Quercus is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four Quercus section Cyclobalanopsis species (Q. poilanei, Q. helferiana, Q. camusiae, and Q. semiserrata) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus Quercus. These four chloroplast genomes ranged from 160,784 bp (Q. poilanei) to 161,632 bp (Q. camusiae) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other Quercus species. We identified seven regions with relatively high variability (rps16, ndhk, accD, ycf1, psbZ—trnG-GCC, rbcL—accD, and rpl32—trnL-UAG) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within Quercus. Our phylogenetic tree supported the idea that the genus Quercus forms two well-differentiated lineages (corresponding to the subgenera Quercus and Cerris). Of the three sections in the subgenus Cerris, the section Ilex was split into two clusters, each nested in the other two sections. Moreover, Q. camusiae and Q. semiserrata detected in this study diverged first in the section Cyclobalanopsis and mixed with Q. engleriana in the section Ilex. In particular, 11 protein coding genes (atpF, ndhA, ndhD, ndhF, ndhK, petB, petD, rbcL, rpl22, ycf1, and ycf3) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of Quercus, which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus.

The interplay between historical biogeography and environmental selection shapes the genetic architecture of species; however, their relative contributions in widespread and ecologically important tree species remain poorly understood. In the Sino-Japanese Floristic Region, the East China Sea has alternately acted as a barrier and a corridor during glacial-interglacial cycles, influencing species isolation and contact. However, the extent to which these historical dynamics, along with environmental gradients, have driven adaptive evolution in dominant forest trees remains unresolved. In the present study, we integrated phylogeographic reconstruction and landscape genomics based on whole-genome resequencing data from 171 individuals across 35 populations to investigate the evolutionary history and adaptive mechanisms of Quercus gilva, a keystone evergreen oak, in East Asian subtropical forests. Population genomic analyses revealed two deeply divergent genetic groups: the China group and the Japan–Korea group, and demographic modeling indicated that their divergence dates back to the Miocene epoch. The relatively high genomic diversity of Q. gilva may result from the absence of severe genetic bottlenecks throughout its evolutionary history, multiple microrefugia during the glacial periods, and postglacial secondary contact. Notably, Quaternary glacial cycles repeatedly facilitated gene flow and admixture between these groups via exposed land bridges. Landscape genomic analyses further demonstrated that adaptive divergence in Q. gilva is shaped by both geographic isolation and environmental gradients, with annual precipitation emerging as the primary climatic driver. This study provides a genome-wide perspective on how historical biogeography and environmental selection interact to shape the genetic architecture of a dominant subtropical evergreen forest species, offering novel insights into the evolutionary dynamics and adaptive evolution across East Asian biodiversity hotspots.