Mathematical models will be studied that use DNA sequence data to estimate the amount of mutation and the amount of Darwinian selection that have acted in the past within a biological species. These methods are based on the distribution of site configurations within a set of aligned DNA sequences from a set of individuals at the same gene. The technique can be applied both at ``silent sites'' (which do not change the gene product) and ``replacement sites'' (which cause a different protein or enzyme). The ratio of the two mutation rates gives an estimate of the number of nonlethal changes possible in the protein, and selection rates at silent sites give an estimate of codon bias. These methods will be extended and applied to DNA sequences from a variety of genes in a variety of species, and to aligned DNA sequences from two or more related species. The latter will allow more data to be analyzed, and will allow estimation of the selective differences between related species. Other extensions and similar procedures will also be studied. Mathematical models will be studied that use DNA sequence data to estimate the amount of mutation and the amount of Darwinian selection that have acted in the past within a biological species. These methods will be extended and applied to DNA sequences from a variety of genes in a variety of species, and to aligned DNA sequences from two or more related species. The latter will allow more data to be analyzed, and will allow estimation of the selective differences between related species. Other extensions and similar procedures will also be studied.
