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Honey bees contribute substantially to the world economy through pollination services and honey production. In the U.S. alone, honey bee pollination is estimated to contribute at least $11 billion annually, primarily through the pollination of specialty crops. However, beekeepers lose about half of their hives every season due to disease, insecticides, and other environmental factors. Here, we explore and validate a spatiotemporal statistical model ofVarroa destructormite burden (in mites/300 bees) in managed honey bee colonies, exploring the impact of both environmental factors and beekeeper behaviors. We examine risk factors forVarroainfestation using apiary inspection data collected across the state of Illinois over 2018–2019, and we test the models using inspection data from 2020–2021. After accounting for spatial and temporal trends, we find that most environmental factors (e.g., floral quality, insecticide load) are not predictive ofVarroaintensity, while lower numbers of nearby apiaries and several beekeeper behaviors (e.g., supplemental feeding and mite monitoring/treatment) are protective againstVarroa. Interestingly, while monitoringandtreating forVarroais protective, treatingwithoutmonitoring is no more effective than not treating at all. This is an important result supporting Integrated Pest Management (IPM) approaches. 

ABSTRACT The opportunistic human pathogenPseudomonas aeruginosais naturally infected by a large class of temperate, transposable, Mu-like phages. We examined the genotypic and phenotypic diversity ofP. aeruginosaPA14 lysogen populations as they resolve clustered regularly interspaced short palindromic repeat(CRISPR) autoimmunity, mediated by an imperfect CRISPR match to the Mu-like DMS3 prophage. After 12 days of evolution, we measured a decrease in spontaneous induction in both exponential and stationary phase growth. Co-existing variation in spontaneous induction rates in the exponential phase depended on the way the coexisting strains resolved genetic conflict. Multiple mutational modes to resolve genetic conflict between host and phage resulted in coexistence in evolved populations of single lysogens that maintained CRISPR immunity to other phages and polylysogens that lost immunity completely. This work highlights a new dimension of the role of lysogenic phages in the evolution of their hosts.IMPORTANCEThe chronic opportunistic multi-drug-resistant pathogenPseudomonas aeruginosais persistently infected by temperate phages. We assess the contribution of temperate phage infection to the evolution of the clinically relevant strain UCBPP-PA14. We found that a low level of clustered regularly interspaced short palindromic repeat (CRISPR)-mediated self-targeting resulted in polylysogeny evolution and large genome rearrangements in lysogens; we also found extensive diversification in CRISPR spacers andcasgenes. These genomic modifications resulted in decreased spontaneous induction in both exponential and stationary phase growth, increasing lysogen fitness. This work shows the importance of considering latent phage infection in characterizing the evolution of bacterial populations.