DOI: 10.5061/dryad.zpc866tft
title: Data from: Widely acclaimed but poorly named - phylogeny and systematics of the charismatic African daisy genus Dimorphotheca Vaill. ex Moench (Asteraceae, Calenduleae)

description: 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 thus support the modern, enlarged circumscription
 of the genus incorporating the former genus Castalis and Osteospermum
 sections Acanthotheca and Blaxium. Major subclades within Dimorphotheca
 are largely cohesive in terms of geographic distribution and morphological
 traits such as growth form and cypsela structure. While many species are
 resolved as monophyletic, the polyphyly of a few species suggests a need
 for taxonomic re-evaluation. On the basis of both morphological and
 molecular data, we describe one new species, and elevate one variety to
 species level. A full taxonomic key to the enlarged genus is presented for
 the first time. Ancestral reconstructions show that capitulum sexual
 system and ray lamina colour are not evolutionarily conserved and that
 neither can therefore be used to delimit major lineages within
 Dimorphotheca. While our findings resolve some taxonomic problems, they
 also highlight the need for further species-level taxonomic work on
 Dimorphotheca.
description: # 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 the two different methodologies
 used to deal with incongruence described in the paper: (1)
 Parker-et-al-2024-decomposed-alignment.nex represents the alignment where
 accessions demonstrating incongruence between gene regions were decomposed
 into a pair of accessions, one representing each incongruent element. If
 for example, incongruence was present between nuclear and plastid regions
 in a sample, that sample was decomposed into an accession comprising only
 the plastid sequence data (nuclear sequence represented as missing) and an
 accession comprising only nuclear sequence data (plastid sequence
 represented as missing). Thus accessions displaying gene tree incongruence
 are represented twice. Decomposed accessions which were deemed to have the
 'false' biological placement in the tree are denoted by an
 epithet indicating which gene region they correspond to (e.g. TRN for
 trnl-trnF or NUC for nuclear) 2\) Parker-et-al-2024-deleted-alignment.nex
 represents the alignment where we used consistency with morphology to
 choose amongst the alternative placements suggested by the contradictory
 loci. Under this approach, the sequences of loci that suggest
 morphologically less-consistent placements were replaced with missing data
 symbols prior to analysis. Thus, each accession is represented just once.
 For more information please refer to the cited paper.