A gene tree is an essential descriptor of any evolutionary process, for the semi-conservative replication of the DNA double helix automatically produces a bifurcating gene tree. It should be emphasized that the genealogical relationship of genes is independent of the mutation process, especially when neutral evolution (Kimura, 1983) is considered. The former is a direct product of DNA replication, while the latter may or may not happen within a certain time period and DNA region. Therefore, even if many nucleotide sequences happened to be identical, there must be a genealogical relationship for those sequences. However, it is impossible to reconstruct the genealogical relationship without mutational events. In this respect, extraction of mutations from genes and their products is critical for reconstructing phylogenetic trees.

We can, therefore, best estimate a gene tree according to the mutation events realized on its expected gene tree (see Fig. 18.1 (a)). We call this ideal reconstruction of the gene tree the realized gene tree (see Fig. 18.1 (b)), while the reconstructed one from observed data is called the ‘estimated’ gene tree (Saitou, 1995b). Branch lengths of realized and estimated genes tree are proportional to mutational events. These mutational events are not necessarily proportional to physical time. Because of limitations in information, estimated gene trees are often unrooted.