Biogeography from a food matrix: a temporal distribution map of Apis mellifera mitochondrial DNA lineages across Italy, obtained from honey samples

The genetic integrity of European Apis mellifera subspecies has been increasingly threatened. Mitochondrial DNA (mtDNA) analysis is widely used to investigate honey bee lineage distribution. Honey represents a valuable source of environmental DNA (eDNA), containing traces of all the organisms involved in its production, including the honey bees, and can therefore be used to obtain insights on honey bee population genetics. In this study, DNA was extracted from 4292 honey samples produced in all regions of the Italian Peninsula plus Sardinia and Sicily, from 1985 to 2023, and used to provide a temporal snapshot of the distribution of the main A. mellifera mtDNA lineages. The C lineage was the most frequent mtDNA throughout Italy, except in Sicily where the A lineage was predominant. MtDNA from the A and M lineages were present in all Italian regions. The frequency of the A mtDNA lineage has increased in many Italian regions over the last years, following a climatic gradient over the Peninsula. Beekeeping practices that used non-native genetic stocks, with the subsequent potential combination of genetic adaptation of honey bees carrying the A lineage to climatic conditions, may explain the observed changes over years in the Italian A. mellifera population genetic structure. This is the first temporal biogeographic study obtained from eDNA extracted from a food matrix, namely honey.