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

Abstract

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 Pedicularis siphonantha 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 Pedicularis. To resolve taxonomic confusion in the Pedicularis siphonantha complex, we reconstructed phylogenies of the complex using nrITS and four plastid DNA loci (matK, rbcL, trnH-psbA, and trnL-F). 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, Pedicularis milliana and Pedicularis tenuituba. Based on morphological, geographical, and genetic evidence, we suggest that hybridization/introgression has occurred between P. milliana and Pedicularis sigmoidea/Pedicularis sp. 1 in the Yulong Snow Mountain of Lijiang, northwest Yunnan, and between P. tenuituba and Pedicularis leptosiphon in Ninglang, northwest Yunnan. After removing conflicting DNA regions in Pedicularis dolichosiphon (nrITS) and P. milliana (ptDNA), the concatenated nrITS and ptDNA phylogenies distinguish 11 species in the P. siphonantha complex, including two undescribed species, from the Jiaozi and Yulong Snow Mountains, respectively. Phylogeographical analyses indicate that the P. siponantha 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.

Chromosome‐scale assembly and analysis of Melilotus officinalis genome for SSR development and nodulation genes analysis

“…Isolation of the geographical environment and artificial selection lead to the divergence and evolution of species T A B L E 2 Numbers and frequencies of the density of total simple sequence repeats (SSRs) and di-, tri-, and tetranucleotide with repeat unit numbers greater than five on each of the eight chromosomes. (Liu et al, 2022). M. officinalis and M. albus had the highest genome structure similarity at the chromosome level.…”

“…Isolation of the geographical environment and artificial selection lead to the divergence and evolution of species (Liu et al., 2022). M. officinalis and M. albus had the highest genome structure similarity at the chromosome level.…”

Pleistocene glaciation advances the cryptic speciation of Stellera chamaejasme L. in a major biodiversity hotspot

“…In the HM, many plants once thought to be single species, are now being recognized as cryptic species, in the midst of evolving into separate entities (Li et al, 2021; Ma et al, 2021; Zhao et al, 2021; Liu et al, 2022; Sun et al, 2022) (Table 1). This is particularly evident in the case of S. chamaejasme .…”

“…Despite evidence of limited glacial extensions in the HM between 0.46 and 0.71 Mya (Xu et al, 2010;Wang et al, 2017), the overall influence of the Pleistocene on current mountain plant diversity remains uncertain. This period likely fostered species diversification, especially through allopatric speciation in presence of geographically isolated mountains (Liu et al, 2013(Liu et al, , 2019(Liu et al, , 2022Smyčka et al, 2022). These migrations, influenced by geographical habitats, led to species variations like the high-altitude RW morph versus the valley-dwelling PP.…”

Responses of Three Pedicularis Species to Geological and Climatic Changes in the Qinling Mountains and Adjacent Areas in East Asia

“…Yu et al (2015) constructed a backbone phylogeny of Pedicularis, with extensive species sampling from the Himalaya-Hengduan Mountains, using sequences of the nuclear ribosomal internal transcribed spacer (nrITS) and three plastid regions (matK, rbcL, and trnL-F) [31]. Liu et al (2022) reconstructed evolutionary relationships of the Pedicularis siphonantha Don complex using nrITS and four plastid DNA loci (matK, rbcL, trnH-psbA, and trnL-F) to resolve taxonomic confusion [32].…”