DOI: 10.5061/dryad.1jwstqk0j
title: Alignments and tree files from: Phylogenetic relationships within tribe Hibisceae (Malvaceae) reveal complex patterns of polyphyly in Hibiscus and Pavonia

description: The diverse and spectacular Hibisceae tribe comprises over 750 species. No
 studies, however, have broadly sampled across the dozens of genera in the
 tribe, leading to uncertainty in the relationships among genera. The
 non-monophyly of the genus Hibiscus is infamous and challenging, whereas
 the monophyly of most other genera in the tribe has yet to be assessed,
 including the large genus Pavonia. Here we significantly increase taxon
 sampling in the most complete phylogenetic study of the tribe to date. We
 assess monophyly of most currently recognized genera in the tribe and
 include three and thirteen newly sampled sections of Hibiscus and Pavonia,
 respectively. We also include five rarely sampled genera and 137 species
 previously unsampled. Our phylogenetic trees demonstrate that Hibiscus, as
 traditionally defined, encompasses at least 20 additional genera. The
 status of Pavonia emerges as comparable in complexity to Hibiscus. We
 offer clarity in the phylogenetic placement of several taxa of uncertain
 affinity (e.g., Helicteropsis, Hibiscadelphus, Jumelleanthus, and
 Wercklea). We also identify two new clades and elevate them to the generic
 rank with the recognition of two, new monotypic genera: 1) Blanchardia
 M.M.Hanes & R.L.Barrett is a surprising Caribbean lineage that is
 sister to the entire tribe, and 2) Astrohibiscus McLay &
 R.L.Barrett represents former members of Hibiscus caesius s.l. Cravenia
 McLay & R.L.Barrett is also described as a new genus for the
 Hibiscus panduriformis clade which is allied to Abelmoschus. Finally, we
 introduce a new classification for the tribe and clarify the boundaries of
 Hibiscus and Pavonia.
description: Sequences were derived from Sanger sequencing, Illumina genome
 skimming, and GenBank. Alignments were made using MAFFT & Muscle,
 then checked by eye. Phylogenetic trees were computed using IQ-TREE and
 MrBayes. Specimen names and collecting numbers correspond to Appendix 1 in
 the manuscript. 
description: Anything that can open nexus (.nex) and newick files (.new,
 .tre), including Geneious, Aliview, FigTree, R, or standard text editors
 such as Wordpad and TextEdit.  Supp. Fig. 1 can be
 opened with pdf readers such as Adobe Acrobat Reader, Foxit PDF Reader, or
 internet browsers such as Google Chrome, and Microsoft Edge. 
description: # Title of Dataset Alignments and tree files from Hanes et al.
 "Phylogenetic relationships within tribe Hibisceae (Malvaceae) reveal
 complex patterns of polyphyly in Hibiscus and Pavonia" ## Description
 of the data and file structure Sequences were derived from Sanger
 sequencing, Illumina genome skimming, and GenBank. Alignments were made
 using MAFFT & Muscle, then checked by eye. Phylogenetic trees were
 computed using IQ-TREE and MrBayes. Specimen names and collecting numbers
 correspond to Appendix 1 in the manuscript. The Supplementary Figure
 (Supp. Fig 1. Hanes-et-al_Hibisceae_MrBayes_4genes.pdf) is a pdf version
 of the additional file
 'Hanes-et-al_Hibisceae_MrBayes_4genes.tre'. ## Data was derived
 from the following sources: * GenBank * New sequences using Sanger and
 Illumina sequencing. * See Appendix 1 for GenBank numbers for all
 sequences used in this study. ## Files in dataset *
 Hanes-et-al_Hibisceae_IQTREE_4genes.treefile *
 Hanes-et-al_Hibisceae_4genes-alignment.nex *
 Hanes-et-al_Hibisceae_MrBayes_4genes.tre *
 Supp._Fig_1._Hanes-et-al_Hibisceae_MrBayes_4genes.pdf