Nucleotide Substitution Models and Evolutionary Distances

  • Xuhua Xia


Genomes change over time, so are the interactions of genes and gene products that breathe life into a genome. To have the most advantageous view of genomes, genes and their interactions, we need to see things from the very beginning. Substitution models enable us to trace history back to the very early forms of life, by reconstructing the genomic “books” erased and obliterated by billions of years of mutations. This chapter focuses on nucleotide-based substitution models, presenting three different ways of deriving, for various substitution models, transition probability matrices that are needed to compute evolutionary distances and to compute likelihood of a tree. These three different ways should allow students of different mathematical background to understand substitution models and their uses in phylogenetics. Almost all frequently used substitution models are nested models with the simple one being a special case of the more general one. The likelihood ratio test, as well as the information-theoretic indices as an alternative approach to model selection, is numerically illustrated in choosing the substitution model that best describes the aligned sequences.


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