title: Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution.
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.
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Chien-Hsun
authors.initials: CH
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Renran
authors.initials: R
authors.lastname: Sun
authors.affiliation: Department of Biology, The Huck Institute of the Life Sciences, Pennsylvania State University.
authors.forename: Yi
authors.initials: Y
authors.lastname: Hu
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Liping
authors.initials: L
authors.lastname: Zeng
authors.affiliation: Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Liming
authors.initials: L
authors.lastname: Cai
authors.affiliation: Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Biodiversity and Plant Systematics, Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany.
authors.forename: Marcus A
authors.initials: MA
authors.lastname: Koch
authors.affiliation: Missouri Botanical Garden, St. Louis.
authors.forename: Ihsan
authors.initials: I
authors.lastname: Al-Shehbaz
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing.
authors.forename: Patrick P
authors.initials: PP
authors.lastname: Edger
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia.
authors.forename: J Chris
authors.initials: JC
authors.lastname: Pires
authors.affiliation: Xinjiang Key Laboratory of Grassland Resources and Ecology, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Ürümqi, China.
authors.forename: Dun-Yan
authors.initials: DY
authors.lastname: Tan
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China hongma@fudan.edu.cn.
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
mesh_terms: D005075:Biological Evolution; D019607:Brassicaceae / Q000145:classification* / Q000235:genetics* / Q000528:radiation effects; D018628:Gene Dosage; D020869:Gene Expression Profiling; D017343:Genes, Plant; D010641:Phenotype; D010802:Phylogeny; D011827:Radiation; D059467:Transcriptome
keywords: Brassicaceae; ancestral character reconstruction; divergence time estimation; orthologous nuclear gene; phylogeny; transcriptome