Urban bumblebees diversify their foraging strategy to maintain nutrient intake
Data files
Apr 28, 2025 version files 280.08 KB
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Bumblebee_diet_PRSB.zip
262.06 KB
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README.md
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Abstract
Anthropogenic ecosystems can alter individual functions and ecological processes such as resource use and species interactions. While variability on morphological traits involved in dietand resource use has been observed between urban and non-urban populations of pollinators, theconsequences on the dietary and pollen transportation patterns remain poorly understood. Here, we investigate the variability in the diet breadth of rural and urban individuals of two bumblebeespecies and the consequences for nutrient intake and pollen transportation. We show that urbanbumblebees exhibit a broader diet breadth than their rural counterparts, driven by the enhancedfloral diversity in cities. However, we found that the nutrient intake remained similar across urbanand rural ecosystems. Finally, we found distinct pollen transportation patterns between urban andrural individuals. Our findings highlight the importance of considering complementary facets of species’ diet and interactions when assessing the effects of anthropogenic ecosystems.
title: "README"
output: html_document
date: "2024-10-30"
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https://doi.org/10.5061/dryad.59zw3r2jn
General information
The following repository includes the necessary information regarding the data and code to repeat the analyses for the manuscript "Urban bumblebees diversify their foraging strategy to maintain nutrient intake". The repository Dryad repository provides the process data, the R project structure, and the code. The raw data that is also necessary is archived externally (repository ENVIDAT and NCBI) but described in this repository with guidance on how to download it and re-use it in the sections below.
This dataset has been generated following intraspecific trait measurements on bumblebees (published in Eggenberger et al., 2019, https://doi.org/10.1111/1365-2656.13051), DNA metabarcoding and pollen chemistry analyses on amino acids and fatty acids (methods and data published in https://doi.org/10.1038/s41597-025-04585-w), and plant traits (methods and data published in https://doi.org/10.1038/s41597-025-04585-w). DNA reads from the metabarcoding analyses were uploaded and archived in the National Centre of Biotechnology Information (NCBI) (https://identifiers.org/ncbi/insdc.sra:SRP520777). Metabarcoding data, chemical pollen data and plant traits are archived in the ENVIDAT repository (https://www.doi.org/10.16904/envidat.532).
Corresponding author information
Name: Joan Casanelles Abella
Orcid: 0000-0003-1924-9298
Affiliation: Urban Productive Ecosystems, Technical University of Munich, Freising, Germany
email: joan.casanelles@tum.de
Alternative contact information
Name: Marco Moretti
Orcid: 0000-0002-5845-3198
Affiliation: Biodiversity and Conservation, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
email: marco.moretti@wsl.ch
Associated publication
Selva, S.; Moretti, M.; Ruedenauer, F.A.; Keller, A.; Fournier, B.; Leonhardt, S.D.; Eggenberger, H.; Casanelles-Abella, J. Urban bumblebees diversify their foraging strategy to maintain nutrient intake
Description of the data and file structure
Project structure
The compressed file "Bumblebee_diet_PRSB" contains three main directories, that is, "Data", "Code" and "output" and a series of subfolders in the following, hierarchical structure, necessary to run the scripts, load the data and produce the output:
Bumblebee_diet
├── Data
│ ├── bumblebee_traits
│ ├── Metabarcoding
│ ├── Nutrient_intake
│ ├── Site_description
├── Code
├── output
│ ├── figures
│ │ ├── figure_1
│ │ ├── figure_2
│ │ ├── figure_3
│ │ ├── figure_4
│ │ ├── figure_5
│ │ ├── figure_6
│ │ ├── figure_7
│ │ ├── figure_s3
│ │ ├── figure_s4
│ │ ├── figure_s5
│ │ ├── figure_s6
│ │ ├── figure_s7
│ │ ├── figure_s8
│ │ ├── figure_s9
│ │ ├── figure_s10
│ │ ├── figure_s11
│ │ ├── figure_s12
│ ├── phylogeny
│ ├── psems
│ ├── tables
│ │ ├── FD
- Directory "Code" contains the R scripts. They are described in the section "Code" below in this README
- Directory "Data" contains four subdirectories (bumblebee traits, Metbarcoding, Nutrientintake, Site_description) that either contain data or have to be populated with external files archived in the repository ENVIDAT. Instructions for downloading the files and where to place them is explained in the section "REQUIRED DATA/External Data" below in this README.
- Directory "output" contains four subdirectories (figures, phylogeny, psems and tables), which are empty and will be automatically populated when running the scripts.
Provided data in this repository
Bumblebee morphological traits
Filename: Bumblebee_Data_Eggenberger_et.al_JAE_2019.csv
Location: This dataset is found under the following path: Data/bumblebee_traits/
Description: The following dataset contains the measurements of the morphological traits from Eggenberger et al. 2019 (https://doi.org/10.1111/1365-2656.13051). The dataset in a CSV file and is structured as described below:
ID: Identification code for the bumblebees, one bumblebee individual for each ID
Number: bumblebee number
Species: the two bumblebee species, with levels B.p = B. pascuorum; B.l = B.lapidarius
Date: Collection date, DD.MM.YY
x: X coordinate LV95
y: y coordinate LV95
City: canton, with levels Zürichm Bern and Basel
Site: replicate, with levels ZH-A to ZH-E (for Zurich); BS-A to BS-E (for Basel). BE-A to BE-D (for Bern)
Rural_Urban: with levels ZH-urban and ZH-rural (for Zurich), BS-urban and BS-rural (for Basel), BE-urban and BE-rural (for Bern)
Habitat: landscape type, urban or rural
Intertegular_distance: distance between the two tegulas (in mm)
Glossa: length glossa (in mm)
Prementum: length premetum (in mm)
Proboscis_length: length proboscis (in mm)
proboscis_ratio: ratio proboscis and ITD
fore_wing_length: length of the fore wing (in mm)
fore_wing_ratio: ratio fore wing and ITD
corbicula_length: length of the corbicula (in mm)
corbicula_ratio: ratio corbicula and ITD
Processed metabarcoding data with plant traits
Filename: Metabarcoding_data_traits.csv
Location: This dataset is found under the following path: Data/Metabarcoding/
Description: The following dataset is a CSV file and contains the plant species list found in the pollen loads of the bumblebees in the corbicula and body structures. For each plant, a list of seven traits are provided.
ID: Combining bumblebee ID, location, landscape and replica
site: contains the location, landscape and replicate
plant.speices: full scientific plant name
location: region (Canton) of sampling, with levels BE (Bern), ZH -(Zurich) and BS (Basel).
landscape: urban (U) or rural (R)
replicate: sampling site within a location and landscape, identified with the letters A-E.
bbspecies: two bumblebee species, B.pascuorum and B.lapidarius
bborgan: pollen transportation organ, two levels: leg-baskets (L) and body (B).
Kingdom: taxonomic level.
Phylum: taxonomic level.
Order: taxonomic level.
Family: taxonomic level.
Genus: taxonomic level.
Species: full scientific name.
Abundance: relative abundance.
native_exotic: origin status.
pollination mode: vector of pollination.
Flowering_months_duration: Number of flowering months.
start_flowering: month of the starting of the flowering.
growth_form_category: plant growth form.
growth_form_numeric: numeric values for the growth form.
plant-height: plant height in meters.
reference: specific reference for traits when applicable. NA refers to not applicable.
inflorescence: Logic, plant with single flowers (0) or inflorescences (1). essibility of the flowers.
structural_blossom_class: depicting the accessibility of the flowers.
structural_blossom_numeric: numeric values for the structural blossom class.
symmetry: floral symmetry.
symmetry_numeric: numeric values for the symmetry.
nectar: logic, nectar present.
pollen: logic, pollen rewards present.
oil: logic. oil present.
sugar.concentration: the amount of sugar present in the nectar, in mg.
Externally archived data
The following files are archived in the repository EnViDAT under the doi: https://www.doi.org/10.16904/envidat.532 and must be downloaded directly from there and added in the specified folders within the R project as described below.
Site description
Filename: Dataset2_sites.csv
Location: This dataset has to be added: Data/Site_description/
Description: The dataset contains the information on the 16 study sites. The columns are:
Location: the three Swiss cantons studied. Levels: Bern =BE; Basel = BS; Zurich =ZH
Landscape: the two types of human-dominated ecosystems, nested to the Swiss canton. Levels: Urban = U; Rural = R
Replicate: sampling place (800-m buffer) nested with the location and the landscape. Levels: A-E.
Site_ID: combination of location, landscape and replicate
X: X coordinate, WGS84
Y: Y coordinate WGS84
Plant S in landscape: Plant species richness within the 800 m calculated using both information from the Global Biodiversity Information. Facility (GBIF) and InfoFlora ([www.infoflora.ch](http://www.infoflora.ch)).
% Buildings: the proportion of buildings and other impervious surfaces within 800 m radius.
% Agricultural: the proportion of agricultural land and other impervious surfaces within 800 m radius.
% Water: the proportion of water and other impervious surfaces within 800 m radius.
% Meadows & grasslands: the proportion of meadows and grasslands and other impervious surfaces within 800 m radius.
Amino acid data
Filename: Dataset3_Aminoacids.csv
Location: This dataset has to be added: Data/Nutrient_intake/
Description: The dataset contains the amino acid content and ratios for the two bumblebees. The columns are:
SampleID_chemical: The ID for chemical analyses
Location: the three Swiss cantons studied. Levels: Bern =BE; Basel = BS; Zurich =ZH
Landscape: the two types of human-dominated ecosystems, nested to the Swiss canton. Levels: Urban = U; Rural = R
Replicate: sampling place (800-m buffer) nested with the location and the landscape. Levels: A-E.
Bumblebee_species: the two studied species, levels: B.pasquorum; B. lapidarius
LocationLandscape: Combining location and landscape
Asp, Thr, ..., Arg: Content of individual amino acids. Amino acids are written as abbreviated names. Full names can be checked here: [https://en.wikipedia.org/wiki/Amino_acid](https://en.wikipedia.org/wiki/Amino_acid)
sum: total sum of amino acid content (mg)
sumessential: total sum essential amino acids (mg)
sumnon-essential: total sum non-essential amino acids (mg)
proportionnonessentialessential: proportion between essential and non-essential amino acids.
Fatty acid data
Filename: Dataset4_Fattyacids.csv
*Location: *This dataset has to be added: Data/Nutrient_intake/
Description: The dataset contains the fatty acid content and ratios for the two bumblebees. The columns are:
SampleID_chemical: The ID for chemical analyses
Location: the three Swiss cantons studied. Levels: Bern =BE; Basel = BS; Zurich =ZH
Landscape: the two types of human-dominated ecosystems, nested to the Swiss canton. Levels: Urban = U; Rural = R
Replicate: sampling place (800-m buffer) nested with the location and the landscape. Levels: A-E.
Bumblebee_species: the two studied species, levels: B.pasquorum; B. lapidarius
LocationLandscape: combination between location and landscape
Caprylic, Pelargonic, ..., Lacceroic: Content of individual fatty acids.
sum: total sum of fatty acid content (mg)
unsaturatedsum: total sum unsaturated fatty acids (mg)
saturatedsum: total sum saturated fatty acids (mg)
omega3sum: total sum Omega 3 fatty acids (mg)
omega6sum: total sum Omega 6 fatty acids (mg)
omega9sum: total sum Omega 9 fatty acids (mg)
omega6to3ratio: ratio Omega 6 to Omega3 fatty acids
-saturatedtounsaturatedration: ratio between saturated and unsaturated fatty acids
Taxonomic diversity
Filename: Dataset5_Species_richness.csv
*Location: *This dataset has to be added: Data/Metabarcoding/
Description: Processed data. The dataset contains the plant species richness in the leg-baskets per bumblebee individual. The columns are:
SampleID: Combining bumblebee ID, location, landscape and replica
Location: canton, levels: Bern =BE; Basel = BS; Zurich =ZH
Landscape: landscape type, levels: Urban = U; Rural = R
Replicate: sampling place (800-m buffer) within location and landscape. Levels: A-E.
LocationLandscape: combining location and landscape
Bumblebee_species: the two studied species, levels: B.pasquorum; B. lapidarius
Plant species richness: the number of plant species found in the pollen of the leg-baskets.
Functional diversity
Filename: Dataset6_Functional_Diversity.csv
*Location: *This dataset has to be added: Data/Metabarcoding
Description: The dataset contains the functional diversity metrics based on the plant composition from the leg-baskets per bumblebee individual. The columns are:
SampleID: Combining bumblebee ID, location, landscape and replica
Location: canton, levels: Bern =BE; Basel = BS; Zurich =ZH
Landscape: landscape type, levels: Urban = U; Rural = R
Replicate: sampling place (800-m buffer) within location and landscape. Levels: A-E.
LocationLandscape: combining location and landscape
Bumblebee_species: the two studied species, levels: B.pasquorum; B. lapidarius
Fric.w: Weighted functional richness
-Fric: functional richness
-FEve.w: Weighted functional evenness
FEve: functional evenness
FDiv.w: weighted functional divergence
FDiv: functional divergence
Phylogenetic diversity
Filename: Dataset7_Phylogenetic_Diversity.csv
Location: This dataset has to be added: Data/Metabarcoding/
Description: The dataset contains the phylogenetic diversity metrics based on the plant composition from the leg-baskets per bumblebee individual. The columns are:
SampleID: Combining bumblebee ID, location, landscape and replica
Location: canton, levels: Bern =BE; Basel = BS; Zurich =ZH
Landscape: landscape type, levels: Urban = U; Rural = R
Replicate: sampling place (800-m buffer) within location and landscape. Levels: A-E.
LocationLandscape: combining location and landscape
Bumblebee_species: the two studied species, levels: B.pasquorum; B. lapidarius
PVar: phylogenetic variance
PRic: Phylogenetic richness
PEve: Phylogenetic evenness
PClu: Phylogenetic clustering
Sharing/Access information
- Bumblebee morphological traits. Derived from:
* Eggenberger et al., 2019, Journal of Applied Ecology ([https://doi.org/10.1111/1365-2656.13051](https://doi.org/10.1111/1365-2656.13051))
- Plant traits: Derived from:
* Casanelles-Abella et al. 2021, Data in Brief (<https://doi.org/10.1016/j.dib.2021.107243>)
* Filipiak et al., 2022, Ecology (<https://doi.org/10.1002/ecy.3705>)
* Tew et al., 2023, Ecological Solutions and Evidence (<https://doi.org/10.1002/2688-8319.12248>)
- Plant species richness at 1500m radius. Derived from:
* GBIF, 2022:Occurrence Download. The Global Biodiversity Information Facility. <https://doi.org/10.15468/DL.KKWG72>
* InfoFlora, 2022: The National Data and Information Center on the Swiss Flora (Swiss National Databank of Vascular Plants) [Data set]. (<https://www.infoflora.ch>) Data is available under request.
- Raw metabarcoding reads. Archived in:
* PRJNA1137320(https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1137320)
* National Centre of Biotechnology Information (NCBI) ([https://identifiers.org/ncbi/insdc.sra:SRP520777](https://identifiers.org/ncbi/insdc.sra:SRP520777))
- Raw data: archived at the repository EnviDAT (https://www.doi.org/10.16904/envidat.532)
Code
The R scripts provided were written in R Version 4.2.1. The scripts include the following:
* A01_Diet_breadth_descriptive.R:
* Description:the R script produces supplementary plots on diet breadth
* Input: Metabarcoding_data_traits.csv
* A02_Diet_breadth_contrasts.R:
* Description: the R script computes the contrasts between the
taxonomic, functional and phylogenetic diversity metrics between
urban and rural landscapes for both bumblebee species The script
also perfoms the Chi-squared test on the proportion of plant
trait levels between urban and rural populations for the two
bumblebee species.
* Input: Metabarcoding_data_traits.csv;
Dataset6_Functional_Diversity.csv;
Dataset7_Phylogenetic_Diversity.csv
* A03.Diet_breadth_psem.R:
* Description: The script calculates the psems for taxonomic,
functional and phylogenetic metrics. It produces the results for
* Input: Metabarcoding_data_traits.csv;
Dataset5_Species_richness.csv;
Dataset6_Functional_Diversity.csv;
Dataset7_Phylogenetic_Diversity.csv;
Data/bumblebee_traits/Bumblebee_Data_Eggenberger_et.al_JAE_2019.csv
* A04_Plots_pSEM.R:
* Description: the scrip produces the plots pSEM analyses
* Input: Metabarcoding_data_traits.csv;
Dataset5_Species_richness.csv;
Dataset6_Functional_Diversity.csv;
Dataset7_Phylogenetic_Diversity.csv;
Data/bumblebee_traits/Bumblebee_Data_Eggenberger_et.al_JAE_2019.csv
* A06_Nutrient_intake.R:
* Description: the script calculates the contrasts of the
aminoacids and fatty acid metrics used to infer nutrients
intake, separately for the two bumblebee species.
* Input: Dataset4_Aminoacids.csv; Dataset4_Fattyacids.csv
* A07_tranportation_pollen.R
* Description: the script analyses the pollen transportation
patterns and networks.
* Input: Metabarcoding_data_traits.csv
* D01_Calculate_functional_phylogenetic_metrics.R
* Description: the script calculates the functional and phylogenetic metrics