title: Re-evaluating the phylogeny of allopolyploid Gossypium L.
abstract: The formation of allopolyploid cotton precipitated a rapid diversification and colonization of dry coastal American tropical and subtropical regions. Previous phylogenetic analyses, combined with molecular divergence analyses, have offered a temporal framework for this radiation, but provide only weak support for some of the resolved branches. Moreover, these earlier analyses did not include the recently recognized sixth polyploid species, G. ekmanianum Wittmack. Here we use targeted sequence capture of multiple loci in conjunction with both concatenated and Bayesian concordance analyses to reevaluate the phylogeny of allopolyploid cotton species. Although phylogenetic resolution afforded by individual genes is often low, sufficient signal was attained both through the concatenated and concordance analyses to provide robust support for the Gossypium polyploid clade, which is reported here.
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, United States. Electronic address: corrinne@iastate.edu.
authors.forename: Corrinne E
authors.initials: CE
authors.lastname: Grover
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, United States.
authors.forename: Joseph P
authors.initials: JP
authors.lastname: Gallagher
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, United States.
authors.forename: Josef J
authors.initials: JJ
authors.lastname: Jareczek
authors.affiliation: Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, United States.
authors.forename: Justin T
authors.initials: JT
authors.lastname: Page
authors.affiliation: Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, United States.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Udall
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Gore
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, United States.
authors.forename: Jonathan F
authors.initials: JF
authors.lastname: Wendel
mesh_terms: D001499:Bayes Theorem; D017343:Genes, Plant / Q000235:genetics; D003368:Gossypium / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography; D011123:Polyploidy; D017422:Sequence Analysis, DNA
keywords: Allopolyploid; Cotton; Gossypium; Phylogeny; Sequence capture