Hybrid populations from numerous plant and animal species, including humans, have been extensively studied by population geneticists to infer historical migrations, detect signatures of natural selection, and identify genomic regions related to phenotypes of interest. Most of these studies considered a simple statistical framework describing the admixture levels of hybrid populations and inferred the influence of a single founding admixture event on their genetic diversity. However, these statistical models do not capture the known complexity of admixture processes in which several source populations can contribute in varying amounts to the hybrid population over many generations. For example, in the case of biodiversity conservation, reintroduction programs often involve complex admixture processes over time with recurrent introductions and hybridizations with pre-existing populations. In humans, isolated populations have historically come into contact through colonization waves, forced displacements, and population migrations. Finally, admixture between communities is often determined by sociocultural rules on intermarriages in contexts of ethnic conflicts or discrimination, slavery, and clan or caste systems. Realistic models of admixture are needed to accurately reconstruct the histories of admixture of hybrid populations from genetic data, and to understand and predict how complex admixture processes influence genetic diversity within and among hybrid populations. To accurately model complex historical admixture, we recently published a general admixture model that considers multiple source populations contributing to the gene-pool of a hybrid population, with potentially variable contributions over time. Theoretically, we have shown that this model allows reconstructing unknown histories of admixture from genetic data. The METHIS project aims to develop a novel comprehensive population-genetic framework for studying, reconstructing and predicting how complex admixture events influence the genetic diversity and evolution of hybrid populations. First, we will expand our admixture model to incorporate several often neglected forces, such as assortative mating and natural selection, known to influence the genetic diversity of hybrid populations. This will allow us to capture these frequently-occurring processes and widen the application spectrum of our approach. Second, we will develop several computer programs to facilitate the application of these theoretical models to the study of admixed populations using genetic data. In particular, we will develop a simulator of genome-wide genetic data based on our admixture models, which can be used to predict the admixture structure and genetic diversity patterns expected in hybrid populations for specific scenarios of interest to researchers. We will integrate this new simulator into an Approximate Bayesian Computation framework that we will specifically adapt to infer, using genetic data, the parameters of complex admixture processes that gave rise to hybrid populations. We will make these new tools publically available. We will apply this new methodology to two case-studies. First, using available genetic data, we will reconstruct and predict the influence of admixture processes on the survival and adaptation of Arenaria grandiflora, a plant species targeted by a hybrid re-introduction program conducted since 1999 in the Fontainebleau forest to restore its nearly extinct population. Second, we will investigate recent histories of admixture in human populations. Indeed, we will generate genome-wide genotypes for 400 individuals from Cape Verde. Merging this new data with publicly available data from African, European, Caribbean and American populations we will reconstruct how variable admixture histories influenced the genomic diversity of these populations descending, on each side of the Atlantic, from the history of European colonization and the Atlantic Slave Trade.

The urbanisation process around the world, which started in High-Income countries, favours obesogenic environmental conditions. The development of transport and tertiary sector, as well as processed energy-dense food, associated with sociocultural factors, such as urban stress, together participate in the creation of living spaces exposing individuals to obesity-related cardiometabolic diseases. This is known as the nutrition transition. Most Low- and Middle-Income Countries in Africa are experiencing a faster nutrition transition leading to an epidemic explosion of obesity. If African populations are faced with a globalized urban environment presenting some uniform physical obesogenic characteristics, their respective evolutionary and cultural history in different socio-ecosystems might determine their adaptive trajectory within urban environments. Yet, most programs aiming to reduce obesity use a uni-disciplinary approach to understand its aetiology. This could explain the current failure of health institutions to prevent obesity. Furthermore, the biocultural background of populations is insufficiently considered to assess their particular adaptive capacity to evolve in new urban environments, and minimize their exposure to obesity. Although the generic determinants of obesity are well identified, their respective effect as well as systemic interactions in body weight regulation remain poorly understood. Our original project, ANTHROPOLISTIC, will develop a novel holistic understanding of body weight regulation, by considering together sociocultural and biological factors, in two anthropologically different African populations (Senegalese and Cameroonians) experiencing the nutrition transition. To do so, ANTHROPOLISTIC will consist of a cross-sectional integrative interdisciplinary study reuniting the two major branches of anthropology (sociocultural and biological) to explore holistically the main biocultural drivers of body weight in both Cameroonian and Senegalese populations in the context of the nutrition transition. Hence, a mixed-methods biocultural anthropological study, collecting qualitative and quantitative data on body weight drivers in 4 rural-urban Senegalese and Cameroonian groups, will be conducted. For the quantitative study, eligible participants will complete a series of questionnaires and measurements to (1) collect their main socio-demographic characteristics, (2) administer validated wellbeing, body image, physical activity and food questionnaires, (3) undertake a complete anthropometric protocol (height, weight, fat mass, etc.), and (4) objectively assess daily pattern of physical activity and metabolic regulations, as well as (5) indicators of the metabolic syndrome (i.e. fasting glucose, blood lipids, WC, blood pressure) of participants. We will also (6) extract DNA to determine the genetic factors associated with body shape. For the qualitative study, we will conduct (1) focus groups discussions to identify the daily social norms, perceptions and practices (orally declared) on body weight, diet and physical activity; (2) individual in-depth semi-structured interviews to explore idiosyncratic postures towards these norms and all aspects of participants’ wellbeing (e.g. poor material conditions, social isolation, social pressures, stress); (3) a photovoice approach based on a self-description by participants of their living environment characteristics associated with these dimensions, and (4) a participant observation phase based on visual data collection and informal unstructured interviews to rigorously characterize practices related to sociocultural perceptions collected. Because this unique interdisciplinary project around a systemic anthropological approach will improve our understanding of the etiology of obesity in Africa, the scientific, medical, cultural and economic benefits of ANTHROPOLISTIC will be major, and disseminate at local, national and international scales.

Human populations are evolving in close interaction with their environment, that they in turn shape. However, this intimate adequacy has been challenged many times during human evolutionary history, for example at the Neolithic revolution 10,000 years ago during the transition from a nomadic hunter-gatherer to a sedentary farming mode of subsistence, or more recently with the industrialization of human societies. While the influence of human activities on various ecosystems is largely recognized, little is know about the effect of ancient and recent changes in lifestyle, notably dietary regimes and access to medicine, on the symbiotic relationship we maintain with the microorganisms living in our guts, the gut microbiome. Our own gut microbial ecosystem is however currently considered to be essential for human health, and seems notably implicated in multiple metabolic and immune diseases. It also appears to be highly variable among individuals and populations, and at least partially heritable, making it a potential target for natural selection. The human gut microbiome therefore represents a phenotype of evolutionary, ecological and medical relevance. Although it appears that the gut microbiome interacts with its host (through e.g., diet, antibiotics use and the immune response) and with other intestinal communities (parasites, viruses), the respective influence of various environmental (whether ecological or cultural) and genetic factors on its composition is not clear. Notably, the loss of microbial biodiversity observed in urban industrialized populations (as compared to rural developing countries) could be due to their dietary specialization, hygiene practices, and/or other variables. This project aims at disentangling the interactions that exist between these different factors to understand (i) how the microbial ecosystem has coevolved in the long-term with humans dietary regimes and parasitism since the Neolithic revolution 10,000 years ago, (ii) how rapid changes in lifestyle, notably industrialisation, has impacted the gut microbial diversity and (iii) what is the influence of genetic determinants on the microbiome composition. To tackle these issues, we propose to sample and compare the gut microbiome of individuals from contrasted subsistence modes (hunter-gatherers versus farmers) and along a gradient of urbanisation (from African rural villages to African cities to a European city) in Cameroon and France. We will collect both anthropological data (nutritional, medical and ethnological questionnaires, and anthropometric measures) and biological data (intestinal parasitism, microbial and human genetic data), and jointly analyze the influence of variables of interest on the gut microbiome, using various statistical and bioinformatics tools. Bringing together classical biological anthropology approaches and next-generation sequencing technologies, this innovative project aims at dissecting how various ecological, cultural and genetic factors have impacted the gut microbial communities in the past, and likely continue to do so in the future, in the context of a rapid homogenization of food and hygiene practices across the World. This project will likely have an important impact in the fields of anthropology, ecology and evolution, as well as substantial implications in public health.

Human societies are interacting with a growing number of nonhuman animal species, including exotic species during visits to zoological parks. And yet, the existence of zoos remains polemical, despite their increasing contribution to biodiversity conservation, because of ethical issues of maintaining wild animals in captivity. Few studies however assessed whether the behaviour and attitude of visitors influence zoo animals, especially nonhuman primates that are so closely related to humans. Besides, humans often lack ability to correctly perceive the emotional state of nonhuman animals, our representations of specific animal species being biologically and culturally driven. This is thus crucial for zoos to understand how captive nonhuman primates and human visitors perceive each other and to identify and promote pedagogic tools that could improve public perceptions. The PRIMAZOO project proposes to develop an integrative approach to study intersecting perceptions and representations underpinning human-animal interactions in zoos. We will mobilize theoretical and methodological concepts from both biological sciences and social sciences and humanities, to understand (i) how nonhuman primates and humans perceive each other according to a variety of individual and environmental factors and (ii) how human visitors represent nonhuman primates and their captivity, depending on their participation in interactive zoo mediation displaying citizen science. The principal investigator, Audrey Maille, and her pluri-disciplinary team composed of 18 collaborators (including 5 persons hired for the project), will carry out five research tasks and one coordination task to achieve the aims of the PRIMAZOO project. TASK 1 will consist of adapting existing infrastructures at Haute-Touche Zoological Reserve (MNHN, Indre), in order to accommodate studies on macaques (Macaca tonkeana) and visitors in the first zoo-based Primate Study Centre to be established in a public zoo being part of a national research institution. TASK 2 will assess whether macaques and humans are able to attribute emotions to members of the other species by processing multimodal cues, such as facial expressions, body postures or vocalizations. TASK 3 will evaluate how the behaviour of one species affects the behaviour of the other species when interacting during zoo visits. TASK 4 will investigate whether participation in zoo mediation displaying citizen science influences those intersecting perceptions and the visitors’ representations of nonhuman primates. Finally, the transversal TASK 5, will study how behaviours and attitudes of human participants toward macaques are affected by knowledge and representations about zoo primates. The PRIMAZOO project, will contribute to improve scientific knowledge about the human-environment interactions as it aims to better characterize the relationships between human and nonhuman primates in a zoo setting through an innovative and holistic approach of animal captivity. This project has the potential to provide new insights on the putative effects of captivity on behaviour of primates, increasing our understanding of primate welfare in zoological parks. This project should also provide scientific tools from life and social sciences for evaluating the influence of environmental education developed in zoo settings on public engagement with zoos as actors of biodiversity conservation, and more generally with environmental issues. The PRIMAZOO project will thus have both scientific and societal implications, in helping to guide the decision-making process in the zoo community.

Two important dimensions of the socio-environmental crisis are climate change and biodiversity loss. One of the main challenges of our century is to promote sustainable solutions adapted to the specificities of each social-ecological system (SES) and to integrate climate change and biodiversity loss in a single environmental policy. Whereas environmental policies against climate change and biodiversity loss are mainly designed and implemented independently, we urgently need a better integrated approach associating these two dimensions and well-being of human beings. Fragmented forest habitats are very interesting areas to better understand the entanglement of the dynamics impulsed by local people subsistence activities, carbon storage and biodiversity conservation policies. The Congo Basin Forest is the 2nd most important equatorial forest representing a unique biodiversity hotspot, carbon sink and source of primary resources for humans. Integrating climate change and biodiversity loss in this region is thus crucial for effective environmental policies at both local and global levels. The FRAGPAN proposal is focused on interactions between bonobos (Pan paniscus) as an endangered and flagship species, humans and a fragmented habitat in Democratic Republic of the Congo (DRC) where both biodiversity conservation and carbon storage policies have been implemented. Bonobos being a male philopatric species, females emigrate from their native group. Thus, the forest connectivity is probably crucial to maintain bonobos genetic viability. The probability of bonobo presence is negatively correlated with the degree of forest fragmentation and human proximity, except in savanna-mosaic habitats located West of the species range, in the Maï-Ndombe Province (DRC). This sub-population is probably genetically isolated, challenging its mid-term viability. However, no information is available on bonobo presence and potential migration between this subpopulation and the central subpopulation. Studying this particular area is crucial to improve our knowledge on bonobo socio-ecological flexibility and to adapt conservation strategies. The primary objective of this project is to analyze the dynamics and the sustainability of the human-bonobo co-existence in this fragmented landscape, and to promote strategies to ensure both bonobo populations viability and local human populations’ needs. The specific objectives are: 1) to characterize the bonobo socio-ecology and biological diversity locally and regionally based on spatialized behavioral and genetic data; 2) to analyze the evolution of the forest cover and connectivity since the late 1950’s, based on aerial and satellite images; 3) to identify changes in human practices and representations (both from local human populations and stakeholders from forest management) of the forest, the bonobos and the habitat dynamics based on interviews, participant observations and archives; 4) to assess the potential for bonobos’ mobility in this fragmented landscape and the consequences on the viability of the studied sub-population, by integrating the previous findings on bonobos, humans and habitat dynamics in a habitat network model; 5) to propose and promote sustainable solutions to maintain and improve human-bonobo co-existence, accounting for human needs, bonobo needs, and the conservation and carbon storage policies. We will conduct this project in the Maï-Ndombe Province where the coordinator of the FRAGPAN proposal has 15 years of experience, in close partnership with the local NGO Mbou-Mon-Tour. Our theoretical framework is based on the resilience of SES, which allows us to better understand changes in complex systems and to guide governance. Beyond our study area, we expect that our results will contribute to the bonobo conservation strategy on its entire distribution area, other great ape species conservation and more generally to the understanding of the forest fragmentation impact on animal dispersion.