Comparative methods and evolution

Comparative biology provides a framework for the study of evolution, by seeking answers to the question of why traits evolved. However, the difficulties of making inferences about the biological causes of trait variation and covariation resulted in the development of very different approaches to comparative analyses, which are outlined and contrasted here. The Homology approach differs from all other approaches as it attempts to explain historical uniques, whereas the various homoplasy approaches draw inferences from repeated origination of correlated traits. A distinction is made between those approaches deriving information from correlated transitions of characters on a cladogram (Homoplasy I) and those that simply extract correlated differences between pairs of phylogenetically independent taxa (Homoplasy II). The latter approach has been implemented in well-developed analytical procedures ("comparative methods") which, however, are principally non-historical and thus their inferences about evolution are indirect. In contrast, the study of correlation of character transitions seeks to explain trait variation as the outcome of evolution, but is hampered by the difficulty of reconstructing ancestral character states, a prerequisite for the analysis of correlated transitions. Model-based techniques for ancestral state reconstruction are being developed, but the lack of data contained in single characters limits the biological reality of parameter-intensive models.