ERC FUNDED PROJECTS

Appreciation of endosymbiosis, a type of symbiosis in which a microbial partner lives within its host cells, as an important source of evolutionary novelty has developed relatively recently. In this proposal, we investigate a fundamental evolutionary process influenced by bacterial endosymbionts: the mechanisms of sex determination of their eukaryotic hosts. In animals, the most common system of sex determination is genetic. It can also be affected by inherited bacterial endosymbionts. However, very few systems have been analyzed and there is no extensive empirical evidence of how endosymbionts can shape host sex-determining systems. In the isopod crustacean Armadillidium vulgare, genetic sex determination follows female heterogamety. However, many A. vulgare populations harbour Wolbachia bacterial endosymbionts which can invert genetic males into phenotypic functional females. Other sex-determining factors have been identified in A. vulgare: a feminizing f element which may be a Wolbachia genome fragment carrying feminization information inserted into the host nuclear genome, and a masculinizing gene which can restore the male sex in the presence of the f element, as a result of a genetic conflict. Thus, sex determination mechanisms in A. vulgare seem to be largely driven by Wolbachia endosymbionts. However, the molecular genetic basis and evolutionary history of all these sex-determining factors is unknown. The A. vulgare/Wolbachia model provides a unique opportunity for directly investigating the impact of endosymbionts on the evolution of host sex determination mechanisms at the molecular genetic level. We will address this issue using the latest developments of molecular genetics technologies, such as next-generation DNA sequencing and high throughput genotyping.

1 403 285 €

Start date: 2011-01-01, End date: 2015-12-31

Prokaryotes evolve rapidly new functionalities by horizontal gene transfer delivered by mobile genetic elements (MGE). MGE increase relatedness between individuals and thereby might also promote the establishment of microbial social networks. Many studies have detailed the dynamics of specific systems in specific MGE. Yet, how MGE key and accessory functions evolve as a whole at the face of social dilemmas arising in microbial communities is largely ignored. Here, I aim at an integrative identification and analysis of self-mobilizable elements to unravel an evolutionary framework of MGE contributions to prokaryotic evolution. We will use sequence similarity, phylogeny and population genetics techniques to detail how elements propagate and are maintained in populations. We will investigate how accessory functions work together in relation to interactions between MGE and of MGE with the host. We will then quantify the long-term impact of MGE to the gene repertoires of prokaryotes by analysis of the patterns of their degradation and/or domestication using regulatory networks and population genetics. The analysis of secretion systems and effectors in mobile elements will enlighten the role of gene mobility in promoting social behaviours thorugh production of public goods. The previous results will then be used to query metagenomics datasets about the roles of gene mobility and secretion in the social evolution of natural microbial populations. This work will pioneer the application of theoretical works in population genetics and social evolution to the study of natural microbial communities by way of evolutionary genomics. Its integrative outlook will also provide essential breakthroughs in the understanding of the evolutionary history of mechanisms of gene mobility, e.g. conjugation. Finally, this project will pinpoint how manipulation of MGE might allows control of virulence, antibiotic resistance and other phenomena related with microbial social interactions.

1 298 925 €

Start date: 2012-07-01, End date: 2017-12-31

Temporal environmental variation in natural systems includes a large component of random fluctuations, the magnitude and predictability of which is modified under current climate change. The need for predicting eco-evolutionary impacts of plastic and evolutionary responses to changing environments is still hampered by lack of strong experimental evidence. FluctEvol aims at shedding a new light on population responses to stochastic environments, and facilitating their prediction, using a unique combination of approaches. First, theoretical models of evolution and demography under a randomly changing optimum phenotype will be designed and analysed, producing new quantitative predictions. Second, statistical methodologies will be developed, and employed in meta-analyses of long-term datasets from natural populations. And third, large-scale and automated experimental evolution in stochastic environments will be carried out with the micro-alga Dunaliella salina, an extremophile that thrives at high and variable salinities. We will manipulate the magnitude and predictability of fluctuations in salinity, and use high-throughput phenotyping and candidate-gene sequencing to analyse the evolution of plasticity for traits involved in salinity adaptation in this species: glycerol and carotene content. We will thus combine the benefits of experimental evolution in microbes (short generations, ample replication) with a priori knowledge of ecologically relevant adaptive traits, allowing for hypothesis-driven experiments. The success of this project in increasing our predictive power about eco-evolutionary dynamics is warranted by the experience of the PI, at the interface between theoretical and empirical approaches. Our experiments will have relevance beyond academia, as we will modify through evolution the plasticity of traits (accumulation of energetic cell metabolites) that are direct targets for bioindustry, thus potentially overcoming current limitations in productivity.

1 499 665 €

Start date: 2016-03-01, End date: 2021-02-28

"The dramatic success of infectious agents comes from their ability to adapt to both immune and pharmaceutical selective pressures. To uncover the dynamics of bacterial adaptation, experimental evolution has been widely used, focusing mostly on organismal fitness. Many of the observation derived from these experiments have been captured by Fisher's Geometric model of Adaptation (FGMA). Despite its success, this top-down phenotypic model is relatively abstract. In fact, its most important parameter, the number of independent phenotypes an organism expose to the action of natural selection, or phenotypic complexity, remains completely disconnected from a genetic perspective. More recently, bottom-up genotype to phenotype maps from system biology have provided an alternative to unravel the constraints regulating bacterial evolution. In the present project, I want to connect these different approaches. The interpretation of system biology models in terms of FGMA will (i) uncover the genetic determinants of phenotypic complexity, giving more genetic context to FGMA, and, (ii) transpose our understanding of evolution through FGMA to complex genotype to phenotype maps. Four different levels of integration will be used: the gene, the metabolic network, the organism and the species. I will use -antibiotic resistance gene, TEM1, to connect thermodynamic models of protein evolution to FGMA, and characterize the phenotypic complexity of a single gene, -computational models of metabolic network and experimental modification of a biochemical pathway regulation to assess the meaning of phenotypic complexity in networks, -in vitro and in vivo experimental evolution coupled with genome sequencing and mutant reconstruction to assess the molecular bases of changes in beneficial mutation rates during organismal adaptation, - faeces of well characterised human twins to assess the factors of the human gut's environment that shape the genetic diversity of the Escherichia coli species."

1 485 600 €

Start date: 2013-05-01, End date: 2018-04-30