Effects of Persistent Introgression on Mitochondrial DNA Genetic Structure and Diversity in the Apis cerana cerana Population

Continuous human-mediated introduction of colonies and queens promotes genetic introgression and reshapes the genetic diversity and structure of local honeybee populations. According to reports, multiple non-native honeybee colonies and queens have been introduced into the DL region, leading to continuous genetic introgression. Here, we assessed the effects of continuous introgression on indigenous <i>Apis cerana</i> in the DL region using mtDNA and genome-wide SNP markers. We sequenced the mitochondrial tRNA ^leu-COII from 217 individuals sampled at 7 DL sites and identified 26 haplotypes defined by 18 polymorphic sites. The ΦST values indicated no internal differentiation within the <i>Apis cerana</i> populations in the DL region. Phylogenetic, network, ABBA-BABA test, and <i>f</i>3 statistic suggested introgression from both northern and southern sources. The <i>f</i>4-ratio indicates that approximately 16% of the ancestry in the DL group is derived from the Aba group. Genetic diversity varied widely within the DL region (<i>Hd</i>: 0.2907-0.8220; <i>π</i>: 0.0009-0.0038; <i>K</i>: 0.3140-1.3980), indicating different stages of introgression. The genetic structure within the DL group appears to be unstable, necessitating long-term monitoring of evolutionary processes and genetic diversity dynamics in <i>A. c. cerana</i> for further insights.