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Background Exploration of adaptive evolution of organisms in response to environmental change can help to understand the evolutionary history of species and the underlying mechanisms of adaptation to local environments, thus guiding future conservation programmes. Before the introduction of  Apis mellifera  in China, eastern honey bees ( Apis cerana ) were the only species used for beekeeping in this region. In the mountains of Changbai, populations of  A. cerana  are considered a distinct ecotype of the species which formed through the distinct selective pressures in this area over time. Result We performed a measure of 300 wing specimens of eastern honey bees and obtained the geometric morphological variation in the wing of  A. cerana  in Changbai Mountain. A total of 3,859,573 high-quality SNP loci were yielded via the whole-genome resequencing of 130 individuals in 5 geographic regions. Conclusion Corresponding geometric morphology and population genomics confirmed the particularity of the  A. cerana  in Changbai Mountain. Genetic differentiation at the subspecies level exists between populations in Changbai Mountain and remaining geographic regions, and a significant reduction in the effective population size and an excessive degree of inbreeding may be responsible for a substantial loss of population genetic diversity. Candidate genes potentially associated with cold environmental adaptations in populations under natural selection were identified, which may represent local adaptations in populations. Our study provided insights into the evolutionary history and adaptation of  A. cerana  in Changbai Mountain, as well as its conservation.

Geometric morphology and population genomics provide insights into the adaptive evolution of Apis cerana in Changbai Mountain