Phylogenomics of Perityleae (Compositae) provides new insights into morphological and chromosomal evolution of the rock daisies

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, our results suggest that morphological characters
traditionally used to classify members of Perityleae have evolved multiple
times within the group. A base chromosome number of x=18 gave rise to
lower base numbers in subtribe Peritylinae (x=12, 13, 16, 17, and 19) by
descending dysploidization. Most taxa constitute a monophyletic lineage
with a base chromosome number of x=17, with many 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