Medieval agriculture in the western Mediterranean is said to have experienced two major events between the 8th and 16th centuries that had a significant impact on its evolution: the Muslim expansion, which would have sparked a “green revolution”, and the expansion into Iberia of the Christian kingdoms, often found under the debated name of “Reconquista”. Although the impact of Muslim expansion on the medieval West is undeniable, it remains unevenly studied, and the actual expansion of Arab-Berber agriculture in the western Mediterranean, its chronology of implementation and the “new” plants and techniques that were supposed to accompany it is yet to be documented, especially in the rural zones, to determine whether or not it was a uniformly widespread phenomenon throughout the medieval Muslim Western world. Concerning the 'Reconquista', its impact on the agricultural world and material culture has been little explored, and the weight of Andalusian agricultural legacy in the newly Christianized areas of the peninsula, and the dynamics and rhythms of the diffusion of new plants and practices to other Christian dominated areas, such as southern France, remain to be explored. To address these questions, ISEMA proposes to use an international (Spain, France), innovative (archaeobotany, quantitative eco-anatomy, geometric morphometrics, stable isotopic analyses) and broadly interdisciplinary approach, in order to tackle a complex agricultural reality that is difficult to grasp using textual archives alone. Through the study of a corpus of more than sixty archaeological sites (10th-16th c.) distributed between Mediterranean France and continental and insular Spain, ISEMA will seek to document medieval agrosystems (exploited plants, farming practices, agricultural landscapes) and their evolution over time. The objective will be to evaluate how medieval societies developed their agrarian strategies, according to the evolution of the cultural, socio-economic and environmental context, and to determine the role of socio-economic dynamics in the large-scale diffusion of certain agricultural productions.

Horses and humans share a long history of interactions from the initial domestication to the standardization of modern breeds. Domesticated horses revolutionized mobility and transformed the organization of past human societies. In turn, humans have optimised their performance, improving their speed, strength or endurance. Whereas variation within current horse breeds is easy to perceive, past forms are poorly comprehended. Indeed, most of our knowledge of the past role of the horse and its breeding is based upon written sources, but they generally provide limited information about the horse itself. In that respect, archaeological horse bones represent the best surviving testimony of the morphological but also functional characteristics of past animals. My project investigates how humans have shaped horses over the four last millenia. The aim will be to better understand the evolution of their interactions and thus to gain insight into how horses have in turn impacted human history. Cutting-edge approaches will be used to characterize bone structure both externally, internally and biomechanically. These data will then be confronted to historical narratives, to document past horse uses and breeding. Besides its contribution to the knowledge about past horse roles, this project will enhance our understanding of the human impact on animal diversity.

Fungi are a remarkably diverse kingdom with an estimated 1.5 million species. They form intimate interactions with a broad array of other organisms, including mutualisms, symbioses and as decomposers. Yet their essential role supporting life on earth has often been matched by their ability to cause devastating diseases in humans, animals and plants. Given that emerging fungal infectious diseases pose serious threats to public and wildlife health, food security, and ecosystem stability, understanding fungal evolution and adaptations to biotic and abiotic factors has never been more urgent. We argue that an in-depth study, combining population and comparative genomics, of one fungal clade containing pathogenic and non-pathogenic species will be critical to better understand the genomic determinants of fungal adaptation. Indeed, these two complementary approaches extract information on different timeframes and as a result draw a more complete and accurate picture of events and processes acting across fungal genomes. We propose to investigate the fungal genus Pseudogymnoascus, comprising one pathogenic species infecting bats (Pd) and more than 45 closely related species not pathogenic to bats. We will (1) characterise the Pd pangenome architecture, content and variability, and test if the species follows the two-speed genome model, (2) identify Pd genomic regions that are involved in local adaptation generally and those that are associated with key biotic and abiotic adaptations specifically, (3) Identify genomic characteristics differentiating pathogenic and non-pathogenic species, and (4) extent our work to characterise the relationship between life-history traits, genome properties and evolutionary processes across Ascomycota.

DockEvol aims to be the first project of a long-term integrative research program on "biological portuarization", defined as the evolution of marine species in harbour-ecosystems under human-altered selective pressures. Humans have built ever larger and numerous ports on all the coasts of the world. These new habitats are like giant mesocosms, often isolated from the open sea by locks, where species find themselves in novel abiotic environments, and within a novel assemblage of exotic and native species that sometimes interbreed. Ports can thus be thought of as Darwinian field-labs in which parallel replay evolution experiments unfold in a replicated fashion for moderate timescales. DockEvol will focus on three species for which we have preliminary evidences of a portuarization syndrome, surveyed in in-port, middle-port and out-port sites in three study ports. Our framework is to study the genotype-phenotype-environment triangular relationship, which is key to allow fine-tuned understanding of evolutionary processes, but rarely examined simultaneously. We will combine high-throughput genome sequencing, condition indexex and microbiome profiling, and monitoring of the abiotic as well as the biotic environment using environmental DNA metabarcoding. In addition, we will build a predictive model using fitness landscapes, adjusted to the genotype-phenotype maps controlled for environmental variations. Finally, lab experimentations will be conducted to investigate the functional effects of two candidate variations we recently identified in portuarized populations of two of our target species: a 15-fold tandem repeat of a cytochrome P450 gene in Ciona, and two radical amino-acid change of the period gene in Mytilus. DockEvol will report how the port environment shapes selection pressures at the species level but also how it modifies organism demography and movement in human-altered seascapes.

Speciation is the process by which populations diverge and accumulate reproductive isolation barriers up to the point they become separate species. Although evolutionary biologists are now able to score genetic differentiation at the whole genome scale, the factors determining the rate of divergence and the likelihood of speciation still remain elusive. The main objective of the CoGeDiv project is to address the unknown role of demographic factors in speciation using a multispecies comparative genomic framework. Major biogeographic suture zones offer ideal study systems to implement such a comparative approach. They concentrate across a wide variety of taxa the coexistence of cryptic species-pairs separated by physical or ecological barriers, which continue to exchange genes despite being partially reproductively isolated. Because these semi-species have originally diversified in a shared historical and ecological context, they provide a suitable framework to identify the evolutionary processes which affect species diversification in phylogenetically diverse groups. The CoGeDiv project will focus on 16 littoral marine species-pairs distributed across a major biogeographic boundary comprising dispersal and ecological barriers: the Atlantic-Mediterranean transition zone. These species-pairs display variable degrees of reproductive isolation and are characterized by a wide range of life-history traits that impact their demography in different ways. A standardized population genomic approach will be implemented to evaluate the rate at which speciation proceeds in these different taxa. Genome-wide differentiation patterns will be characterized for each species-pair using individual RNA-Sequencing in population samples. An integrated bioinformatic pipeline will be used to score polymorphisms and compute population genetic statistics. For each species-pair, the joint demographic history will be inferred using statistical methods that separately capture historical, demographic and selective effects. Estimated divergence parameters will be compared among species-pairs to link species biology and ecology with their propensity to speciate in a shared biogeographical context. By generating a comprehensive and high-dimensional dataset to address testable predictions, we expect to bring significant progress beyond the state-of-the-art on several fundamental questions that remain unanswered. (i) How the balance between selection and gene flow affects divergence across the speciation continuum? (ii) Is heterogeneous genomic divergence shaped by differential gene flow and/or linked selection? (iii) What is the role of cytonuclear incompatibilities in speciation? (iv) How life-history traits and species demographic characteristics affect speciation? By generating an unprecedented analysis of species genetic diversity beyond the classically recognized conservation units, we expect to provide a mechanistic understanding of species responses to contemporary climate change, and to improve our knowledge of cryptic diversity in a littoral marine diversity hotspot.