Selecting models of evolution

Phylogenetic reconstruction is a problem of statistical inference. Since statistical inferences cannot be drawn in the absence of probabilities, the use of a model of nucleotide substitution or amino acid replacement – a model of evolution – becomes indispensable when using DNA or protein sequences to estimate phylogenetic relationships among taxa. Models of evolution are sets of assumptions about the process of nucleotide or amino acid substitution (see Chapters 4 and 9). They describe the different probabilities of change from one nucleotide or amino acid to another along a phylogenetic tree, allowing us to choose among different phylogenetic hypotheses to explain the data at hand. Comprehensive reviews of models of evolution are offered elsewhere (Swofford et al., 1996; Liò & Goldman, 1998).