Character coding of secondary chemical variation for use in phylogenetic analyses

A coding procedure is presented for secondary chemical data whereby putative biogenetic pathways are coded as phylogenetic characters with enzymatic conversions between compounds representing the corresponding character states. A character state tree or stepmatrix allows direct representation of the secondary chemical biogenetic pathway and avoids problems of non-independence associated with coding schemes that score presence/absence of individual compounds. Stepmatrices are the most biosynthetically realistic character definitions because individual and population level polymorphisms can be scored, reticulate enzymatic conversions within pathways may be represented, and down-weighting of pathway loss versus gain is possible. The stepmatrix approach unifies analyses of secondary chemicals, allozymes, and developmental characters because the biological unity of the pathway, locus, or character ontogeny is preserved. Empirical investigation of the stepmatrix and character state tree coding methods using floral fragrance data in Cypripedium (Orchidaceae) resulted in cladistic relationships which were largely congruent with those suggested from recent DNA and allozyme studies. This character coding methodology provides an effective means for including secondary compound data in total evidence studies. Furthermore, ancestral state reconstructions provide a phylogenetic context within which biochemical pathway evolution may be studied.