title: Deep phylogenetic incongruence in the angiosperm clade Rosidae.
abstract: Analysis of large data sets can help resolve difficult nodes in the tree of life and also reveal complex evolutionary histories. The placement of the Celastrales-Oxalidales-Malpighiales (COM) clade within Rosidae remains one of the most confounding phylogenetic questions in angiosperms, with previous analyses placing it with either Fabidae or Malvidae. To elucidate the position of COM, we assembled multi-gene matrices of chloroplast, mitochondrial, and nuclear sequences, as well as large single- and multi-copy nuclear gene data sets. Analyses of multi-gene data sets demonstrate conflict between the chloroplast and both nuclear and mitochondrial data sets, and the results are robust to various character-coding and data-exclusion treatments. Analyses of single- and multi-copy nuclear loci indicate that most loci support the placement of COM with Malvidae, fewer loci support COM with Fabidae, and almost no loci support COM outside a clade of Fabidae and Malvidae. Although incomplete lineage sorting and ancient introgressive hybridization remain as plausible explanations for the conflict among loci, more complete sampling is necessary to evaluate these hypotheses fully. Our results emphasize the importance of genomic data sets for revealing deep incongruence and complex patterns of evolution.
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
authors.forename: Miao
authors.initials: M
authors.lastname: Sun
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA. Electronic address: dsoltis@botany.ufl.edu.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.affiliation: School of Life Science, Nantong University, Nantong 226007, China.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Zhu
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
authors.forename: J Gordon
authors.initials: JG
authors.lastname: Burleigh
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China. Electronic address: zhiduan@ibcas.ac.cn.
authors.forename: Zhiduan
authors.initials: Z
authors.lastname: Chen
mesh_terms: D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D006824:Hybridization, Genetic; D016013:Likelihood Functions; D019684:Magnoliopsida / Q000145:classification* / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant
keywords: COM clade; Hybridization; Incomplete lineage sorting; Incongruence; Introgression; Phylogenomics