Genetic diversity and population differentiation of eastern honey bees (Apis cerana) in Sichuan, China, based on mtDNA cox1 gene sequences

To better understand the genetic diversity, population differentiation, and maternal origin of eastern honey bees (Apis cerana) in Sichuan Province, China, we analyzed mitochondrial DNA cox1 sequences from 10 geographical populations. A total of 308 cox1 gene sequences were obtained, forming 41 distinct haplotypes. The average haplotype diversity (Hd) was 0.833, and the average nucleotide diversity (Pi) was 0.00188, indicating a high level of genetic diversity in A. cerana populations in Sichuan. Notably, Hap3 was identified as the most frequent and widely distributed haplotype, suggesting it may represent the ancestral haplotype of A. cerana in this region. Analysis of molecular variance (AMOVA) revealed that the majority of genetic variation was concentrated within populations. Pairwise fixation index (Fst) and gene flow (Nm) results showed that a significant genetic differentiation was observed in population from Aba (AB), Batang (BT), and Derong (DR) compared to other regions, with mountain barriers potentially driving this spatial genetic structuring. The haplotype phylogenetic tree and haplotype network analysis further revealed that haplotypes from DR and BT clustered into two independent groups, suggesting unique genetic characteristics in these areas. Neutrality tests suggested potential historical demographic expansion in A. cerana populations from Sichuan. These findings demonstrate that Sichuan’s A. cerana populations maintain rich genetic diversity with significant geographic differentiation, providing critical insights for formulating regional conservation strategies and sustainable utilization of this ecologically important pollinator.