Data from: Widely acclaimed but poorly named - phylogeny and systematics of the charismatic African daisy genus Dimorphotheca Vaill. ex Moench (Asteraceae, Calenduleae)
Data files
May 30, 2024 version files 491.29 KB
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Parker-et-al-2024-decomposed-alignment.nex
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Parker-et-al-2024-deleted-alignment.nex
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README.md
Abstract
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.
README: Data from: Widely acclaimed but poorly named - phylogeny and systematics of the charismatic African daisy genus Dimorphotheca Vaill. ex Moench (Asteraceae, Calenduleae)
https://doi.org/10.5061/dryad.zpc866tft
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.