Data for phylogenomic study of Australian Gnaphalieae

Target file, data matrices, likelihood trees from concatenated analysis, bootstrap samples, and gene trees for the manuscript "Phylogenomic data resolve major clades of Australian Gnaphalieae (Asteraceae)".\nLineage: Genomic DNA was extracted from 5-15 mg silica dried leaf tissue or herbarium material. Fragment size was reduced to approximately 350 bp with sonication. Library preparation followed Schuster & al. (2018) with minor modifications. Library pools were enriched for COS loci using the myBaits Compositae bait set. Enriched library pools were sequenced on Illumina NexSeq 150 cycles paired end. In addition, we shotgun sequenced libraries on NexSeq to be able to assemble the chloroplast genes when we found that coverage for these genes was too low after enrichment.\n\nWe used Trimmomatic to clean raw reads. COS loci and 53 protein coding chloroplast genes were assembled with HybPiper without supercontig construction. COS paralogs were resolved with the 1to1 method of Yang & Smith (2014).\n\nAll alignments were produced with MAFFT (Katoh & Standley, 2013) under auto-selection of alignment strategy. Gene trees for COS loci were inferred with IQ-TREE 1.6.12 after model testing and partition finding on codon positions as starting partitions. Likelihood analysis of concatenated chloroplast and concatenated COS data was done with IQ-TREE after model testing and partition finding on codon positions. 1,000 UltraFast Bootstrap (UFB) samples were used as support values. Gene trees of COS loci were used for coalescent analysis with the 'shortcut' approach using ASTRAL 5.6.3 inferring local posterior probability as support values We rooted COS phylogenies on Oedera squarrosa and chloroplast phylogenies on Gnaphalium diamantinense and Vellereophyton dealbatum.