Relaxation of selective strength, manifested as a reduction in the efficiency or intensity of
natural selection, can drive evolutionary innovation and presage lineage extinction or loss of …

Population geneticists have long sought to understand the contribution of natural selection
to molecular evolution. A variety of approaches have been proposed that use population …

Phylogenetic tests of adaptive evolution, such as the widely used branch-site test (BST),
assume that nucleotide substitutions occur singly and independently. Recent research has …

A number of tests have been developed to detect positive selection at the molecular level.
These tests are based on DNA polymorphism within and divergence between species …

The genomic signatures of positive selection and evolutionary constraints can be detected
by analyses of nucleotide sequences. One of the most widely used programs for this …

The selective pressure at the protein level is usually measured by the nonsynonymous/
synonymous rate ratio (ω= d N/d S), with ω< 1, ω= 1, and ω> 1 indicating purifying (or …

The historical signal in nucleotide sequences becomes eroded over time by substitutions
occurring repeatedly at the same sites. This phenomenon, known as substitution saturation …

Selection modulates gene sequence evolution in different ways by constraining potential
changes of amino acid sequences (purifying selection) or by favoring new and adaptive …

The branch-site test is a likelihood ratio test to detect positive selection along prespecified
lineages on a phylogeny that affects only a subset of codons in a protein-coding gene, with …

The selective pressure on a protein-coding gene can be measured by comparing silent
(synonymous) and replacement (nonsynonymous) substitution rates. Higher replacement …