Phylogenetic and molecular dating analyses of Chinese endemic genus Dipelta (Caprifoliaceae) based on nuclear RAD‐Seq and chloroplast genome data.

<italic>Dipelta</italic> Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, <italic>Dipelta floribunda, Dipelta yunnanensis</italic>, and <italic>Dipelta elegans</italic>. Recent progress in the systematics and phylogeographics of <italic>Dipelta</italic> has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population‐level genomic data restriction site‐associated DNA‐single nucleotide polymorphisms (RAD‐SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between <italic>D. elegans</italic> and the <italic>D. yunnanensis</italic>–<italic>D. floribunda</italic> group, but with cyto‐nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil‐calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD‐SNPs simultaneously suggested that the three species of <italic>Dipelta</italic> diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai–Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid‐Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for <italic>D. floribunda</italic> and <italic>D. yunnanensis</italic> regardless of bidirectional gene flow. Based on both plastid and nuclear genome‐scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for <italic>Dipelta</italic> and enable further understanding of the origin and evolution of floristic endemisms of China. [ABSTRACT FROM AUTHOR]