Barkman lab of plant phylogenetics and evolutionary biochemistry
Evolution of plant biochemistry
Plant specialized metabolism is responsible for the production of many thousands of small molecules that affect development and mediate interactions with the environment. While primary metabolites and many specialized molecules are found throughout the plant tree of life, others are often restricted to particular lineages or have evolved by convergence. Our lab is particularly interested in understanding how different lineages of plants evolved enzymes and pathways to produce diverse metabolites. To do this, we use Ancestral Sequence Resurrection to revive ancient enzymes and study their properties. We focus on the SABATH family of methyltransferases that are well known for being involved in the production of important metabolites such as methyl salicylate, methyl jasmonate and caffeine, in addition to others. Our studies are mostly aimed at understanding enzyme family diversification, especially as it relates to mechanisms of convergent evolution and the nature of enzyme substrate preference switches. This work requires the combination of molecular phylogenetics with molecular biology, biochemistry and analytical chemistry techniques.
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Huang et al. 2012. Enzyme functional evolution through improved catalysis of ancestrally non-preferred substrates. Proceedings of the National Academy of Sciences, USA. 109: 2966-2971.
Huang, et al. 2016. Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes. Proceedings of the National Academy of Sciences, USA. 113: 10613-10618
O’Donnell, et al. 2021. Convergent biochemical pathways for xanthine alkaloid production in plants evolved from ancestral enzymes with different catalytic properties. Molecular Biology and Evolution. 38:2704-2714.
Parasitic plant phylogeny and genome evolution
Parasitism has evolved at least 12 times in flowering plant history. These lineages include some of the most spectacular plants on earth and have evolved varying degrees of photosynthetic loss. The phylogenetic affinities had remained obscure for many of the extreme parasitic lineages but our use of mitochondrial DNA provided novel insights and resulted in the confident placement of nearly all groups, although horizontal gene transfers from host to parasite has led to challenges. Aside from phylogeny, our studies of parasitic plant plastid and mitochondrial genomes in collaboration with Jeff Palmer, Claude dePamphilis and H. J. Su have revealed that they are nearly as interesting as the morphology and biology of the plants themselves!
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Barkman et al. 2004. Mitochondrial DNA sequences reveal the photosynthetic relatives of Rafflesia, the world’s largest flower. Proceedings of the National Academy of Sciences, USA. 787-792.
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Barkman et al. 2007. Mitochondrial DNA suggests 12 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evolutionary Biology 7: 248.
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Skippington et al. 2015. The miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes. Proceedings of the National Academy of Sciences, USA. 112 (27) E3515-E3524.
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Su et al. 2018. A novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proceedings of the National Academy of Sciences, USA. 116 (3): 934-943.
Phylogeny and systematics of plants in Sabah, Malaysia
Sabah, Malaysia is home to some of the most biodiverse places on earth and in spite of intense studies numerous new species await description and taxonomic confusion persists. Thus, our emphasis has been to contribute to the systematics and taxonomy of various groups, especially Schefflera (now Heptapleurum): in collaboration with Aida Shafreena Ahmad Puad and the late David Frodin we described 17 novel species and documented aspects of the natural history and diversity of the incredible group in Sabah. Our earliest work was largely centered on studies of high elevation endemics in the orchid genus Dendrochilum found on Mount Kinabalu. More recent studies have focussed on phylogeny, taxonomy and biogeography of parasitic plant families including Rafflesiaceae, Balanophoraceae, Viscaceae and Loranthaceae all in collaboration with our Malaysian colleagues.
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Barkman, T. J. and Simpson, B. B. 2002. Hybrid origin and parentage of Dendrochilum acuiferum (Orchidaceae) inferred in a phylogenetic context using nuclear and plastid DNA sequence data. Systematic Botany 27: 209-220.
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Barkman, T. J., M. Bendiksby, S.-H. Lim, K. Mat Salleh, J. Nais, D. Madulid and T. Schumacher 2008. Accelerated rates of floral evolution at the upper size limit for flowers Current Biology 18:1508-1513.
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Mika Bendiksby, Galina Gussarova, Jamili Nais, Kamarudin Mat-Salleh, Nery Sofiyanti, Domingo Madulid, Trond Schumacher, and Todd Barkman. 2010. Elucidating the evolutionary history of the Southeast Asian holoparasitic giant-flowered Rafflesiaceae: Pliocene vicariance, morphological convergence and character displacement. Molecular Phylogenetics and Evolution 57: 620-633.
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Barkman, T. J., R. Repin, and J. Sugau. 2016. The parasitic plant families Loranthaceae and Viscaceae in Sabah, Malaysia. Sandakania 21: 131-169.
Ahmad Puad, Aida Shafreena, Frodin, D. G and T. J. Barkman. The Genus Schefflera in Sabah, Malaysian Borneo. 2018. Natural History Publications (Borneo) Sdn. Bhd. ISBN: 978-983-812-184-2
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