title: Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times.
abstract: Angiosperms are the most successful plants and support human livelihood and ecosystems. Angiosperm phylogeny is the foundation of studies of gene function and phenotypic evolution, divergence time estimation and biogeography. The relationship of the five divergent groups of the Mesangiospermae (~99.95% of extant angiosperms) remains uncertain, with multiple hypotheses reported in the literature. Here transcriptome data sets are obtained from 26 species lacking sequenced genomes, representing each of the five groups: eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae. Phylogenetic analyses using 59 carefully selected low-copy nuclear genes resulted in highly supported relationships: sisterhood of eudicots and a clade containing Chloranthaceae and Ceratophyllaceae, with magnoliids being the next sister group, followed by monocots. Our topology allows a re-examination of the evolutionary patterns of 110 morphological characters. The molecular clock estimates of Mesangiospermae diversification during the late to middle Jurassic correspond well to the origins of some insects, which may have been a factor facilitating early angiosperm radiation.
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, 220 Handan Road, Yangpu District, Shanghai 200433, China.
authors.forename: Liping
authors.initials: L
authors.lastname: Zeng
authors.affiliation: 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: 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, 220 Handan Road, Yangpu District, Shanghai 200433, China.
authors.forename: Renran
authors.initials: R
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
authors.forename: Hongzhi
authors.initials: H
authors.lastname: Kong
authors.affiliation: 1] 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, 220 Handan Road, Yangpu District, Shanghai 200433, China [2] Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington DC 20560, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: 1] 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, 220 Handan Road, Yangpu District, Shanghai 200433, China [2] Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics*; D005580:Fossils; D020869:Gene Expression Profiling; D016013:Likelihood Functions; D019684:Magnoliopsida / Q000033:anatomy & histology* / Q000145:classification* / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013997:Time Factors