Widely acclaimed but poorly named - phylogeny and systematics of the charismatic African daisy genus Dimorphotheca Vaill. ex Moench (Asteraceae, Calenduleae)

Phylogenetic relationships in the South African daisy genus Dimorphotheca have long been uncertain, with the taxonomy of the genus relying on a few morphological traits, most prominently capitulum sexual system (i.e., cypsela type) and ray colour, which may not be evolutionarily conserved. Here we present the first well-sampled molecular phylogeny of Dimorphotheca, based on nuclear ribosomal (ITS and ETS) and plastid trnL-trnF region DNA sequences from multiple accessions per species. Although the relationships suggested by these markers are broadly congruent, we do find some instances of incongruence which we resolve using a combined decomposition and deletion approach. Using our best estimate of phylogenetic relationships, we reconstruct the evolution of capitulum fertility and ray colour to assess the evolutionary conservatism of these traits and their taxonomic utility. We find support for the monophyly of Dimorphotheca, excluding the recently segregated O. polypterum, and our data ..., , , # Data from: Widely acclaimed but poorly named - phylogeny and systematics of the charismatic African daisy genus Dimorphotheca Vaill. ex Moench (Asteraceae, Calenduleae)

Gene alignments used to produce phylogenetic trees and analysis for the cited study on the African daisy genus Dimorphotheca

## Description of the data and file structure

This dataset contains two concatenated DNA gene alignments in nexus format: where each line contains a sample followed by the nucleotides (standard IUPAC codes) which make up the sequenced gene regions for that sample. Sequencing was done using the Sanger sequencing methodology for each sample. Each alignment file includes three gene regions: two nuclear (ITS and ETS) and one chloroplast region. The position where each gene regions starts is indicated in a text block (character set block) at the bottom of the file. Where a gene region or nucleotides are missing or there is a gap, this is indicated by a - symbol.

The two alignments correspond to ...