Date of Degree


Document Type


Degree Name





Edward J. Kennelly

Committee Members

Douglas C. Daly

Benjamin M. Torke

Cameron L. McNeil

William J. Hurst

Subject Categories

Biology | Botany | Food Science | Pharmacology | Plant Sciences


caffeine, purine alkaloid, methylxanthine, metabolomics, cacao, Amazon


Biosynthesis of purine alkaloids has arisen by convergent evolution in several plant families across the angiosperm phylogeny. Global secondary metabolite variation in these derived taxa is not well understood within the context of their congeners and related lineages. Wild crop relatives represent the evolutionary background of edible and medicinal plants, enabling an understanding of the origins of species by correlating diversification with concomitant phenotypic changes prior to human-mediated selection and domestication. Chemotaxonomy, as part of an integrative taxonomy uniting botany, phytochemistry, and systematics, is an analytical methodology for identifying significant changes in metabolite composition across taxa in order to understand species chemodiversity within a phylogenetic context.

In the current work, the chemotaxonomy of caffeine-containing plants is developed via liquid chromatography-mass spectrometry-based (LC-MS) metabolomics of Ilex L. (Aquifoliaceae) and Theobroma L. and Herrania Goudot (Byttneriodeae, Malvaceae) species. Caffeine-containing species were identified and targeted for comparative phytochemical analyses with their wild relatives, assessing purine alkaloid variability, identifying unique secondary metabolite markers, and testing metabolome-lineage relationships as part of chemotaxonomic species delimitation and phytochemical lineage reconstruction. Metabolomes of caffeine-containing taxa were profiled to differentiate species, taxonomic sections, and genera using multivariate statistics and chemometrics methodologies, including principal component analysis (PCA), non-metric multidimensional scaling (NMDS), hierarchical clustering analysis (HCA), discriminant analysis (OPLS-DA), and S-plot modeling. Significant qualitative and quantitative metabolite markers were identified and profiled across species. Parallel upregulation of purine alkaloids and other secondary metabolites are suggested for clades within Ilex and for Theobroma and Herrania species. Evidence from LC-MS metabolomics-based chemotaxonomy of caffeine-containing species and their wild relatives demonstrate how secondary metabolite chemistry and global metabolome divergence track taxonomic relationships, providing new insights via synthesis within a phylogenetic framework.

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