Next-generation sequencing-based population genetics unravels the evolutionary history of Rhodomyrtus tomentosa in China

Abstract Background Rhodomyrtus tomentosa (Ait.) Hassk. is useful for its ornamental, medicinal, and ecological characteristics, and is considered a “Neglected and Underutilized Crop Species”. However, our understanding of the geographic structure and evolutionary history of its wild populations is limited. To address this gap, we investigated genomic data from 284 samples of R. tomentosa from 28 wild populations in southern China. Results The genetic diversity of populations in different regions revealed the similar trends using whole-genome and RAD-seq data, and Hainan Island having a higher genetic diversity than other regions. The 28 populations clustered into three distinct groups: (a) GROUP1 on the eastern mainland within Guangdong, Fujian, and Hunan Provinces; (b) GROUP2 on the western mainland within Guangxi and Yunnan Provinces; and (c) GROUP3 on Hainan Island. Mantel tests and redundancy analyses revealed population differentiation was affected by distance and environmental factors such as annual average radiation. Demographic history and gene flow analyses indicated the mainland populations and the Hainan Island populations diverged around 0.93 MYA, with gene flow primarily occurring from Hainan Island and the coastal regions (such as Zhanjiang in Guangdong and Fangchenggang in Guangxi) towards the mainland, reflecting an expansion trend within the species. PSMC’ analyses indicated that the populations of the three groups underwent a bottleneck during the Pleistocene due to glacial-interglacial cycles and geological events. Niche analysis revealed that the ice ages caused habitat contraction for the species, and populations with higher genetic diversity are generally distributed in areas with more suitable habitats. Conclusions This study elucidates the current genetic distribution of the species within China and suggests that drastic Pleistocene climate change and geographical events caused population divergence and fluctuations in effective population size, shaping the current genetic distribution of R. tomentosa. These findings provide a theoretical basis for the genetic conservation and improvement of R. tomentosa.