Genetic variation and demographic history of <i>Vatica mangachapoi</i> Blanco (Dipterocarpaceae), a dominant tree in the lowland rainforests of Hainan Island, China

Abstract Vatica mangachapoi is the only dipterocarp species forming dominant stands in the lowland rainforests of Hainan Island. Understanding its population history is essential for elucidating the assembly of local rainforest communities on the island. In this study, we collected 266 individuals from 15 populations and genotyped them using 12 polymorphic microsatellites markers to assess genetic diversity, population structure, and demographic history. The results showed that V. mangachapoi exhibited relatively high genetic diversity (Na = 5.583, He = 0.698) compared with threatened dipterocarps. STRUCTURE analyses revealed two distinct genetic clusters, from which three groups of populations with varying proportions of the genetic clusters were identified. Principal coordinates analysis and neighbour-joining tree reconstruction also supported the division of populations into three groups. Based on approximate Bayesian computation implemented in DIYABC v.2.1.0, the V. mangachapoi on Hainan Island was inferred to experience population expansion ∼70 kya, then contraction near 21 kya, and subsequent lineage divergence at ∼18 kya, suggesting that Quaternary glacial–interglacial cycles probably played an important role in shaping its population history on this Island. Overall, our findings highlight the impact of Quaternary climatic oscillations on the demographic history of V. mangachapoi and provide a valuable framework for developing effective conservation strategies to preserve its long-term adaptive potential.