A comprehensive meta-analysis of the use of mtDNA and microsatellite markers in the study of phylogeography and conservation of the gene pool of Apis mellifera L.

Asset ZHYLKİBAYEV, Kudiyarov Rahim, Serik D. Nurbaev, Yu. A. Yuldashbaev, Elvira Pocheshkhova, Макпал Каргаева

2026

Full text Open access: Gold Metadata (CSL-JSON)
DOI 10.1590/1519-6984.307227
Data confidence 70 medium
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Abstract

Abstract The Western honey bee (Apis mellifera L.) is a key pollinator species and an important object of beekeeping; however, anthropogenic introgression of genes from commercial breeds threatens the preservation of local gene pools. To systematize data from contemporary studies on the application of mitochondrial DNA (mtDNA) markers (COI–COII locus) and nuclear microsatellites (SSR) for phylogeographic research and monitoring the genetic purity of A. mellifera populations. A systematic search was conducted in the databases Scopus, Web of Science Core Collection, RSCI, and PubMed for the period 1998-2025 using combinations of the following keywords: (“Apis mellifera” OR “honey bee”) AND (“mtDNA” OR “mitochondrial DNA” OR “COI–COII”) AND (“microsatellite*” OR “SSR”) AND (“phylogeograph*” OR “population genetic*” OR “introgression”). Inclusion criteria were: (1) original studies containing data on polymorphism of the COI–COII locus and/or SSR loci; (2) analysis of A. mellifera populations with clear geographic attribution; (3) availability of quantitative data on allele frequencies or levels of introgression. Study selection and data extraction were performed by two independent researchers. The quality of the studies was assessed using an adapted checklist for population genetic research. The meta-analysis included 15 studies (n = 3,847 bee colonies from 28 regions). The mtDNA COI–COII locus demonstrated high reliability for determining maternal affiliation with evolutionary lineages (M, C, A, O), with a sensitivity of 98.7% [95% CI: 96.2-99.5%]. A panel of five SSR loci (A043, Ap081, Ap049, A113, mrjp3) enabled differentiation between subspecies of the M and C lineages with an accuracy of 99.1% (AUC = 0.994). The pooled estimate of the PQQ allele frequency (a marker of the M lineage) was 0.67 [0.62-0.72], with significant heterogeneity among studies (I2 = 68.4%, p < 0.001). Five reserves of Apis mellifera mellifera were identified in the Ural and Volga regions with introgression levels <5%. The Altai population retains a core gene pool of the M lineage (proportion of purebred colonies 75% [68-81%]).