The Role of Functional Analysis in Phylogenetic Inference: Examples from the History of the Xiphosura

Abstract

SYNOPSIS. Conventional cladistic analyses of phylogeny can be interpreted as operating at the level of phylogenetic trees. They assume that all “evolutionary steps” (transitions from one character state to the next, along a morphocline) are independent and equal, and, on that basis, select the cladogram which is consistent with the most parsimonious trees. Evaluation of the assumptions of independence and equality requires consideration of hypotheses at the levelof scenarios. In some cases, arguments based on functional analysis can suggest revised interpretations of either homology or polarity. If properly formulated, these arguments can alter the evaluation of parsimony for trees to the extent that even the choice of cladogram is affected. The structure of scenario level arguments is identical to that of arguments operating at tree level. Examples of phylogenetic inference in the context of xiphosurans (horseshoe crabs), using both comparative morphological and functional analysis, illustrate this approach. In different cases, orthodox interpretations of relationship are either challenged or corroborated. Although the introduction of functional analysis into the process of phylogenetic inference may appear to compromise the usefulness of the reconstructed phylogeny for testing hypotheses concerning the role of natural selection in evolution, it actually increases the strength of such tests.