title: Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage.
abstract: The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.
authors.affiliation: Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley , Berkeley, CA , United States.
authors.forename: Chodon
authors.initials: C
authors.lastname: Sass
authors.affiliation: Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley , Berkeley, CA , United States.
authors.forename: William J D
authors.initials: WJ
authors.lastname: Iles
authors.affiliation: Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States; Department of Biology, California State University, Los Angeles, Los Angeles, CA, United States.
authors.forename: Craig F
authors.initials: CF
authors.lastname: Barrett
authors.affiliation: Department of Earth & Environmental Sciences and the Museum of Paleontology, University of Michigan , Ann Arbor, MI , United States.
authors.forename: Selena Y
authors.initials: SY
authors.lastname: Smith
authors.affiliation: Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley , Berkeley, CA , United States.
authors.forename: Chelsea D
authors.initials: CD
authors.lastname: Specht
keywords: Ancient radiation; Array-based capture; Banana; Exon capture; Gingers; HTS; Heliconiaceae; High-throughput sequencing; Musaceae
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