Alignments and tree files from: Phylogenetic relationships within tribe Hibisceae (Malvaceae) reveal complex patterns of polyphyly in Hibiscus and Pavonia

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..., 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. , 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. , # 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-ali...