Abstract paml, currently in version 4, is a package of programs for phylogenetic analyses of
DNA and protein sequences using maximum likelihood (ML). The programs may be used to …

The past few years have seen the development of powerful statistical methods for detecting
adaptive molecular evolution. These methods compare synonymous and nonsynonymous …

The growing availability of human genetic variation has given rise to novel methods of
measuring genetic tolerance that better interpret variants of unknown significance. We …

Many genes that mediate sexual reproduction, such as those involved in gamete
recognition, diverge rapidly, often as a result of adaptive evolution. This widespread …

Population Genetics and Microevolutionary Theory Explore the fundamentals of the
biological implications of population genetic theory In the newly revised Second Edition of …

Maximum-likelihood methods based on models of codon substitution accounting for
heterogeneous selective pressures across sites have proved to be powerful in detecting …

Sequence comparisons of genomes or expressed sequence tags (ESTs) from related
organisms provide insight into functional conservation and diversification. We compare the …

Examining genomic data for traces of selection provides a powerful tool for identifying
genomic regions of functional importance. Many methods for identifying such regions have …

Rapid evolution driven by positive Darwinian selection is a recurrent theme in male
reproductive protein evolution. In contrast, positive selection has never been demonstrated …

Successful reproduction requires contributions from both the male and the female. In
Drosophila, contributions from the male include accessory gland proteins (Acps) that are …