DOI: 10.6084/m9.figshare.30281617.v1
title: Data from Knauer et al., Pesticides and habitat loss additively reduce wild bees in crop fields

description: We conducted a global analysis of 36 primary datasets, which were selected based on a systematic literature search of published field studies on the effects of pesticide use and the loss of semi-natural habitats (SNH) on wild bee assemblages in crop fields. The collected datasets covered 681 agricultural fields across various crop types on the African, European, and North American continents and included information on the abundance and potential response traits (body size, lecty, sociality, nest location, nesting strategy, and kleptoparasitism) of 910 bee species (19,593 specimens).Based on the raw data, we calculated a range of alpha diversity metrics for each site, including abundance, species richness, functional diversity, functional mean pairwise distance, functional evenness, functional specialization, phylogenetic diversity, and phylogenetic mean pairwise distance (Laliberté & Legendre 2010; Grab<i> et al.</i> 2019; Woodcock<i> et al.</i> 2019; Magneville<i> et al.</i> 2022; Weekers<i> et al.</i> 2022).Additionally, we calculated multiple beta diversity metrics to analyze patterns of species composition across agroecosystems with varying levels of intensification. As a measure of nestedness, we used abundance-weighted nestedness of bee assemblages based on overlap and decreasing fill (WNODF) (Almeida-Neto & Ulrich 2011). WNODF was calculated separately for each dataset across comparable assemblages recorded in the same region, crop and during the same year(s). To understand patterns of nestedness and turnover of species occurrence in bee assemblages along gradients of increasing pesticide hazard quotient (HQ) and decreasing proportion of SNH, we additionally measured turnover and nestedness across sites experiencing increasing anthropogenic stressors (Schmera et al. 2022).wo measurements of pesticide hazard in focal fields were used: (a) high versus low intensity of pesticide use based on production systems (conventional or organic), additionally supported by information on typical pesticide management (e.g., through farmer interviews), available for 27 datasets; or (b) hazard quotients (HQ), which incorporate application rates and the toxicity of applied pesticides to bees (Park et al. 2015), available for 28 datasets with a total of 6,667 individual pesticide applications.<br>ReferencesAlmeida-Neto, M. & Ulrich, W. (2011). A straightforward computational approach for measuring nestedness using quantitative matrices. <i>Environmental Modelling & Software</i>, 26, 173-178.Grab, H., Branstetter, M.G., Amon, N., Urban-Mead, K.R., Park, M.G., Gibbs, J.<i> et al.</i> (2019). Agriculturally dominated landscapes reduce bee phylogenetic diversity and pollination services. <i>Science</i>, 363, 282-284.Laliberté, E. & Legendre, P. (2010). A distance‐based framework for measuring functional diversity from multiple traits. <i>Ecology</i>, 91, 299-305.Magneville, C., Loiseau, N., Albouy, C., Casajus, N., Claverie, T., Escalas, A.<i> et al.</i> (2022). mFD: an R package to compute and illustrate the multiple facets of functional diversity. <i>Ecography, </i>2022, e05904.Park, M.G., Blitzer, E., Gibbs, J., Losey, J.E. & Danforth, B.N. (2015). Negative effects of pesticides on wild bee communities can be buffered by landscape context. <i>Proceedings of the Royal Society B</i>, 282, 20150299.Schmera, D., Legendre, P., Erős, T., Tóth, M., Magyari, E.K., Baur, B.<i> et al.</i> (2022). New measures for quantifying directional changes in presence-absence community data. <i>Ecological Indicators</i>, 136, 108618.Weekers, T., Marshall, L., Leclercq, N., Wood, T.J., Cejas, D., Drepper, B.<i> et al.</i> (2022). Dominance of honey bees is negatively associated with wild bee diversity in commercial apple orchards regardless of management practices. <i>Agriculture, Ecosystems & Environment</i>, 323, 107697.Woodcock, B.A., Garratt, M.P.D., Powney, G.D., Shaw, R.F., Osborne, J.L., Soroka, J.<i> et al.</i> (2019). Meta-analysis reveals that pollinator functional diversity and abundance enhance crop pollination and yield. <i>Nature Communications</i>, 10, 1481.<br><br><b>Description of the files</b>alpha_data: contains the main data used for the analysis of alpha diversity including measures of bee community diversity - Abundance (Abundance), species richness (Species.richness), rarefied species richness (Species.richness.rf), Functional diversity (Funct.div), functional MPD (Funct.mpd), functional evenness (Funct.eve), functional specialization (Funct.spec), phylogenetic diversity (Phyl.div), phylogenetic MPD (Phyl.mpd). Also included are both measures of pesticide hazard (HQ, Pesticide.intensity), semi-natural habitat (SNH), edge density (ED), the size of the focal field (Field.size), its crop type(Crop)and bee attractiveness (Bee.attractive). The data file additionally contains the Study ID (Study), Dataset ID (Dataset) and the continent (Continent) where the study was conducted).alpha_corr_coef_hq and alpha_corr_coef_snh: Contain the data used to create the Extended data Figure 2. This includes all types of pesticide hazard quotients (HQ) and semi-natural habitats in landscapes (SNH) and their correlation coefficients with different metrics of bee community diversity (Abundance, Species.richness, Functional.diversity, Phylogenetic.diversity).alpha_estimates_additive_models and alpha_estimates_interaction_models contain the model outputs from the models run in the code Knauer_etal_R_alpha used to create the forest plots.beta_wnodf_hq and beta_wnodf_snh contain the WNODF measures for each study measured along gradients of increasing pesticide HQ and decreasing proportions of SNH in landscapes respectively.beta_turnover_hq and beta_turnover_snh contain the measures of gaining and losing turnover (Gain.turn and Loss.turn) for each study, their standard deviation (SD.gain.turn and SD.loss.turn) and the study's sample size (N) along gradients of increasing pesticide HQ and decreasing proportions of SNH in landscapes respectively.beta_nestedness_hq and beta_nestedness_snh contain the measures of gaining and losing nestedness (Gain.nest and Loss.nest) for each study, their standard deviation (SD.gain.nest and SD.loss.nest) and the study's sample size (N) along gradients of increasing pesticide HQ and decreasing proportions of SNH in landscapes respectively.<br>