Apis mellifera (the Western honey bee) is a predominantly human managed pollinator consisting of different evolutionary lineages each containing a number of subspecies. Apis mellifera is threatened by various factors for example, parasites, viruses and pesticide use. The native subspecies of the British Isles Apis mellifera mellifera is additionally threatened by introgression resulting from the importation of foreign subspecies perceived to have more desirable characteristics. This thesis investigates the integrity of Apis mellifera mellifera in the UK and how that can be assessed. Initially, introgression levels over time in a conservation program were assessed. This revealed temporal decreases in introgression, indicating that some bee keeping management strategies can be effective in the conservation of this subspecies. Next, an assessment of different methods for measuring introgression in a social insects such as honey bees revealed that pooled colony approaches can be a powerful tool in the assessment of colony level introgression. Following this, an assessment of the status of Apis mellifera mellifera in the wider British Isles was performed using whole genome data. This revealed a largely introgressed population across the British Isles with the exception of a few key locations: Ireland, the South West of England, the Inner Hebrides, Northern Scotland, the Isle of Man, and Jersey. Finally, an examination of the ‘purity’ of subspecies in a phenotypic monitoring project and an assessment the genomic differences between subspecies highlights the importance of genetic assessment in scientific studies and indicates regions of high differentiation between subspecies. This work has implications for introgression assessment in social insects and future directions for A. m. mellifera conservation in the British Isles and further afield.

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