The same format followed in Figure 1 is used here to demonstrate how rapid acquisition of gene function of a single sample might affect tree outcome in a phenetic analysis. In (A), four arrays are shown. Expressed genes are shown as green dots. The hierarchy depicted in (B) depicts a situation in which the gene expressions in the arrays are related to each other in a hierarchical pattern in which sample 4 acquires several new gene expressions. The events that occurred in each cell to produce its array profile are outlined in the same color as the array above. (C) The UPGMA (Sokal and Michener 1958) solution to the array data set. (D) The parsimony solution. The phenetic result is at odds with the parsimony result, which once again represents the “true” groupings of the cell lines.
