DOI: 10.5061/dryad.mkkwh710c
title: Data from: Habitat quality influences pollinator pathogen prevalence through both habitat–disease and biodiversity–disease pathways

description: The dilution effect hypothesis posits that increasing biodiversity reduces
 infectious disease transmission. Here, we propose that habitat quality
 might modulate this negative biodiversity–disease relationship. Habitat
 may influence pathogen prevalence directly by affecting host traits like
 nutrition and immune response (we coined this as the ‘habitat–disease
 relationship’) or indirectly by changing host biodiversity
 (biodiversity–disease relationship). We used a path model to test the
 relative strength of links between habitat, biodiversity, and pathogen
 prevalence in a pollinator–virus system. High-quality habitat metrics were
 directly associated with viral prevalence, providing evidence for a
 habitat–disease relationship. However, the strength and direction of
 specific habitat effects on viral prevalence varied based on the
 characteristics of the habitat, host, and pathogen. In general, more
 natural area and richness of landcover types were directly associated with
 increased viral prevalence, while greater floral density was associated
 with reduced viral prevalence. More natural habitat was also indirectly
 associated with reduced prevalence of two key viruses (black queen cell
 virus and deformed wing virus) via increased pollinator species richness,
 providing evidence for a habitat-mediated dilution effect on viral
 prevalence. Biodiversity–disease relationships varied across viruses, as
 prevalence of sacbrood virus was not associated with any habitat quality
 or pollinator community metrics. Across all viruses and hosts,
 habitat–disease and biodiversity–disease paths had effects of similar
 magnitude on viral prevalence. Therefore, habitat quality is a key driver
 of variation in pathogen prevalence among communities via both direct
 habitat–disease and indirect biodiversity–disease pathways, though the
 specific patterns varied among different viruses and host species.
 Critically, habitat–disease relationships could either contribute to or
 obscure dilution effects in natural systems depending on the relative
 strength and direction of the habitat–disease and biodiversity–disease
 pathways in that host–pathogen system. Therefore, habitat may be an
 important driver in the complex interactions between hosts and pathogens.
description: We collected pollinator community species richness and abundance
 data by sampling pollinators from each community with hand nets and pan
 traps. At each collection site, we measured the density of flowers and
 species richness of flowering plants (including native and non-native
 plants) to assess local habitat quality along the same transects that
 pollinators were collected from. To assess landscape habitat quality for
 pollinators, we used the USDA cropland data layer to quantify the
 proportion of natural area (including forest, wetland, and grassland) and
 the landscape richness (the number of different landcover types) within a
 1000 m radius of each collection site. Landowner permission was given for
 pollinator collection at each site.  A subset of
 <em>Apis mellifera</em>, <em>Bombus
 impatiens</em>, <em>Lasioglossum </em>spp.
 and <em>Eucera pruinosa</em> was tested for the presence of
 deformed wing virus (DWV), black queen cell virus (BQCV), and sacbrood
 virus (SBV). Viral data was recorded as binary presence or absence of each
 virus for each individual tested. Each bee in the study was tested for all
 three viruses. We used a path model to test the
 relative effects of habitat quality characteristics and pollinator
 community characteristics on patterns of viral prevalence. The path model
 allows us to rigorously disentangle the effects of habitat characteristics
 on patterns of pathogen prevalence through the newly proposed
 habitat–disease relationship and the well-established biodiversity–disease
 relationship.
description: <strong>Summary of field and virus prevalence
 data</strong><br>Field collected data examining the
 relative impact of local- and landscape-level habitat quality
 characteristics and pollinator community diversity and abundance on viral
 prevalence in a natural multihost-multipathogen system. This data uses
 pollinator communities sampled from winter squash farms along a landscape
 gradient from low to high proportion natural area and vary substantially
 in pollinator diversity and abundance to evaluate patterns of deformed
 wing virus (DWV), black queen cell virus (BQCV), and sacbrood virus (SBV)
 prevalence within four focal host species: <em>Apis
 mellifera</em>, <em>Bombus
 impatiens</em>, <em>Lasioglossum </em>spp., and
 <em>Eucera pruinosa</em>. A subset of the four host species
 collected from each site was used to test for the presence or absence of
 DWV, BQCV, and SBV using RT-PCR with virus-specific
 primers.<br>Virus_Positive_Community+Habitat_Covariates_1Mar2022.csv<br>README_for_Fearon,Wood,Tibbetts_Ecology.txt <strong>R script for path models </strong><br>The code used to run the main and species-specific path analyses presented in the manuscript. This code produces the information presented in Figures 1–4, and all tables in Appendix S2 and Appendix S3.<br>BeeVirusHabitat+CommunityPathModels_29Sept2022.R <strong>Calculations of relative strength of direct, indirect, and total effects from the main path model (Figure 4)</strong><br>These calculations were done in Microsoft Excel based on the significant scale standardized coefficients produced from the main path model (Figure 4).<br>Fig 4_indirect and total effect calculations from main path model.xlsx Original pollinator community data and compilation and analysis of the prevalence of the viral negative strand in each host species, indicative of active viral replication and infection, from the bee specimen used in this study can be found in Data from: Pollinator community species richness dilutes prevalence of multiple viruses within multiple host species (https://doi.org/10.5061/dryad.zpc866t7g).