Data from: Global taxonomic, functional, and phylogenetic diversity of bees in apple orchards
Data files
Aug 11, 2023 version files 369.50 KB
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Community_matrix.csv
263.82 KB
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README.md
11.02 KB
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Species_list.csv
94.66 KB
Aug 11, 2023 version files 369.34 KB
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Community_matrix.csv
263.82 KB
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README.md
10.87 KB
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Species_list.csv
94.66 KB
Abstract
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.
This README file was generated on 2023-08-10 by Nicolas Leclercq.
GENERAL INFORMATION
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Title of Dataset: Global taxonomic, functional, and phylogenetic diversity of bees in apple orchards
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Author Information
A. Principal Author Contact Information
Name: Nicolas Vereecken
Institution: Universit Libre de Bruxelles
Email: nicolas.vereecken@ulb.beB. Associate Author Contact Information
Name: Nicolas Leclercq
Institution: Universit Libre de Bruxelles
Email: nicolas.leclercq@ulb.be -
Date of data collection : 2019 (2020 for Bhutan)
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Geographic location of data collection: World
SHARING/ACCESS INFORMATION
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Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
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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, https://doi.org/10.1016/j.scitotenv.2023.165933
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Links to other publicly accessible locations of the data: None
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Links/relationships to ancillary data sets: None
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Was data derived from another source? No
A. If yes, list source(s): NA -
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. https://doi.org/10.5061/dryad.cfxpnvxb8
DATA & FILE OVERVIEW
- File List:
A) Community_matrix.csv
B) Species_list.csv
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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.
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Additional related data collected that was not included in the current data package: None
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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
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DATA-SPECIFIC INFORMATION FOR: Community_matrix.csv
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Number of variables: 663 (Either categorical: Sites’ information or numerical: Latitude, Longitude and species/morphospecies abundances)
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Number of rows: 177 (Sites sampled - apple orchards)
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Variable List:
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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.
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Country: Country of each site
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Sampler.identity: Sometimes different groups of people from different scientific teams sampled the same country/region. We differentiate those groups in this column.
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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)
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Longitude: Longitude (decimal degrees)
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Management: Non-Organic or Organic management
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Yield: Yield in 2018 (Ton/ha) - information given by the farmer (NA when unavailable)
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Size: Size of the apple orchards (ha) - information given by the farmer (NA when unavailable)
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Hives: Number of honeybee hives within the apple orchards - information given by the farmer (NA when unavailable)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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.
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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.
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Missing data codes: None
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Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: Species_list.csv
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Number of variables: 14 (categorical variables: phylogenetic and functional traits information)
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Number of cases/rows: 644 (Species/morphospecies)
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Variable List:
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Binomial: Bee species/morphospecies scientific name. Morphospecies designations were specific to each country (subgenus provided when available).
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Superfamily: Apoidea superfamily
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Position: Phylogenetic relatedness between families (Col+Hali: Colletidae + Halictidae; Api+Meg: Apidea + Megachilidae; And: Andrenidae)
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Family: Bee families
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Subfamily: Bee subfamilies
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Tribe: Bee tribes
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Genus: Bee genera
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Subgenus: Bee subgenera
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Managed: Species either considered as wild species or managed/manageable species in the study
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Size: Small:inter-tegular distance (ITD) < 2 mm; medium: 2 mm ITD 3 mm; and
large: ITD > 3 mm -
Nesting: Nesting type (above-ground, below-ground, both below and aboveground)
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Sociality: Sociality (cleptoparasite, communal, eusocial, primitively eusocial, primitively social, social parasite, solitary, solitary and communal, solitary and primitively social)
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Pollen: Pollen transportation (abdomen, accidental, corbiculae, crop, legs, both legs and body)
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Tongue: Tongue length (short, long)
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Missing data codes: NA (data not available)
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Specialized formats or other abbreviations used: None
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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
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
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.
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.
Csv file