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

## TL;DR

This study shows that non-native honeybee introductions in the DL region have caused genetic mixing and instability in local Apis cerana cerana populations.

## Contribution

The study identifies two distinct introgression sources and highlights the instability of genetic structure due to continuous gene flow.

## Key findings

- Mitochondrial analysis revealed 26 haplotypes and introgression from both northern and southern sources.
- Genetic diversity varied widely within the DL region, indicating different stages of introgression.
- ΦST values showed no internal differentiation, suggesting continuous gene flow has disrupted population stability.

## Abstract

The prevalence of non-native subspecies introductions in the Daloushan (DL) region raises questions about their specific impact on population structure and population diversity. This study examined the tRNA leu-COII sequence of 217 samples in the region, identified genetic lineage admixture, and detected two distinct types of introgression within Apis cerana cerana from southern and northern origins. This finding was confirmed through gene flow analysis using whole-genome data. Furthermore, there is inconsistency in the internal genetic structure of the DL population, with varying levels of genetic diversity. This suggests that continuous gene flow has kept the Apis cerana populations in the region in a state of instability, emphasizing the necessity of early protection for honeybees with local genetic characteristics.

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 Apis cerana 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 Apis cerana populations in the DL region. Phylogenetic, network, ABBA-BABA test, and f3 statistic suggested introgression from both northern and southern sources. The f4-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 (Hd: 0.2907–0.8220; π: 0.0009–0.0038; K: 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 A. c. cerana for further insights.