It’s important to discover new resources and expand knowledge of the
distribution range of Apis cerana for the conservation and utilization
of genetic resources. Here, we newly sequenced genomes and apply
population genetic and morphological analysis methods using publicly
available genome-wide datasets to investigate the origin and adaptation
of A.cerana sanshasis from Yongxing Island. The results showed SanshaId
colony was significantly genetically differentiated from others with an
average Fst of 0.2669, indicating a level of subspecies differentiation.
Morphological clustering also showed significant differences, especially
the tongue length of SanshaId colony was significantly smaller than that
of others. In summary, we concluded that A.cerana sanshasis is a
subspecies of A.cerana. Population history analysis showed SanshaId
population has a recent common ancestral feature with Hainan’s, and
subspecies differentiation occurred around 0.57 Ma due to geological
movements causing geographic isolation. We examined the genetic
variation between the recently marginalized colonies from HainanId and
SanshaId, and found high frequency nonsynonymous mutations gene in
SanshaId colony involved in Glutathione metabolism and other signaling
pathways, among which a gene potentially related to tongue length
morphology, Cuticular, was subject to evolutionary selection; meanwhile,
differential tissue expression profiles showed a correlation with
glucose metabolism genes are highly expressed in the midgut, suggesting
these genes may be associated with adaptation to tropical island
environments. Our results expand the understanding of the distribution
range of Asian honeybee and provide the basis for understanding the
population dynamics of A.cerana sanshasis and the molecular evolutionary
mechanisms of adaptation to tropical island environments.