Phylogeography of Bombus huntii (Hymenoptera: Apidae) using whole-genome sequences from natural history collection specimens

Bumble bees are widespread pollinators, and species often span heterogeneous landscapes with varying environmental complexity. Complex topography, along with historical climate, can shape genetic diversity and act as barriers to gene flow, potentially leading to speciation. Bombus huntii (Greene, 1860) is a bumble bee species featuring a broad geographic range, spanning from the southern portion of Canada, the western United States, to the central portion of Mexico. Prior microsatellite work identified signatures of population structure between the northern portion of B. huntii’s range, in the United States and Canada, and the northern and central portions in Mexico. Utilizing a newly assembled reference genome and whole-genome resequencing of natural history collection specimens, we aimed to characterize patterns of population structure, genetic diversity, and inbreeding for northern and southern populations of B. huntii and test for potential speciation based on prior microsatellite results. We found strong population structure between the northern and southern lineages and identified reduced genetic diversity in the southern populations with evidence of increased inbreeding compared to the north. Our phylogenomic results lacked strong support for splitting the north and south populations into separate species, with demographic analysis suggesting some gene flow in the direction of south to north. Overall, our results suggest that while there is a lack of strong support for speciation occurring between these 2 geographic populations, there is evidence of decreased genetic diversity and increased levels of inbreeding in the Mexico population, indicating that these 2 populations do warrant consideration as evolutionary significant units.