RAD-Seq and Ecological Niche Reveal Genetic Diversity, Phylogeny, and Geographic Distribution of and Its Closely Related Species.

Most plants of have economic value and medicinal application. Among them, and its closely related species have been demonstrated to have definite efficacy. However, the taxonomy and phylogenetic relationship of in terms of morphology and commonly used gene regions remain controversial, which adversely affects its rational application. In this study, a total of 107 individuals of , , , , and were studied from the perspectives of genetic diversity, phylogeny, and ecology single nucleotide polymorphisms (SNPs) developed through restriction site-associated DNA sequencing (RAD-seq). Based on these SNPs, the genetic diversity, phylogenetic reconstruction, and population genetic structure were analyzed. Subsequently, divergence time estimation and differentiation scenario simulation were performed. Meanwhile, according to the species distribution records and bioclimatic variables, the Last Glacial Maximum and current potential distributions of five species were constructed, and the main ecological factors affecting the distribution of different species were extracted. The calculated showed that there was a moderate degree of differentiation among , , and , and there was a high degree of genetic differentiation between and the above species. The phylogenetic tree indicated that each of the species was monophyletic. The results of population genetic structure and divergence scenario simulation and D-statistics showed that there were admixture and gene flow among , , and . The results of ecological niche modeling indicated that the distribution areas and the bioclimatic variables affecting the distribution of and its related species were different. This study explored the differences in the genetic divergence and geographical distribution patterns of and its related species, clarifying the uniqueness of compared to its relatives and providing a reference for their rational application in the future.