Among the projects that we are currently working on, we would like to highlight the following:
1. Effect of the accumulation of deleterious mutations in TEV fitness on its natural hosts Nicotiana tabacum. Characterization of the level of epistasis among deleterious mutations both, within and among genes.
2. Statistical characterization of the distribution of mutational effects on TEV fitness and virulence on tobacco and on new hosts. Epistasis-by-host interactions.
3. Characterization of the molecular basis of differences in virulence. Correlation between viral replicative fitness and virulence. Evolution of virulence under multiple-infections dynamics and vector-mediated transmission.
4. Characterization of adaptive dynamics of TEV to new hosts (Arabidopsis thaliana and Capsicum annuum). Host range and evolutionary correlated response to new hosts. Tradeoffs in simultaneous adaptation to different hosts. How does the pattern of plant gene expression changes as a consequence of viral adaptation?
5. Experimental test of the model of clonal interference among beneficial mutations (TEV). Molecular characterization of beneficial mutations fixed at successive adaptive steps and its effect on the rate of adaptation.
6. Evolutionary significance of genome segmentation.
7. Evolution of mechanisms of genetic robustness in highly mutable RNA genomes (TEV). The role of population size and mutation rate in the evolution of genetic robustness. Genetic robustness as a correlated response to environmental robustness. Neutral networks and the evolution of robustness in viroid species.
8. The suppression of post-transcriptional gene silencing as a viral evolutionary strategy to overcome plant defences. Characterization of mutational effects on the suppressor protein (HC-Pro) of TEV. Compensatory evolution of suppression function and genetic architecture of the trait. Molecular evolution of viral suppressor proteins.
9. Evolutionary stability of A. thaliana transgenic plants that express amiRNAs targeting TuMV HC-Pro. Estimation of the likelihood of resistance-breaking by evolving TuMV populations. Molecular basis of resistance-breaking. In cooperation with Prof. Nam-Hai Chua (Rockefeller University).
10. Synergistic interactions among viruses coinfecting the same plant (TuMV and CaMV infecting A. thaliana). Coevolutionary dynamics. In cooperation with Dr. Rémy Froissart (CNRS, Montpellier).
11. Molecular evolution and phylogenetic studies of different plant viruses.
12. Development and systemic analysis of in silico and analytical models of viral gene interaction networks. Models of cell-to-cell and systemic movement. Epidemiological models. In cooperation with Prof. Ricard V. Solé (Universitat Pompeu Fabra) and Dr. Alfonso Jaramillo (École Polytechnique).
13. Optimal mutation rate and the relationship between mutational robustness and evolvability in digital organisms. In cooperation with Prof. R.E. Lenski and Dr. C. Ofria (Michigan State University) and Dr. Rafael Sanjuán (Universitat de València).