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

Abstract

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.

Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family

“…Few studies have used Compositae1061 to investigate infrageneric relationships in different Compositae tribes, while there are currently no published reports of the use of Angiosperms353 in the Compositae. Lichter-Marck et al (2020) and Thapa et al (2020) investigated infrageneric relationships within Perityle Benth. (Perityleae) and Antennaria (Gnaphalieae), respectively, and compared the effects of concatenated vs. gene tree analyses.…”

“…Since 2014, this probe set has been used to study the family‐wide phylogeny (Mandel et al, 2015, 2017, 2019); the relationships among different tribes (Watson et al, 2020); the relationships at the tribe level in the Cardueae (Herrando‐Moraira et al, 2018, 2019), Vernonieae (Siniscalchi et al, 2019a), and Perityleae (Lichter‐Marck et al, 2020); and the infrageneric relationships in Antennaria Gaertn. (Thapa et al, 2020).…”

Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

“…Among the genome‐scale methods developed to date, target enrichment, also known as Hyb‐Seq, has been shown as the most efficient and cost‐effective approach for obtaining large data sets of SCNs for plant systematics (Lemmon et al, 2012; Mandel et al, 2014; Weitemier et al, 2014; Dodsworth et al, 2019). Targeted nuclear sequences from Hyb‐Seq have been corroborated to be effective for providing greater phylogenetic resolution both at shallow and deep levels (Villaverde et al, 2018; Kleinkopf et al, 2019; Li et al, 2019; Lichter‐Marck et al, 2020; Watson et al, 2020; Ma et al, 2021). Hyb‐Seq has gained popularity in recent phylogenomic studies due to its good performance with degraded DNA from silica gel‐dried and herbarium specimens (Weitemier et al, 2014; Villaverde et al, 2018; Wang et al, 2021), unlike whole‐genome sequencing (WGS) and transcriptome sequencing (RNAseq) that require fresh or flash‐frozen materials (Xiang et al, 2017).…”

Edaphic specialization onto bare, rocky outcrops as a factor in the evolution of desert angiosperms

“…Disjunct populations are also present in the Atacama Desert in Chile (19)(20). Within the NA deserts, Perityleae show characteristics suggestive of an insular radiation, including high species diversity, geographic speciation, divergent life history strategies, and specialization into disparate ecological niches (20)(21). A remarkable aspect of this group's natural history is the extreme edaphic specialization demonstrated by some taxa, which grow exclusively on bare, rocky outcrops, including steep canyon walls and cliffs on the slopes of desert mountains.…”