Phylogenomics of the rock daisy tribe (Perityleae; Asteraceae) provides new insights into morphological and chromosome evolution

Rock daisies (Perityleae; Compositae) are a diverse clade of seven genera and ca. 84 minimum-rank taxa that mostly occur as narrow endemics on sheer rock-cliffs throughout the southwest U.S. and northern Mexico. Taxonomy of Perityleae has traditionally been based on morphology and cytogenetics. To test taxonomic hypotheses and utility of characters emphasized in past treatments, we present the first densely sampled molecular phylogenies of Perityleae and reconstruct trait and chromosome evolution. We inferred phylogenetic trees from whole chloroplast genomes, nuclear ribosomal cistrons, and hundreds of low-copy nuclear genes using genome skimming and target-capture. Discordance between sources of molecular data suggests a underappreciated history of hybridization in Perityleae. Phylogenies support the monophyly of subtribe Peritylinae, a distinctive group possessing a four-lobed disc corolla; however, all of the phylogenetic trees generated in this study reject the monophyly of the most species-rich genus, Perityle as well as its sections Perityle sect. Perityle, Perityle sect. Laphamia, and Perityle sect. Pappothrix. Using reversible jump MCMC and Bayesian inference, our results suggest irreversible directional evolution of pappus bristles, callous fruit margins, ciliate fruit margins and disk corolla color, while a model of bi-directional change was maximally supported for ray corolla color, pappus scales, and transitions between radiate and discoid inflorescence forms. A base chromosome number of x=9 gave rise to higher base numbers in subtribe Peritylinae (x=12, 13, 16, 17, 18 and 19) through two independent polyploidizationsfollowe dby ascending or descending aneuploidy. Most taxa constitute a monophyletic lineage with a base chromosome number of x=17, with many neo-polyploidization events. These results demonstrate the advantages and obstacles to next-generation sequencing approaches in synantherology while laying the foundation for taxonomic revision and comparative study of the evolutionary ecology of Perityleae.