Molecular evolution of viruses; 'trees', 'clocks' and 'modules'

Comparisons of the nucleotide sequences of viral genomes, and derived amino acid sequences, mostly confirm the traditional taxonomic groupings of viruses. These comparisons have also shown unexpected homologies between genes of viruses from different groups previously thought to be unrelated, and between some viral and non-viral genes. Comparisons of the three-dimensional structures of the particle proteins of some viruses have also revealed unexpected relationship, and, together with the sequence homologies, suggest that some ancestral viruses had 'modular' origins. Some of the sequence differences have been used to construct phylogenies. However, there is evidence that viral gene 'molecular clocks' do not always keep time consistently over very long or very short evolutionary time periods. Clues on evolution mostly come from comparative studies of living or fossil organisms. Fossils of viruses are not known, and thus clues of the origins and evolution of viruses are obtained by comparing extant forms. For example, by comparing isolates of different viruses, or strains of viruses, one can infer the properties of their ancestors, and by comparing isolates obtained during an epidemic, and sequentially related to one another, one can observe directly the type and timing of evolutionary changes.