Character coding of secondary chemical variation for use in phylogenetic analyses

Abstract

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 de"nitions 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 uni"es 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 #oral 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 e!ective 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.

Chemical composition of anther volatiles in Ranunculaceae: genera‐specific profiles in Anemone, Aquilegia, Caltha, Pulsatilla, Ranunculus, and Trollius species

“…In addition to their ecological significance, floral fragrances have been recognized as chemotaxonomic markers in some plant taxa (Gerlach and Schill, 1989;Dahl et al, 1990;Harborne, 1993;Knudsen, 1994;Knudsen and Mori, 1996). Floral odor compounds are somewhat limited markers however, due to homoplasy and high intraspecific variation (see Williams and Whitten, 1999;Azuma et al, 2001;Barkman, 2001;Levin et al, 2001).…”

Floral scent analysis in Hieracium subgenus Pilosella and its taxonomical implications

“…An objection to the use of floral scent patterns in systematics is that convergence of floral scents may play an important role in plants in general, caused by similar pollinator pressures acting on plants of independent origin (Dobson et al, 2005). Nevertheless, comparative studies of floral scent and DNA data in orchids (Barkman, 2001;Williams and Whitten, 1998) as well as in Nyctaginaceae (Levin et al, 2003) revealed that the tree topologies generated by non-coding DNA markers are in some cases congruent with those based on floral scent data.…”

“…The methods to analyse scent patterns for taxonomical questions are manifold (Barkman, 2001;Levin et al, 2003). The simplest method is the use of presence/ absence data of different flower volatiles.…”

Relações na tribo Bocageeae Endlicher baseadas em fitoquímica e sequências de DNA

“…Seaman e Funk (1983) desenvolveram um método para codificar a presença e a ausência de determinada via metabólica e de cada substância dentro da via. Barkman (2001) propôs a utilização da via biossintética como caráter e das suas conversões enzimáticas como estados de caráter.…”

“…Como as substâncias de uma dada via estão relacionadas e dependem umas das outras durante o processo de biossíntese, elas não podem ser definidas como caracteres. É mais adequado que sejam consideradas estados de um caráter, nesse caso a própria via em que são produzidas (Barkman, 2001). …”