Purifying selection can obscure the ancient age of viral lineages.

ABSTRACT: Statistical methods for molecular dating of viral origins have been used extensively to infer the time of most common recent ancestor for many rapidly evolving pathogens. However, there are a number of cases, in which epidemiological, historical, or genomic evidence suggests much older viral origins than those obtained via molecular dating. We demonstrate how pervasive purifying selection can mask the ancient origins of recently sampled pathogens, in part due to the inability of nucleotide-based substitution models to properly account for complex patterns of spatial and temporal variability in selective pressures. We use codon-based substitution models to infer the length of branches in viral phylogenies; these models produce estimates that are often considerably longer than those obtained

SUBMITTER: Wertheim JO 

PROVIDER: S-EPMC3247791 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature