Phylogenetic analysis nucleotide substitutions

In the late 1960 s and throughout the 1970 s allozyme characters provided simple genetic information which was useful for phylogenetic analysis (Buth 1984, Swofford and Berlocher 1987). This information reflected nucleotide substitutions in charged amino acids. The work of Coyne and others with varying pH and gel concentrations showed us that a large proportion of hidden alloz3nne variants could be visualized but that a complete picture of variation would require nucleotide sequences (reviewed in Coyne 1982). 

The selection of nucleotide characters for phylogenetic studies is not a simple problem. In general, for a given taxonomic level the best characters are those whose states are constant within taxa and variable among taxa, but not so variable that noise is introduced into the analysis. For molecular data, noise is created by multiple substitutions at a site. 

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