Probabilistic Methods for Bioinformatics

Chapter 10Molecular Evolutionary Genetics

In the previous chapter, we took the gene (locus) as our basic unit and investigated ways in which allele composition can change over time when alleles undergo mutations. An allele that becomes fixed in a population is composed of a sequence that is different from the one it replaces. That is, the substitution of a new allele for an old allele consists of the substitution of a new nucleotide sequence for an old nucleotide sequence. In this chapter, we investigate how nucleotide sequences change over time. We take the nucleotide as our basic unit and develop models for nucleotide substitutions over time. ...