Parasites have high socio-economic impact due to their negative effect on humans, animals and plants welfare. Parasite evolution may lead to emergence of new infectious diseases, and compromise existing disease control strategies. Viruses are one of the most important groups of parasites causing a large fraction of emerging diseases. Adaptation to new environments may lead to population diversification, including speciation events resulting in the appearance of new viruses.

Ecological and genetic factors are important in determining virus evolution. Environmental modifications impose selection pressures, thus changes in host population density or distribution will result in the appearance of new viral strains or species.

Mutation and recombination are the main mechanisms for generating genetic variability in RNA viruses: their high mutation rates allow them to evolve rapidly adapting to new environments. Exchange of gene modules between related viral strains (modular evolution) may also result in new variants with higher fitness. We will analyze the role of these evolutionary mechanisms in the processes of virus speciation using bioinformatic tools applied to genomic sequence datasets.

Analyses will focus on the families Picornaviridae, Coronaviridae and Potyviridae as models for RNA virus evolution. The three families have been widely studied, as they are important human, domestic animals and wildlife, and crop pathogens, with high sociological and agronomic relevance. Sequence data, together with information on host range and geographical distribution, are available for a large number of species and strains of these families. However, despite this data availability, to date there has been no extensive analysis of the patterns and processes of RNA virus speciation.

Understanding virus evolution may be of deep interest as it may help to predict and control viral epidemics, and to understand the processes leading to the emergence of new infectious diseases