Global lability, regional resolution, and majority-rule consensus bias

Evolutionary interpretation of paleontological patterns requires a hypothesis of phylogeny, but our phylogenetic hypotheses may not perfectly mirror organismal phylogeny. Tree summary methods less conservative than strict consensus may increase resolution, but these methods may present a biased summary of the full set of most parsimonious trees. When we fail to acknowledge all equally optimal topologies, we risk disregarding trees that are closer to the correct phylogeny. We discuss a case where two subsets of trees were recovered in the set of most parsimonious trees, each with a profoundly different interpretation of character evolution near the root of Echinodermata. This was caused by the presence of a bimodally labile taxon in the matrix with two different topological subsets, each equally parsimonious but differing in the number of consistent trees. Majority-rule consensus favors the subset with the largest number of trees consistent with the placement of the rogue taxon. This bias favors clusters not because of the biological implications of the tree, but on the basis of great inequality in the sizes of the islands of parsimony. We thus recommend that majority-rule consensus trees not be used to summarize the results of a phylogenetic analysis.