Mitochondrial DNA of Apis dorsata reveals the haplotype differentiations and genetic relationship in Sundaland, Lesser Sunda, and Sulawesi

The giant honey bee Apis dorsata is widely distributed across Asia, including Sundaland and Wallacea. Two giant honey bee subspecies are recognized in Indonesia, i.e., Apis dorsata dorsata, distributed across the archipelago except Sulawesi, and the endemic to Sulawesi, Apis dorsata binghami. Despite the ecological importance, molecular data on A. dorsata in Indonesia are unrevealed. We aim to investigate (1) the genetic and haplotype variation of A. dorsata across Sundaland, Lesser Sunda, and Sulawesi using mitochondrial markers of COI, COII genes, and the intergenic spacer region, and (2) genetic relationships among those regions. We performed genetic diversity median-joining network to uncover the relationships among them. Based on the genetic and haplotype variations, we found two groups of A. d. dorsata: (a) Sundaland and (b) Lesser Sunda, the former exhibits lower genetic diversity and differentiation. The MJ network revealed that Sumatra1 is a common haplotype in Sundaland and an ancestral haplotype of Indonesian giant honey bees. In contrast, we found the high genetic differentiation of A. d. dorsata between the western and eastern parts of the Lesser Sunda; the former was genetically closer to Sundaland. We also confirmed A. d. binghami in Sulawesi and revealed the highest nucleotide variations, genetic differentiation, and two amino acid mutations in COII that serve as the marker of this Sulawesi endemic bee. Our results indicate that the genetic structure of A. dorsata in the Indonesian archipelago was shaped by Pleistocene land connections and present-day island separation, resulting from the rise in sea level.