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.

中文翻译：

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Perityleae（菊科）的系统基因组学为岩雏菊的形态学和染色体进化提供了新的见解

岩雏菊（Perityleae; Compositae）是一个由七个属和约。84 个最低等级的分类群，主要作为狭窄的特有物种出现在整个美国西南部和墨西哥北部的陡峭岩石峭壁上。Perityleae 的分类学传统上基于形态学和细胞遗传学。为了测试过去处理中强调的分类学假设和特征的效用，我们展示了 Perityleae 的第一个密集采样的分子系统发育，并重建了性状和染色体进化。我们使用基因组撇取和目标捕获从整个叶绿体基因组、核核糖体顺反子和数百个低拷贝核基因推断系统发育树。分子数据来源之间的不一致表明 Perityleae 中的杂交历史被低估了。系统发育支持亚部落 Peritylinae 的单一性，一个独特的群体，拥有一个四裂的圆盘花冠；然而，本研究中生成的所有系统发育树都拒绝物种最丰富的属 Perityle 及其部分的单系：Perityle sect。Perityle，Perityle 教派。Laphamia 和 Perityle 教派。帕波丝菌。使用可逆跳跃 MCMC，我们的结果表明，传统上用于对 Perityleae 成员进行分类的形态特征已在该组内多次进化。碱基染色体数 x = 9 通过多倍体化产生更高的亚部落 Peritylinae 碱基数（x = 12、13、16、17、18 和 19），然后是上升或下降的异倍体。大多数分类群构成一个单系谱系，基本染色体数为 x = 17，具有多个新多倍化事件。