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An understanding of the origin and formation of biodiversity and distribution patterns can provide a theoretical foundation for biodiversity conservation. In this study, phylogeny and biogeography analyses based on mitochondrial genomes and niche modeling based on occurrence records were performed to test the hypotheses on the center of origin, diversification, and glacial refugia of honey bees (Apis spp.). The results suggest that the Apis genus originated from tropical Asia during the Miocene, in which the Sundaland was the ancestral region of most clusters in the Apis genus and a glacial refuge of A. cerana and A. andreniformis. The diversification rate declined with time, and climate change may have a potential impact on the suitable regions of honey bees in the future. This study advances our understanding of the origin, climate change response, and diversification of honey bees. [ABSTRACT FROM AUTHOR]