Resolution of brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution

Chien Hsun Huang, Renran Sun, Yi Hu, Liping Zeng, Ning Zhang, Liming Cai, Qiang Zhang, Marcus A. Koch, Ihsan Al-Shehbaz, Patrick P. Edger, J. Chris Pires, Dun Yan Tan, Yang Zhong, Hong Ma

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117 Scopus citations

Abstract

Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene-Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.

Original languageEnglish (US)
Pages (from-to)394-412
Number of pages19
JournalMolecular biology and evolution
Volume33
Issue number2
DOIs
StatePublished - Feb 1 2016

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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    Huang, C. H., Sun, R., Hu, Y., Zeng, L., Zhang, N., Cai, L., Zhang, Q., Koch, M. A., Al-Shehbaz, I., Edger, P. P., Pires, J. C., Tan, D. Y., Zhong, Y., & Ma, H. (2016). Resolution of brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Molecular biology and evolution, 33(2), 394-412. https://doi.org/10.1093/molbev/msv226