Multiple molecular data provide new insights into phylogeny and historical biogeography of East Asian <i>Artemisia</i> L. (Asteraceae)

Abstract Artemisia L. is one of the most diverse genera in the Asteraceae, widely used in agriculture and medicine, with a giant range of complicated taxa. The task of establishing the phylogeny difficulties owing to the highly similar morphological characters. East Asia, a biodiversity hotspot and major usage area for Artemisia, has received limited attention. Here, we collected 71 species (two subspecies, 94 samples) of Artemisia and its allies from East Asia and its neighbouring regions, and combined with public databases, ensuring representation of all East Asian subgenera. The phylogeny and historical biogeography of Artemisia and its allies in East Asia were reconstructed using plastome, nuclear ribosomal DNA (nrDNA), and nuclear single nucleotide polymorphism data obtained by genome skimming technology. Under the phylogenetic framework, we inferred introgression, divergence, and historical biogeography. We reveal strong nucleoplasmic conflicts in Artemisia, its allies, and subgenera. Past classifications could not classify most subgenera under Artemisia as monophyletic. East Asian Artemisia was probably diversified in situ in the Early Oligocene with the influences of climatic oscillations and geographic activities. A. pectinate, A. palustris, A. keiskeana, and A. hedinii appeared to belong to the early divergent lineages of modern East Asian Artemisia. These findings provide new insights into the evolution of Artemisia.