Molecular Systematics of Philadelphus and Molecular Evolution of LFY in the Core Eudicots

Abstract

Phylogenetic analysis is a powerful tool for elucidate evolutionary relationships of organisms and genes and for testing taxonomic and evolutionary hypotheses. I conducted phylogenetic analyses of DNA sequences from five gene regions to evaluate the classification scheme of Philadelphus and used phylogenetic analysis to provide a framework for examining molecular evolution of the LFY gene in plants. Results from my study suggested that Philadelphus is a paraphyletic group with the single species genus Carpenteria nested within. Three evolutionary distinct clades were identified in this large Carpenteria-Philadelphus complex, the subgenus Deutzoides clade, the genus Carpenteria clade, and the remaining Core-Philadelphus clade, each merits the recognition of a genus. Our results mostly agreed with the most recent treatment of genus Philadelphus on the placement of Deutzoides, with the exception of P. hirsutus. However, our result does not support the classification scheme proposed for the rest Philadelphus species. Biogeographic analysis using the Statistical Bayes-DIVA method (S-DIVA) and divergence time dating with the BEAST method resolved the origin of Philadelphus s. l. in southwestern North America in the Oligocene. Several intercontinental migrations from North America to Asia and to Europe occurred at the different times of the later Tertiary to reach a worldwide distribution of the genus. For the molecular evolution study of LFY gene, our results revealed that the evolution of LFY was under strong functional constraint, with the C domain under the strongest selection force and the intervening domain being the most relaxed. Our study also showed that the detection of positive selection using the Branch Site Model was robust to taxon sampling density, but sensitive to sequence length and alignment ambiguity. Our analyses under various conditions consistently detected positive selection in Fabaceae, where FLO/LFY evolved a role of the KNOX1 gene function in regulating compound leaf development. Under the best alignment, we detected adaptive selection at several sites in Asterales, Brassicaceae, and Fabaceae where gene duplication and/or novel function of LFY have been reported.