Phylogenetic methodology has always attracted more than its share of controversy, so I expected critical responses to my 1999 piece on the evolutionary implications of character-taxon matrices. In that piece, I argued that the topology of a clade, as inferred from cladistic parsimony analysis of a rectangular matrix of characters and taxa, is influenced by all the taxa considered, including those that fall outside the clade in question. The inferred pattern of branching in the clade is therefore statistically influenced by and dependent on the inferred evolutionary pattern among the other taxa. This dependence is at odds with the principle that, once sister-groups of eukaryotes have diverged, their subsequent pathways of evolution are independent of each other. I also suggested that, along with evidence from ontogeny, times of appearance of taxa as inferred from stratigraphic data be allowed to influence interpretations of which characters are primitive and which are derived.