Abstract
Biogeographical barriers to gene flow are central to plant phylogeography. There are many physical and geographic boundaries in China, but there are few studies on the natural geographical isolation boundary of the Qinling Mountains-Huaihe River Line (QHL) using molecular ecological evidence. Allium macrostemon is a perennial herb belonging to the family Amaryllidaceae. It is a precious Chinese herb with the same origin as medicine and food, and has a variety of health and healing properties. Five SSR markers, three chloroplast DNA (cpDNA) markers (psbA-trnH, rps16 and trnL-F), one nuclear ribosomal DNA (nrDNA) marker (ITS), and simplified genome GBS sequencing were used to analyze the genetic diversity and genetic structure of A. macrostemon. Combining SSR, cpDNA, nrDNA ITS data and GBS analysis results, A. macrostemon populations could be grouped into northern and southern group, with the southern group further divided into southwestern and central-southeastern group. Niche simulations results show that the distribution area of A. macrostemon will reach its maximum in the future. These data indicate that a geographical barrier and Quaternary climate have maintained the regional separation of A. macrostemon, and the back-and-forth fluctuations of QHL and Quaternary climate play an important role in this process. QHL acts as a north-south dividing line in phylogeography and population genetic structure, promoting physical geographic isolation. This study can provide scientific theoretical basis for the conservation, development and utilization of A. macrostemon resources, further provide reference for the systematic geographical pattern of large-scale spatial distribution of plants in China, and enrich our understanding of the Quaternary plant evolution history in complex terrain areas.