DOI: 10.5061/dryad.j6q573nt5
title: Data from: Interactions of husbandry, landscape, and immunity in regulating viral loads for managed honey bees

description: The western honey bee, Apis mellifera, continues to experience widespread
 die-offs that threaten their critical ecological and agricultural roles.
 Given the recognized impact of viruses on the increased mortality rates,
 it is imperative to understand the forces shaping viral infections. In
 this study, we explore how hive husbandry, landscape, and immunity
 influence viral loads in managed bees. We characterized 43 apiaries across
 Central Florida for eight husbandry interventions, five landscape
 variables, transcription of four immune genes, and infection intensities
 of four viruses: Black Queen Cell Virus (BQCV), Deformed Wing Virus
 (DWV-A), Lake Sinai Virus (LSV-2), and Israeli Acute Paralysis Virus
 (IAPV). We found that colonies surrounded by more floral resources and
 fresh water bodies were associated with increased viral loads and
 increased viral coinfections. We speculate that increased floral resources
 increased pollinator abundance, thereby increasing transmission rates and
 viral richness. We further speculate that increased open water similarly
 increased pollinator abundance and/or exposure to immunity-altering
 pesticides. Last, we show that husbandry interventions aimed at reducing
 Varroa destructor mites can have positive and negative off-target viral
 impacts. Our data underscore the importance of landscape, immunity, and
 husbandry in honey bee disease dynamics and highlight the complexity of
 their interactions.
description: # Data from: Interactions of husbandry, landscape, and immunity in
 regulating viral loads for managed honey bees Dataset DOI:
 [10.5061/dryad.j6q573nt5](10.5061/dryad.j6q573nt5) ## Description of the
 data and file structure This file includes individual-level data on viral
 load, immune gene expression, husbandry practices, and landscape
 characteristics. ### Files and variables #### File: AllData.xlsx
 **Description:** This file includes individual-level data on viral load,
 immune gene expression, husbandry practices, and landscape
 characteristics. **Notes:** * Each sample underwent qPCR twice: once for
 viral assays and once for immune gene assays. Both assays used Actin as a
 reference gene, resulting in two separate Actin Cq values (Act_ct and
 Act_cq). * For final modeling, Actin Cq values were averaged. * Samples
 with missing immune gene data are included but were excluded from relevant
 statistical models. Missing values are indicated by blank cells.
 **Variable Codes:** Husbandry Variables ( 0 = treatment not applied; 1 =
 treatment applied) * SF = supplemental feeding usage * SHB = Small Hive
 Beetle prevention usage * EO = essential oil usage * Api = Apiguard usage
 * Ami = amitraz usage * Hops = hops usage * OA = oxalic acid usage * FA =
 formic acid usage * Miticides = general usage of miticides (umbrella
 term)  Landscape Variables (Values represent proportions within a 2 km
 radius. A +1 was added to zero values for later log transformations.) *
 BFA = Bee Forage Area * IS = Impervious Surfaces * NL = Natural Lands * Ag
 = Agriculture * OW = Open Water (fresh) Immunity Variables: * Act_cq:
 Actin Cq value for immune assays * PPO_cq, Def_cq, Dom_cq, Dic_cq: Raw Cq
 values for PPO, Defensin, Domeless, and Dicer * dPPO, dDef, dDom, dDicer:
 ΔCq = Immune gene Cq – Actin Cq * CN_PPO, CN_Def, CN_Dom, CN_Dic:
 Calculated copy number (methods in manuscript) * PPO, Def, Dome, Dicer:
 log₁₀-transformed copy numbers  Viral Variables: * Act_ct: Actin Cq value
 for viral assays * BQCV_ct, DWV_ct, IAPV_ct, LSV_ct: Raw viral Cq values *
 dBQCV, dDWV, dIAPV, dLSV: ΔCq = Viral gene Cq – Actin Cq * CN_BQCV,
 CN_DWV, CN_IAPV, CN_LSV: Viral copy numbers * BQCV, DWV, IAPV, LSV:
 log₁₀-transformed viral copy numbers  Principal Components & Other
 Calculated Metrics: * PC_virus, PC_virusR: Principal component scores
 summarizing viral load * PC_imm: Principal component of immune gene
 expression * PC_land: Principal component of landscape characteristics *
 PC_hus: Principal component of husbandry variables * Viral_rich: Number of
 detected viruses per sample * Viral_cat: Categorical variable summarizing
 viral co-infection status. Values are represented by single-letter codes
 (one or more letters may appear if multiple viruses were detected). D=
 Deformed Wing Virus; B= Black Queen Cell Virus; I = Israeli Acute
 Paralysis Virus; L= Lake Sinai Virus. #### File: HiveSummary.csv
 **Description:** This file includes colony-level averages of viral
 infection and associated environmental variables. ##### **Variable
 Codes:** Husbandry Variables ( 0 = treatment not applied; 1 = treatment
 applied) * SF = supplemental feeding usage * SHB = Small Hive Beetle
 prevention usage * EO = essential oil usage * Api = Apiguard usage * Ami =
 amitraz usage * Hops = hops usage * OA = oxalic acid usage * FA = formic
 acid usage * Miticides = general usage of miticides (umbrella term)
 Landscape Variables (Values represent proportions within a 2 km radius. A
 +1 was added to zero values for later log transformations.) * BFA = Bee
 Forage Area * IS = Impervious Surfaces * NL = Natural Lands * Ag =
 Agriculture * OW = Open Water (fresh) Viral Load (Colony Averages): *
 Log(BQCV), Log(DWV), Log(IAPV), Log(LSV): Log-transformed mean viral copy
 number per colony