herbs. Observations also suggest that current human disturbances, such as logging activities, as well as climate anomalies, contribute to the rapid expansion of these degraded forests, which could have considerable consequences for local populations. In this project, we will study the mechanisms by which Marantaceae forests may originate and be maintained at different spatial and temporal scales. We will combine observations at the local and regional scales (among which historical data) and parsimonious theoretical models to study the long-term dynamics of Marantaceae forests, the conditions under which stability is expected and the mechanisms by which giant herbs monopolize space and may outcompete trees or restrain their development. The project will be structured in four complementary main work packages (WP): WP0 will be dedicated to synthesize previous studies conducted on Marantaceae forests, of which many were reported as grey literature; WP1 will aim at investigating the main ecological mechanisms underlying the dynamics of Marantaceae forests; WP2 will aim at depicting the contemporary ( 500 yrs) spatio-temporal dynamics of Marantaceae forests based on remote sensing data and historical ecology approaches; and WP3 will consist in devising mathematical models to understand the conditions of a post-disturbance stability of Marantaceae forests and the relative importance of the drivers of this stability. WP3 will thus bridge the scale gap between the local ecological mechanisms (WP1) and the broad scale spatio-temporal dynamics (WP2) of Marantaceae forests. Overall, our project will generate important knowledge on the dynamics of a system that constitutes an important part of the tropical African wet forests and ofglobal concern regarding biodiversity and carbon sequestration in the second largest tropical forest area in the world. It will also contribute to the increased awareness that the dynamics of ecosystems is not systematically reversible and that external forcings may make them shift to alternative stable states. The ultimate goal of the project is to anticipate the potential consequences of global changes on the dynamics of Marantaceae forests and to provide recommendations for forest conservation and management.

The concept of genetic conflict is one of the most important legacies of twentieth century evolutionary biology, and has now become, in the era of massive sequencing, a major foundation of our understanding of genome evolution. Genetic conflicts occur within organisms between different genes that maximize their transmission in different ways. A spectacular example is cytoplasmic male sterility (CMS), whereby maternally transmitted mitochondrial genes suppress the male function in hermaphrodites, to the detriment of nuclear genes. The result is a sexual polymorphism called gynodioecy, whereby hermaphrodites coexist with females in populations. CMS and gynodioecy have been well studied theoretically, and empirically in plants. They have become one of the textbook examples of genetic conflicts. However CMS has surprisingly never been described in animals. In addition, tests of the evolutionary theory of gynodioecy remained indirect, as the long generation time of most gynodioecious plants made it complicated to observe evolutionary dynamics over generations, in real time. We recently discovered the first animal example of CMS in a hermaphroditic freshwater snail Physa acuta (Pa) and propose to use this species as a new model to study genetic conflicts. Capitilizing on the short generation time of this snail - easy to breed in the lab-, and on the preliminary data accumulated in the past two years, we propose a project that will not only open this field of evolutionary genetics to a new clade (animals), but also follow hitherto unexplored, exciting research avenues, such as experimental evolution. MINIGAN is organized along four axes / questions. (i) What is the geographical distribution of CMS and does it occur in specific environmental conditions? (ii) Is male sterility compensated by a female advantage, how and when is this advantage expressed ? (iii) Can we directly observe the co-evolutionary cycles of mitochondrial and nuclear genomes predicted by models, as a consequence of mtDNA suppressing male function while some nuclear genes restore it ? (iv) What is the genomic signature of gynodioecy ? How does CMS affect mitochondrial and nuclear genomes and transcriptomes? We will rely on a variety of approaches already used in plant models including field sampling, PCR, intensive lab experiments, together with more innovative methods such as experimental evolution, genome scans, and transcriptomics. This project is ambitious, requiring long-term (2yr) experimental evolution and a de-novo assembly of the snail genome, and a large re-sequencing effort. This combination of various techniques results in a balanced mix of relatively low-risk and high-risk, high-gain approaches. The diversity of methods also echoes the complementarity of competences present in the three different partners of the consortium and their respective scientific leaders. The project is coordinated by P. David in CEFE (Montpellier), broad-spectrum evolutionary biologist, quantitative and population geneticist, and specialist of animal mating systems with long experience with working with snails as model systems. A whole team, including a specialist of gynodioecy in plants, will assist him in the CEFE. Both E. Luquet and J. Romiguier (respectively leaders of the LEHNA partner in Lyon and ISEM partner in Montpellier) are talented young researchers who, together with their associated teams, will bring their knowledge in life-history evolution, transcriptomics and genomics. Collaboration will be facilitated by geographical proximity, and the succesful past collaborations between the partners on the snail model, already materialized by common publications and by the obtention of the preliminary results forming the basis of this project. Gathering a well-integrated consortium of high-profile research teams with complementary skills, MINIGAN has the potential to shed a new light on the dynamics of CMS, and more generally on genetic conflicts.