title: Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.
abstract: Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots.
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.|Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA.
authors.forename: Liping
authors.initials: L
authors.lastname: Zeng
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.|Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin, 541006, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Institute of Systematic Botany, University of Zurich, Zurich, 8008, Switzerland.
authors.forename: Peter K
authors.initials: PK
authors.lastname: Endress
authors.affiliation: Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin, 541006, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.|Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
mesh_terms: D002467:Cell Nucleus / Q000235:genetics*; D003062:Codon / Q000235:genetics; D030541:Databases, Genetic; D017343:Genes, Plant; D014644:Genetic Variation; D019684:Magnoliopsida / Q000235:genetics*; D010802:Phylogeny; D011123:Polyploidy; D017423:Sequence Analysis, RNA; D013997:Time Factors; D059467:Transcriptome / Q000235:genetics*
chemical_list: D003062:Codon
keywords: Pentapetalae; divergence time; diversification; eudicots; phylogenetics; transcriptome