@ARTICLE{TreeBASE2Ref26793, author = {Liping Zeng and Ning Zhang and qiang zhang and Peter Endress and Jie Huang and Hong Ma}, title = {Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomics and genomic datasets}, year = {2017}, keywords = {eudicots; Pentapetalae; phylogenetics; divergence time; diversification; transcriptome }, doi = {}, url = {http://}, pmid = {}, journal = {New Phytologist}, volume = {}, number = {}, pages = {}, abstract = {? Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain ~ 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and likely have 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 ca. 146 Mya, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within ~ 15 million years. 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 in the evolutionary trend of morphologies and contributions for the diversification of eudicots. } }

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