Using genomics to aid in the conservation of the native Irish honey bee
Smith, Stephen
Smith, Stephen
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Publication Date
2024-08-27
Type
doctoral thesis
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Abstract
Apis mellifera mellifera, or the European dark bee, is a sub-lineage of the European honey bee that is native to North Western Europe including Ireland. Recent studies have shown that the free-living population of honey bees in Ireland is widespread and has a high level of genetic purity. This is threatened by consistent and increasing importation of foreign sub-lineages, namely C-lineage queens from either A. m. ligustica and A. m. carnica, with numbers of importations rising from just over 100 queens per year in 2012 to over 1200 per year in 2021. A survey of Irish beekeepers was undertaken to identify attitudes of Irish beekeepers towards issues such as conservation and scientific research. The results indicated that the overwhelming majority are currently supporting the conservation of the native Irish honey bee through their beekeeping practices with only a small group of respondents keeping a non-native sub-lineage in their apiaries. A whole genome pooled sequencing analysis was undertaken to identify hybrid colonies and model the current population of Irish honey bees. Over 150 Irish honey bee colonies were sampled alongside three UK and five German colonies. The use of the f3-statistics method found an increase in hybridisation rates compared with previous studies and confirmed the reports of increased importations, however, the Irish population was found to contain a large percentage of extremely pure M-lineage honey bee colonies that are an important resource in the conservation of this sub-lineage. The use of pool-seq allowed the data generated in this study to be combined with two pan-European pool-seq datasets to create a network model of European honey bee population. Groups from this model were then extracted for admixture analysis that helped identify the best course of action in regards to the future methods of conservation of the native Irish honey bee. The reliance on abdominal colour alone to detect hybridised honey bees has been challenged in recent studies and pure-black hybrids were also detected in this study. A Cochran-Mantel-Haenszel test followed by a gene ontology analysis discovered genes and processes related to melanin production and cuticle development in honey bees. A microbiome analysis using shotgun metagenomics methods was carried out to investigate if management, and treatment, results in a different microbiome profile in comparison with free-living honey bee colonies. Relative abundance analysis and differential absolute abundance analysis methods both identified differences between managed and free-living honey bee microbiomes.
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University of Galway
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Attribution-NonCommercial-NoDerivatives 4.0 International