Cryptic Species Diversification of the Complex (Orobanchaceae) in the Mountains of Southwest China Since the Pliocene.

Morphological approaches often fail to delimit species in recently derived species complexes. This can be exacerbated in historical collections which may have lost key features in specimen preparation and preservation. Here, we examine the complex, endemic to the Mountains of Southwest China. This complex is characterized by its red/purple/pink and long-tubular corolla, and twisted, beaked galea. However, herbarium specimens are often difficult to identify to species. Molecular approaches using nrITS or nuclear ribosomal internal transcribed spacer (nrITS) + plastid DNA (ptDNA) have been successfully used for species identification in . To resolve taxonomic confusion in the complex, we reconstructed phylogenies of the complex using nrITS and four plastid DNA loci (, , , and ). To recover as much of the phylogenetic history as possible, we sampled individuals at the population level. Topological incongruence between the nrITS and ptDNA datasets was recovered in clades including two widely distributed species, and . Based on morphological, geographical, and genetic evidence, we suggest that hybridization/introgression has occurred between and / sp. 1 in the Yulong Snow Mountain of Lijiang, northwest Yunnan, and between and in Ninglang, northwest Yunnan. After removing conflicting DNA regions in (nrITS) and (ptDNA), the concatenated nrITS and ptDNA phylogenies distinguish 11 species in the complex, including two undescribed species, from the Jiaozi and Yulong Snow Mountains, respectively. Phylogeographical analyses indicate that the complex originated from south of the Hengduan Mountains, expanding north to the Himalayas and the Yunnan-Guizhou Plateau. Moreover, the uplift of the Qinghai-Tibet Plateau and climate oscillations may have driven further diversification in the complex.