CHARACTER CODING OF SECONDARY CHEMICAL VARIATION FOR USE IN PHYLOGENETIC ANALYSES
TODD J. BARKMAN
Department of Biology, Western Michigan University, Kalamazoo, MI 49008 Tel.# 269-387-5610; fax # 269-387-5609. E-mail address, firstname.lastname@example.org
A coding procedure is presented for secondary chemical data whereby putative biogenetic pathways are coded as 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 pathways 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 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 or character-state tree coding methods using parsimony analyses of 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 enhance inferences of biochemical pathway evolution.