Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models.

ABSTRACT:

Background

The vast majority of phylogenetic trees are inferred from molecular sequence data (nucleotides or amino acids) using time-reversible evolutionary models which assume that, for any pair of nucleotide or amino acid characters, the relative rate of X to Y substitution is the same as the relative rate of Y to X substitution. However, this reversibility assumption is unlikely to accurately reflect the actual underlying biochemical and/or evolutionary processes that lead to the fixation of substitutions. Here, we use empirical viral genome sequence data to reveal that evolutionary non-reversibility is pervasive among most groups of viruses. Specifically, we consider two non-reversible nucleotide substitution models: (1) a 6-rate non-reversible model (NREV6) in which Watson-Cri

SUBMITTER: Sianga-Mete R 

PROVIDER: S-EPMC9810213 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature