J Syst Evol ›› 2020, Vol. 58 ›› Issue (6): 853-880.DOI: 10.1111/jse.12711

• Research Articles • Previous Articles     Next Articles

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

Isaac H. Lichter-Marck1 * , William A. Freyman1 , Carolina M. Siniscalchi2 , Jennifer R. Mandel3 , Arturo Castro-Castro4 , Gabriel Johnson5 , and Bruce G. Baldwin1   

  1. 1 Department of Integrative Biology and Jepson Herbarium, University of California, Berkeley, CA 94720, USA
    2 Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
    3 Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, USA
    4 Centro Interdisciplinario de Investigacion para el Desarollo Integral Regional Unidad Durango, Durango, Durango, Mexico
    5 Department of Botany, MRC‐166, National Museum of Natural History, Smithsonian Institution, PO Box 37012 Washington, DC 20013‐7012, USA
  • Received:2020-07-14 Accepted:2020-11-29 Online:2020-12-04 Published:2020-11-01


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 United States 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 an 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 x = 9 gave rise to higher base numbers in subtribe Peritylinae (x = 12, 13, 16, 17, 18, and 19) through polyploidization, followed by ascending or descending dysploidy. Most taxa constitute a monophyletic lineage with a base chromosome number of x = 17, with multiple neo‐polyploidization events. These results demonstrate the advantages and obstacles of next‐generation sequencing approaches in synantherology while laying the foundation for taxonomic revision and comparative study of the evolutionary ecology of Perityleae.

Key words: chromosome evolution, Compositae, genome skimming, Heliantheae, Hyb‐Seq, molecular systematics, morphological evolution, Perityleae, phylogenomics