Phylogenomic data for hyperdiverse daisy tribes

Asteraceae account for 10% of all flowering plant species, and 35-40% of these are in five closely-related tribes that total over 10,000 species. These tribes include Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae, which form one of two enormous clades within Subfamily Asteroideae. We took a phylogenomics approach to resolve evolutionary relationships among these five tribes. We sampled the nuclear and plastid genomes via HybSeq target enrichment and genome skimming, and recovered 74 plastid genes and nearly 1000 nuclear loci, known as Conserved Orthologous Sequences. We tested for conflicting support in both datasets and used network analyses to assess patterns of reticulation to explain the early evolutionary history of this lineage which has experienced whole genome duplications and rapid radiations. We found both concordance and conflicting support in both datasets and documented four ancient hybridization events. Due to the timing of the early radiation of this five-tribe lineage, shortly before the Eocene-Oligocene extinction event (34 MYA), early lineages were likely lost, obscuring some details of their early evolutionary history.

Methods
HybSeq nuclear and chloroplast/plastid bycatch.