Data matrices and phylogenetic tree of Pogonolepis (Asteraceae)

Data matrices and phylogenetic tree of Pogonolepis (Asteraceae) for species delimitation study.\nLineage: 44 specimens labelled as Pogonolepis were selected from herbarium CANB to represent both species approximately evenly and to cover most of their geographic ranges. Very small specimens were excluded because destructive sampling would compromise their quality, as were specimens whose colouration suggested that DNA quality would be very poor. After re-identification of some mislabelled sheets (see below), 21 specimens of each species are present in the dataset.\nThree species of the Angianthus clade were chosen as outgroups, and raw reads produced for the Genomics for Australian Plants consortium were downloaded from the Bioplatforms Australia Data Portal (data.bioplatforms.com): Cephalosorus carpesioides (Turcz.) P.S.Short, Bioplatforms sample ID 80038; Dithyrostegia amplexicaulis A.Gray, 80053; and Hyalochlamys globifera A.Gray, 80073.\n\nLaboratory work was conducted by the Australian Genome Research Facility. Genomic DNA was extracted using the NucleoSpin Plant II Kit (Macherey-Nagel, Düren, Germany) and sonicated using a Covaris (Woburn, MA, USA) AFA plate to a fragment size of approximately 350 base pairs. Libraries were built using NEBNext Ultra II (NEB, Ipswich, MA, USA), and sequence capture was conducted on pools of twelve libraries using the angiosperms353 MYbaits kit (Daicel Arbor Biosciences, Ann Arbor, MI, USA) NovaSeq. Enriched libraries were sequenced on Illumina NovaSeq 6000 SP with v1.5 300 cycle chemistry. Sequence data were obtained for all sampled specimens.\n\nReads were assembled against target sequences using hybpiper-rbgv (Jackson et al. 2021), a Nextflow pipeline adapted from HybPiper (Johnson et al. 2016). The results of HybPiper’s paralog finder were analysed with yang-and-smith-rbgv (Jackson et al. 2021), a Nextflow pipeline implementing the four gene-tree based paralogy resolution algorithms collated by Yang and Smith (2014). Cephalosorus carpesioides, Dithyrostegia amplexicaulis, and Hyalochlamys globifera were used as outgroups. I selected results of the Monophyletic Outgroups algorithm (MO), which recursively moves through each gene tree from the root and removes the smaller of each pair of sister clades sharing sequences from the same sample. This means that at most one ortholog group is retrieved from each gene. Custom-written Python scripts were used to ensure that gene alignments were in frame and to concatenated them into a supermatrix.\n\nPhylogenies of the concatenated supermatrix and of all gene alignments were inferred with IQTREE 2.0.7 and 2.1.3 (Minh, Schmidt, et al. 2020), partitioning the alignment by genes and under automatic model testing. Two branch support measures were inferred: UltraFast Bootstraps (UFB) (Minh et al. 2013) and gene Concordance Factors (gCF) (Minh, Hahn, et al. 2020). The latter calculate the percentage of informative gene trees that support a branch in the species tree. To establish a baseline of gCF expected under free recombination of genes as expected from sexual reproduction, I produced 20 replicate phylogenies after randomly reassigning all gene sequences to samples in the species showing the higher gCF values in the original data.