Much of modern biological research aims to characterize the relationship between genotype
and phenotype. Evolutionary biology is more ambitious. An understanding of how genotype …

A widely used method for studying the evolutionary forces acting on a species is to
sequence homologous genomic regions from a set of randomly chosen individuals. The …

In a wide variety of organisms, synonymous codons are used with different frequencies, a
phenomenon known as codon bias. Population genetic studies have shown that …

Codon-based models of evolution are a relatively new addition to the toolkit of
computational biologists, and in recent years remarkable progress has been made in this …

Evolutionary studies commonly model single nucleotide substitutions and assume that they
occur as independent draws from a unique probability distribution across the sequence …

The phenomenon of codon usage bias has been important in the study of evolution because
it provides examples of weak selection working at the molecular level. During the last two …

Through an analysis of polymorphism within and divergence between species, we can hope
to learn about the distribution of selective effects of mutations in the genome, changes in the …

Background Models of codon evolution have proven useful for investigating the strength and
direction of natural selection. In some cases, a priori biological knowledge has been used …

Phylogenetic codon models are routinely used to characterize selective regimes in coding
sequences. Their parametric design, however, is still a matter of debate, in particular …

Codon usage bias is the nonrandom use of synonymous codons for the same amino acid.
Most population genetic models of codon usage evolution assume that the population is at …