[37] Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences

This chapter describes the significance of maximum parsimony approach to the construction of evolutionary trees from aligned homologous sequences. A maximum parsimony tree accounts for the evolutionary descent or related sequences by the fewest possible genie changes. Such a tree maximizes the genetic likenesses associated with common ancestry while minimizing the incidence of convergent mutations. Calculation of tree length is simplified by removing the root from the tree. Such an unrooted tree or network still retains the interior nodes and the exterior nodes (the OTUs).The maximum parsimony procedure can reconstruct ancestral sequences for each interior node of a tree but cannot determine which interior node or which pair of adjacent interior nodes is closest to the root. The problem of finding the maximum parsimony tree can be broken down into two parts. The first part proved to be easy and was solved by Fitch for homologous nucleotide sequences. The algorithm requires as input data both the OTUs, which are contemporary homologous nucleotide sequences already aligned against one another, and the instructions for a tree or dendrogram specifying any one of the possible dichotomous branching orders for the OTUs.