DOI: 10.5061/dryad.cfxpnvxb8
title: Data from: Global taxonomic, functional, and phylogenetic diversity of bees in apple orchards

description: An essential prerequisite to safeguard pollinator species is
 characterisation of the multifaceted diversity of crop pollinators and
 identification of the drivers of pollinator community changes across
 biogeographical gradients. The extent to which intensive agriculture is
 associated with the homogenisation of biological communities at large
 spatial scales remains poorly understood. In this study, we investigated
 diversity drivers for 644 bee species/morphospecies in 177 commercial
 apple orchards across 33 countries and four global biogeographical biomes.
 Our findings reveal significant taxonomic dissimilarity among
 biogeographical zones. Interestingly, despite this dissimilarity, species
 from different zones share similar higher-level phylogenetic groups and
 similar ecological and behavioural traits (i.e. functional traits), likely
 due to habitat filtering caused by perennial monoculture systems managed
 intensively for crop production. Honey bee species dominated orchard
 communities, while other managed/manageable and wild species were
 collected in lower numbers. Moreover, the presence of herbaceous,
 uncultivated open areas and organic management practices were associated
 with increased wild bee diversity. Overall, our study sheds light on the
 importance of large-scale analyses contributing to the emerging fields of
 functional and phylogenetic diversity, which can be related to ecosystem
 function to promote biodiversity as a key asset in agroecosystems in the
 face of global change pressures.
description: During the apple blooming season in 2019 (except Bhutan in 2020),
 we surveyed 177 commercial apple orchards in 33 countries covering six
 continents following a strict and standardised protocol combining netting
 and pan trapping (3 days). This datasets represents the all community
 matrix used in the article "Global taxonomic, functional, and
 phylogenetic diversity of bees in apple orchards. Each
 site was sampled for three days (consecutive if weather permitting) during
 the peak blooming period. Netting collection incorporated surveying all
 bee specimens seen directly visiting the blossoms over two 90 min sessions
 (morning and afternoon) per day, while walking through orchard rows.
 Passive sampling consisted of deploying of painted pan traps at 9 h00 each
 day, in three trios (fluorescent yellow, fluorescent blue, and white) on
 cleared ground. The pan traps were filled with soapy water and were
 collected at 4 h00. All<br>pan traps were painted at the Agroecology
 Lab (ULB, Belgium) then dispatched to each collaborator to ensure
 comparability of the results. In the present study, we
 only considered bee species as they are the<br>main pollinators of
 apple trees. Each bee specimen was identified by regional experts either
 to species or morphospecies level (except for the Bombus terrestris
 agg.<br>complex) depending on the available knowledge and
 identification tools in the specific country; this sometimes required
 sending of material for expert identification. We aggregated together the
 records of Andrena scotica and A. carantonica (named A. scotica in the
 dataset) due to taxonomic uncertainties. Morphospecies designations were
 specific to each country.
description: Csv file
description: This README file was generated on 2023-08-10 by Nicolas Leclercq. GENERAL
 INFORMATION 1. Title of Dataset: Global taxonomic, functional, and
 phylogenetic diversity of bees in apple orchards 2. Author Information A.
 Principal Author Contact Information Name: Nicolas Vereecken Institution:
 Universit Libre de Bruxelles Email: B.
 Associate Author Contact Information Name: Nicolas Leclercq Institution:
 Universit Libre de Bruxelles Email: 3.
 Date of data collection : 2019 (2020 for Bhutan) 4. Geographic location of
 data collection: World SHARING/ACCESS INFORMATION 1. Licenses/restrictions
 placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to
 publications that cite or use the data: N. Leclercq, L. Marshall, T.
 Weekers, P. Basu, D. Benda, D. Bevk, R. Bhattacharya, P. Bogusch, A.
 Bontutnaja, L. Bortolotti, N. Cabirol, E. Caldern-Uraga, R. Carvalho, S.
 Castro, S. Chatterjee, M. De La Cruz Alquicira, J.R. de Miranda, T.
 Dirilgen, A. Dorchin, K. Dorji, B. Drepper, S. Flaminio, J. Gailis, M.
 Galloni, H. Gaspar, M.W. Gikungu, B.A. Hatteland, I. Hinojosa-Diaz, L.
 Hostinsk, B.G. Howlett, K.-L.J. Hung, L. Hutchinson, R.O. Jesus, N.
 Karklina, M.S. Khan, J. Loureiro, X. Men, J.-M. Molenberg, S.
 Mudri-Stojni, P. Nikolic, E. Normandin, J. Osterman, F. Ouyang, A.S.
 Oygarden, L. Ozolina-Pole, N. Ozols, A. Parra Saldivar, R.J. Paxton, T.
 Pitts-Singer, K. Poveda, K. Prendergast, M. Quaranta, S.F.J. Read, S.
 Reinhardt, M. Rojas-Oropeza, C. Ruiz, M. Rundlf, A. Sade, C. Sandberg, F.
 Sgolastra, S.F. Shah, M.A. Shebl, V. Soon, D.A. Stanley, J. Straka, P.
 Theodorou, E. Tobajas, J.L. Vaca-Uribe, A. Vera, C.A. Villagra, M.-K.
 Williams, M. Wolowski, T.J. Wood, Z. Yan, Q. Zhang & N.J. Vereecken
 (2023). Global taxonomic, functional, and phylogenetic diversity of bees
 in apple orchards. Science of The Total Environment,901, 165933,
 1. Links to other
 publicly accessible locations of the data: None 2. Links/relationships to
 ancillary data sets: None 3. Was data derived from another source? No A.
 If yes, list source(s): NA 4. Recommended citation for this dataset: N.
 Leclercq, L. Marshall, T. Weekers, P. Basu, D. Benda, D. Bevk, R.
 Bhattacharya, P. Bogusch, A. Bontutnaja, L. Bortolotti, N. Cabirol, E.
 Caldern-Uraga, R. Carvalho, S. Castro, S. Chatterjee, M. De La Cruz
 Alquicira, J.R. de Miranda, T. Dirilgen, A. Dorchin, K. Dorji, B. Drepper,
 S. Flaminio, J. Gailis, M. Galloni, H. Gaspar, M.W. Gikungu, B.A.
 Hatteland, I. Hinojosa-Diaz, L. Hostinsk, B.G. Howlett, K.-L.J. Hung, L.
 Hutchinson, R.O. Jesus, N. Karklina, M.S. Khan, J. Loureiro, X. Men, J.-M.
 Molenberg, S. Mudri-Stojni, P. Nikolic, E. Normandin, J. Osterman, F.
 Ouyang, A.S. Oygarden, L. Ozolina-Pole, N. Ozols, A. Parra Saldivar, R.J.
 Paxton, T. Pitts-Singer, K. Poveda, K. Prendergast, M. Quaranta, S.F.J.
 Read, S. Reinhardt, M. Rojas-Oropeza, C. Ruiz, M. Rundlf, A. Sade, C.
 Sandberg, F. Sgolastra, S.F. Shah, M.A. Shebl, V. Soon, D.A. Stanley, J.
 Straka, P. Theodorou, E. Tobajas, J.L. Vaca-Uribe, A. Vera, C.A. Villagra,
 M.-K. Williams, M. Wolowski, T.J. Wood, Z. Yan, Q. Zhang & N.J.
 Vereecken (2023). Data from: Global taxonomic, functional, and
 phylogenetic diversity of bees in apple orchards. Dryad Digital
 Repository. DATA &
 FILE OVERVIEW 1. File List: A) Community_matrix.csv B) Species_list.csv 1.
 Relationship between files, if important: Community_matrix.csv contains
 sites' (apple orchard) information that were used in the study and
 abundances collected of all species/morphospecies.
 Species/morphospecies' information (phylogenetic and functional
 traits) are detailed in the Species_list.csv file. 2. Additional related
 data collected that was not included in the current data package: None 3.
 Are there multiple versions of the dataset? No A. If yes, name of file(s)
 that was updated: NA i. Why was the file updated? NA ii. When was the file
 updated? NA
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Community_matrix.csv 1. Number of
 variables: 663 (Either categorical: Sites' information or numerical:
 Latitude, Longitude and species/morphospecies abundances) 2. Number of
 rows: 177 (Sites sampled - apple orchards) 3. Variable List: * Sites:
 Sites' names/ID. The names are always computed using a 3 letters
 abreviation of the country of each site and a number. Sites are apple
 orchards sampled for the study in 2019. * Country: Country of each site *
 Sampler.identity: Sometimes different groups of people from different
 scientific teams sampled the same country/region. We differentiate those
 groups in this column. * Biogeograhical.zone: Biogeograhical zone of each
 site. We defined a biogeographical zone as a biome (Mediterranean &
 Xeric, Temperate, Tropical & Subtropical, and Mountain) within a
 biogeographical realm (Afrotropic, Australasia, West Palearctic, Central
 Palearctic, East Palearctic, Indomalayan, Nearctic, and Neotropic). We
 used the Resolve Ecoregions 2017 dataset (Dinerstein et al., 2017). We
 merged the following biomes into larger climate biomes to ensure
 sufficient replicates within each biogeographical zone: (i) all temperate
 forests, temperate grasslands, and tundra biomes into the Temperate biome;
 (ii) all tropical & subtropical forests and tropical & subtropical
 grasslands biomes into the Tropical & Subtropical biome; (iii)
 Mediterranean forests, woodlands & scrub and deserts & xeric
 shrublands biomes into the Mediterranean & Xeric biome. The Mountain
 biome was retained. Within the Palearctic realm, China and Pakistan sites
 were very distant from the rest of the locations (Europe, North Africa,
 and the Middle East), and therefore, are very likely to contain different
 bee assemblages (Michener, 2007). Therefore, we decided to divide the
 Palearctic realm into three parts: West Palearctic (Europe, North Africa,
 and the Middle East), Central Palearctic (Pakistan), and East Palearctic
 (China). * Latitude: Latitude (decimal degrees) * Longitude: Longitude
 (decimal degrees) * Management: Non-Organic or Organic management * Yield:
 Yield in 2018 (Ton/ha) - information given by the farmer (NA when
 unavailable) * Size: Size of the apple orchards (ha) - information given
 by the farmer (NA when unavailable) * Hives: Number of honeybee hives
 within the apple orchards - information given by the farmer (NA when
 unavailable) * Water: Proportion of water in a radius of 2000 m around
 sites - Land Use and Land Cover (LULC) proportions were extracted using
 2019 ESA Sentinel-2 imagery at 10 m resolution (Karra et al., 2021) *
 Water: Proportion of water in a radius of 2000 m around sites - Land Use
 and Land Cover (LULC) proportions were extracted using 2019 ESA Sentinel-2
 imagery at 10 m resolution (Karra et al., 2021) * Trees: Proportion of
 trees in a radius of 2000 m around sites - Land Use and Land Cover (LULC)
 proportions were extracted using 2019 ESA Sentinel-2 imagery at 10 m
 resolution (Karra et al., 2021) * Crops: Proportion of crop in a radius of
 2000 m around sites - Land Use and Land Cover (LULC) proportions were
 extracted using 2019 ESA Sentinel-2 imagery at 10 m resolution (Karra et
 al., 2021) * Built_Area: Proportion of built area in a radius of 2000 m
 around sites - Land Use and Land Cover (LULC) proportions were extracted
 using 2019 ESA Sentinel-2 imagery at 10 m resolution (Karra et al., 2021)
 * Bare_Ground: Proportion of bare ground area in a radius of 2000 m around
 sites - Land Use and Land Cover (LULC) proportions were extracted using
 2019 ESA Sentinel-2 imagery at 10 m resolution (Karra et al., 2021) *
 Rangeland: Proportion of rangeland in a radius of 2000 m around sites -
 Land Use and Land Cover (LULC) proportions were extracted using 2019 ESA
 Sentinel-2 imagery at 10 m resolution (Karra et al., 2021) *
 Flooded_Vegetation: Proportion of flooded vegetation in a radius of 2000 m
 around sites - Land Use and Land Cover (LULC) proportions were extracted
 using 2019 ESA Sentinel-2 imagery at 10 m resolution (Karra et al., 2021)
 * Clouds: Proportion of clouds in a radius of 2000 m around sites - Land
 Use and Land Cover (LULC) proportions were extracted using 2019 ESA
 Sentinel-2 imagery at 10 m resolution (Karra et al., 2021). When
 information was not available due to clouds, land was categorized as
 clouds. * Snow_Ice: Proportion of snow and ice in a radius of 2000 m
 around sites - Land Use and Land Cover (LULC) proportions were extracted
 using 2019 ESA Sentinel-2 imagery at 10 m resolution (Karra et al., 2021)
 *Then all 644 species/morphospecies scientific names (from
 Agapostemon.cockerelli to Xylocopa.virginica): Abundance of each
 species/morphospecies collected in each site. Genus and species are
 separated by a full stop. Scientific names match the "Binomial"
 column in the Species_list.csv file. 4. Missing data codes: None 5.
 Specialized formats or other abbreviations used: None
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Species_list.csv 1. Number of variables: 14
 (categorical variables: phylogenetic and functional traits information) 2.
 Number of cases/rows: 644 (Species/morphospecies) 3. Variable List: *
 Binomial: Bee species/morphospecies scientific name. Morphospecies
 designations were specific to each country (subgenus provided when
 available). * Superfamily: Apoidea superfamily * Position: Phylogenetic
 relatedness between families (Col+Hali: Colletidae + Halictidae; Api+Meg:
 Apidea + Megachilidae; And: Andrenidae) * Family: Bee families *
 Subfamily: Bee subfamilies * Tribe: Bee tribes * Genus: Bee genera *
 Subgenus: Bee subgenera * Managed: Species either considered as wild
 species or managed/manageable species in the study * Size:
 Small:inter-tegular distance (ITD) &lt; 2 mm; medium: 2 mm ITD 3 mm; and
 large: ITD &gt; 3 mm * Nesting: Nesting type (above-ground, below-ground,
 both below and aboveground) * Sociality: Sociality (cleptoparasite,
 communal, eusocial, primitively eusocial, primitively social, social
 parasite, solitary, solitary and communal, solitary and primitively
 social) * Pollen: Pollen transportation (abdomen, accidental, corbiculae,
 crop, legs, both legs and body) * Tongue: Tongue length (short, long) 4.
 Missing data codes: NA (data not available) 5. Specialized formats or
 other abbreviations used: None
 \#########################################################################