This doctoral thesis, directed by Santiago F. Elena, presents a series of experimental studies on the strategies of evolutionary capacity and adaptation of viruses to their plant hosts. The results of this research have been published in the journals Scientific Reports, Virus Evolution, PNAS, Archives of Virology and Advances in Virus Research. The thesis was defended on October 13, 2021.

Viruses are the most abundant biological entities on Earth and have a great capacity for evolution and adaptation. Some viruses can infect a wide range of hosts causing damage to a number of important plants, while others infect one host species very well and cause severe damaging symptoms in a short period of time. Over time, viruses can adapt well to new hosts and increase their infectivity and virulence, thereby causing further damage to the host. However, we still do not know how plants respond to viral infection with viruses that have different adaptation histories or host ranges, or how viruses that are differently adapted to the host respond to different environmental stresses. This thesis attempted to answer these questions with an experimental system of turnip mosaic virus (TuMV) that infects the model plant Arabidopsis thaliana. Different TuMV strains with different adaptation histories were used. Some were naïve to Arabidopsis, while others were preadapted to the host with different host ranges (generalist or specialist). A method called genomic association studies (GWAS) was used to relate the plant genes involved in viral infection with the different TuMV strains. Using the GWAS method, plant genes that responded differentially to a generalist virus or a specialized one were identified and characterized. Finally, Arabidopsis was inoculated with the naive and preadapted virus and its genetic robustness (the constancy of the phenotype under mutational changes) and environmental robustness (the constancy of the phenotype under environmental changes) was verified. The results show how adaptation to one environment limits the evolutionary capacity in other alternative environments, thus restricting the ability of the preadapted virus to respond quickly to future environmental changes.

Anamarija Butković's thesis was carried out in the Evolutionary Systems Virology research group of the I²SysBio under the supervision of Santiago F. Elena (Research Professor at the CSIC). During the development of her thesis Anamarija Butković has enjoyed a contract within the Grisolia Program (Generalitat Valenciana) and a short-term EMBO scholarship during her stay in Mart Krupovic's laboratory (Pasteur Institute, Paris). The qualifying panel was made up of Carmen Hernández (IBMCP, CSIC-UPV), Jesús Israel Pagán Muñoz (UPM) and Philippe Roumagnac (Cirad Agricultural Research Center for International Development), who rated the thesis as outstanding.