This review is motivated by the true explosion in the number of recent studies both
developing and ameliorating probabilistic models of codon evolution. Traditionally …

While it has often been assumed that, in humans, synonymous mutations would have no
effect on fitness, let alone cause disease, this position has been questioned over the last …

Comparative analysis of multiple genomes in a phylogenetic framework dramatically
improves the precision and sensitivity of evolutionary inference, producing more robust …

Current models of codon substitution are formulated at the levels of nucleotide substitution
and do not explicitly consider the separate effects of mutation and selection. They are thus …

Non-coding DNA comprises∼ 80% of the euchromatic portion of the Drosophila
melanogaster genome. Non-coding sequences are known to contain functionally important …

Drosophila seminal proteins have an unusually high rate of molecular sequence evolution,
suggesting either a high rate of neutral substitution or rapid adaptive evolution. To further …

Patterns of synonymous codon usage are determined by the forces of mutation, selection
and drift. We elaborate on previous population genetic models of codon usage to …

Selection acting on codon usage can cause patterns of synonymous evolution to deviate
considerably from those expected under neutrality. To investigate the quantitative …

Despite the degeneracy of the genetic code, whereby different codons encode the same
amino acid, alternative codons and amino acids are utilized nonrandomly within and …

The genomic density of sequence polymorphisms critically affects the sensitivity of
inferences about ongoing sequence evolution, function and demographic history. Most …