Nationwide Tracking of A-Lineage Spread in Western Honey Bees Using Haplotype Sharing, Local Ancestry Mapping, and Migration Inference

Understanding the spatial dynamics of genetic ancestry is essential for elucidating historical and contemporary patterns of gene flow among populations. Honey bees in the United States have a 400-year history of importation, management, and adaptation to diverse environments. Genetic diversity is a key factor for colony health and resilience. Notably, the most genetically diverse populations in the country originate from the invasive A-lineage (Africanized or 'Killer' honey bees). In this study, we leveraged a nationwide community-science platform to assemble an extensive genomic dataset of U.S. honey bee populations and used it to ask how this invasive lineage is spreading across the country and how its spread has impacted honey bee genetic diversity nationwide. Using RFMix, we assigned local ancestry across the genome to capture fine-scale ancestry patterns and applied TreeMix to genome-wide allele frequency data to infer directional gene flow among U.S. populations. Our analyses revealed patterns consistent with a strong northward migration, with major source populations in southern states such as Texas (TX), Arizona (AZ), and Florida (FL), and primary targets in northern states including Michigan (MI), New York (NY), and Vermont (VT). Covariance estimates indicated strong genetic connectivity, particularly from TX and AZ. Spatial visualization of migration edges highlighted key routes of A-lineage expansion. Together, these results provide the first genome-wide evidence for a nationwide spread of A-lineage ancestry in the U.S., offering insights to guide breeding strategies and predict the future dynamics of honey bee genetic diversity.