First, in order to date the origin of the East African endemic genera, a previously published DNA sequence data matrix (dataset A in Additional file 1) of the African clade was used (Couvreur et al., 2008, treeBASE SN3554).
RJA assembled the morphological and DNA sequence data matrices (the latter based on an alignment supplied by A. Roca and W. Murphy), designed the web-database, carried out the phylogenetic analyses, and wrote the manuscript.
We here apply clustering optimization to a Hymenogaster internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) data matrix using distinct reference partitions representing distinct species concepts.
We first chose the DNA replication timing data matrix as the input for training a supra-hexagonal map.
We extracted four types of molecular data including gene expression, promoter methylation, somatic mutation and DNA copy number variation, using the "data matrix" tool provided by TCGA data portal.
The final aligned data matrix contained four unlinked nuclear DNA regions and two mitochondrial DNA regions for a total of 4152 characters, of which 1172 were from mitochondrial and 2980 were from nuclear loci (Table 1).
Our approach consists of mining the DNA data in GenBank to construct a supermatrix and analyzing this matrix with model-based phylogenetic inference techniques.
Although missing DNA data from the possibly extinct Chinese species A. sinensis, the morphological character matrix (Tab. S1, S2) strongly inferred the placement of this species in the phylogeny.
The ten Sanger-sequenced nuclear loci were concatenated into one matrix of 7214 bp of protein-coding and ribosomal DNA data, with no missing data for any taxon.
For the woody Sonchus alliance (Asteraceae, subgenus Dendrosonchus and five allied genera), the data matrix based on the internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) [51] was used.
