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Evolutionary genomics of plant paratisism |
Parasitism has evolved around a dozen times in flowering plants, involving remarkable modifications in physiology and morphology. Using the iconic parasitic lineage Raffelesiaceae as a model, I characterized several unusual genomic modifications that challenges our understanding of how deeply a plant genome can be altered. We demonstrated an unprecedented level of gene reduction, expansion of non-coding regions, and horizontal gene transfer (HGT) in the genome of Rafflesiaceae. Especially, phylogenetic reconstruction of the HGTs revealed a dynamic history of former host-parasite associations dating back tens of millions of years, demonstrating the utility of horizontally transferred genes as DNA fossils to investigate the extinct symbiotic history.
Related publication: Cai, L., Arnold, B., Xi, Z., DeCosta, J., Khost, D., Hughes, N., Reardon, C., Barrington, D., Manikam, S., Nikolov, L., Mathews, S., Sackton, T., Davis, C.C.. Deeply altered genome architecture in the endoparasitic flowering plant Sapria himalayana Griff. (Rafflesiaceae). Current Biology. Media coverage: Science Editor's Choice, Harvard Gazette, Sciencenet |
Polyploidization and global upheaval
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Phylogenomic methods |
The field of systematic biology has moved towards the genomic era. An emerging trend in the field is the discovery of conflicting phylogenetic signals across the genome due to deep coalescence, reticulate evolution, and of course, estimation error. One major theme of my research is to understand the phylogenetic relationships within Malpighiales, especially the ancient radiation that gave rise to the majority of the extant family-level diversity. Despite high rate of gene tree estimation error, I demonstrated that both incomplete lineage sorting and reticulate evolution contribute to the recalcitrant relationship of the backbone phylogeny. I also developed a novel method to quantify the relative contribution of biological and analytical factors in generating the conflicting phylogenetic signals.
Related publication: Cai, L.*, Xi, Z., Lemmon, E., Lemmon, A., Mast, A., Buddenhagen, C., Liu, L. and Davis, C.C.*, 2020. The perfect storm: gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales. * co-corresponding author. Systematic Biology. link. |
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Biogeography |
Many plant lineages in Malpighiales have a southern hemisphere origin. The diversification of these ancient lineages are often linked with the geographical events in these areas such as the breakup of Gondwana and the closing of the Isthmus of Panama. During my visit to the Harvard University Herbaria as an undergraduate summer intern, I investigated the biogeography of the aquatic plant family Elatinaceae (Malpighiales). I built the first molecular phylogeny of this family and demonstrated that its early divergence history is associated with Gondwana breakup.
Related publication: Cai, L., Xi, Z., Peterson, K., Rushworth, C., Beaulieu, J. and Davis, C.C., 2016. Phylogeny of Elatinaceae and the tropical Gondwanan origin of the Centroplacaceae (Malpighiaceae, Elatinaceae) Clade. PLOS ONE, 11(9), p.e0161881. link |
Liming Cai
PhD candidate, Department of Organismic and Evolutionary Biology, Harvard University 22 Divinity Ave, Cambridge, MA 02138 |