Comparative biology and the importance of cladistic classification: a case study from the sensory biology of squamate reptiles

Evolutionary taxonomy has all but succumbed to cladistic methodology, but it continues to exert considerable influence in the realm of higher classification. Some systematists accept cladistic methods in phylogeny inference, but allow paraphyly in formal classifications. Most important, however, many traditional classifications based on paraphyletic groups (e.g. 'Reptilia') remain in force, deeply entrenched in the literature. Cladists have argued that such paraphyletic classifications can mislead comparative biologists into false evolutionary generalizations, but this assertion has rarely, if ever, been supported by example. This paper provides a case study, illustrating in detail the influence of a traditional paraphyletic classification of squamate reptiles on the historical development of ideas regarding the evolution of sensory modes (chemoreception vs. vision) in the group. The paraphyletic classification is shown to have led to false generalizations and incorrect conclusions stemming directly from the fact that the classification did not reflect accurately the phylogeny of Squamata, particularly the cladistic relationships of Gekkota. This study provides direct evidence that evolutionary generalization must be rooted in the branching pattern of phylogeny and not the potentially arbitrary categorical ranks of traditional taxonomies. It further supports recent calls for a truly phylogenctic taxonomy that has as its philosophical core the concept of descent.