README: Honey bees (Apis mellifera) modify plant-pollinator network structure, but do not alter wild species interactions

#Abstract

Honey bees (Apis mellifera) are widely used for honey production and crop pollination,
raising concern for wild pollinators, as honey bees may compete with wild pollinators
for floral resources. The first sign of competition, before changes appear in wild
pollinator abundance or diversity, may be changes to wild pollinator interactions with
plants. Such changes for a community can be measured by looking at changes to
metrics of resource use overlap in plant-pollinator interaction networks. Studies of
honey bee effects on plant-pollinator networks have usually not distinguished whether
honey bees alter wild pollinator interactions, or if they merely alter total network
structure by adding their own interactions. To test this question, we experimentally
introduced honey bees to a Canadian grassland and measured plant-pollinator
interactions at varying distances from the introduced hives. We found that honey bees
increased the network metrics of pollinator and plant functional complementarity and
decreased interaction evenness. However, in networks constructed from just wild
pollinator interactions, honey bee abundance did not affect any of the metrics
calculated. Thus, all network structural changes to the full network (including honey
bee interactions) were due only to honey bee-plant interactions, and not to honey bees
causing changes in wild pollinator-plant interactions. Given widespread and increasing
use of honey bees, it is important to establish whether they affect wild pollinator
communities. Our results suggest that honey bees did not alter wild pollinator foraging
patterns in this system, even in a year that was drier than the 20-year average.

#Summary of methods

In southern Alberta, Canada we established eighteen 30 x 2 m transects at 100 m, 500 m, and 5000 m distances on either
side of each of 3 clusters of honey bee hives for a total of six replicates. Between May 28 and August 28, 2019, observers
visited each transect and surveyed insect flower visitation almost once per week for a
total of 10 collection rounds. All insects thatvisibly contacted the anthers or stigma of open flowers were
collected with a hand net and placed in labelled individual vials, frozen, and identified to species in the lab.
Associated flowers were identified to species. The data were entered in Excel and processed and cleaned in R / Rstudio.

The data provided includes interaction data from nineteen transects (originally 18 but F5000 was replaced with G5000 mid-season). Interactions are recorded between pollinators and plants and the dataset also includes flower
species abundance data for each transect sampled. Additionally, transect locations and locations of the bee hives placed are included.

A total of 281 pollinator species and 37 plant species were identified in 1,814 interactions.

Later, some of the pinned insect specimens' body sizes were measured and contributed to the paper: "Pollinator intraspecific body size variation and sociality influence their interactions with plants". 2024. Functional Ecology. Authored by Peralta, Guadalupe; Resasco, Julian; Worthy, Sydney; Frost, Carol; Guevara, Angie; Manning, Isabella; Cagnolo, Luciano; Burkle, Laura.

To take body size measurements, the selected specimens were photographed from the dorsal side with a Nikon COOLPIX 8400 Digital Camera mounted on an OLYMPUS SZX16 stereo microscope. A ruler was placed adjacent to and in the same plane as the insect’s dorsal surface during photography. The images were then imported into ImageJ, calibrated using the ruler as a scale bar, and measured using the line tool to manually delineate the intertegular distance, which is the distance spanning between the wing bases. Only intergegular distances were analyzed in the above paper. However, other distances measured for some specimens included: thorax length (as viewed dorsally and measured along the midpoint), head width, head length, abdomen length, and body length.

Description of the data and file structure

Location information:

The data were obtained on the University of Alberta's Mattheis Research Ranch and surrounding land administered by Eastern Irrigation District, which is in mixedgrass prairie rangeland near the town of Brooks, Alberta, Canada;
GPS locations of sampling coordinates are listed in the sheet called "Transect Locations 2019" along with the number of collection rounds (Each number corresponds to one sampling pass through all the transects that were possible to sample in that round; one week of sampling). The bee hives did not have a collection round and so have NA in their cell.

Data is in excel spreadsheet format.

Column header titles for each excel spreadsheet tab:

#Transect Locations 2019
Longitude - Longitude of the transect or bee hive cluster. Measured with Garmin handheld GPS.
Latitude - Latitude of the transect or bee hive cluster. Measured with Garmin handheld GPS.
Transect - Name of the transect or bee hive cluster. The number at the end of each name refers to the number of hives in the bee hive cluster, or the distance of the transect from the nearest bee hive cluster (in metres), respectively.
Total Hand-Caught Collections - Number of times this transect was sampled in 2019 by netting flower visitors along the 30-m x 2-m transect for 30 min by 2 observers.

#Transect Flower Counts 2019
Date_DMY - Date that the transect was sampled by Date, Month, Year
Collection - This variable is another way of recording the date, with 1 corresponding to the first sampling date, 2 corresponding to the second sampling date, etc., throughout the whole season.
Season - Early, Mid, or Late "season". Rationale for these divisions based on abundance of honey bees (see Worthy et al., 2023, PLOS ONE )
Transect_ID - Transect name. The number at the end of each name refers to the distance of the transect from the nearest bee hive cluster (in metres), though some transects named as 5000 were more than 5000 m from the nearest hive cluster.
Treatment - Distance of the transect from the nearest hive cluster. For some t5000 replicates, the transect was greater than 5000 m from the nearest hive cluster.
Plant_ID - Plant species or morphospecies. Each row represents an individual plant found on the transect with flowers.
Flower_count - Number of flowers counted (or estimated) for that plant individual.

#Interaction Data 2019
Date_DMY - Date that the transect was sampled by Date, Month, Year
Collection - This variable is another way of recording the date, with 1 corresponding to the first sampling date, 2 corresponding to the second sampling date, etc., throughout the whole season.
Coll_round - Each number corresponds to one sampling pass through all the transects that were possible to sample in that round.
Season - Early, Mid, or Late "season". Rationale for these divisions based on abundance of honey bees (see Worthy et al., 2023, PLOS ONE)
Transect_ID - Transect name. The number at the end of each name refers to the distance of the transect from the nearest bee hive cluster (in metres), though some transects named as 5000 were more than 5000 m from the nearest hive cluster.
Treatment - Distance of the transect from the nearest hive cluster. For some t5000 replicates, the transect was greater than 5000 m from the nearest hive cluster.
Temp_C - Temperature (degrees C). Measured with a handheld Brunton Sherpa before starting to sample the transect.
Wind_km - Wind speed (km/hr). Measured with a handheld Brunton Sherpa before starting to sample the transect.
Pressure_kPa - Pressure (kPa). Measured with a handheld Brunton Sherpa before starting to sample the transect.
Insect_ID - Unique ID number for this insect. Number composed of the date on which the insect was collected visiting a flower, a dash, and then a number representing what number individual this was. E.g., -3 means the third insect collected at that transect on that date.
Plant_ID - Plant species name
Species_Comm - Insect species group common name
Species_ID - Insect species or morphospecies name. Genus names are capitalized. Specific epithets are not capitalized. When a name contains two capitalized names, that insect genus ID was undecided between those two genera. NA refers to insects that were observed but unidentifiable (usually because they escaped the net).
Order.group - Latin name for species group (with groupings at different taxonomic levels but generally at the level of Order)
Plant_no - Number corresponding to that plant species (for graphing and analysis)
Species_no - Number corresponding to that insect species (for graphing and analysis)

#Measurements

Insect_ID - Unique (within a transect) ID number for this insect. Number composed of the date on which the insect was collected visiting a flower, a dash, and then a number representing what number individual this was. E.g., -3 means the third insect collected at that transect on that date.

Species_ID - Insect species or morphospecies name. Genus names are capitalized. Specific epithets are not capitalized. When a name contains two capitalized names, that insect genus ID was undecided between those two genera.

Included in Peralta et al 2024 - "Yes" or "No", indicating whether the thorax width measurement was included in the data set analyzed in Peralta et al 2024 (Functional Ecology) or not

Thorax Width (mm) - Thorax width (intertegular distance) measured as described above in the methods, in mm.

Thorax length (mm) - The longitudinal measurement of the thorax from the point where it meets the head to where it meets the abdomen, in mm. VNA (Value Not Available) indicates that this value was not measured.

Head width (mm) - Maximum width of the head (lateral body axis, viewed dorsally), in mm. VNA (Value Not Available) indicates that this value was not measured.

Head length (mm) - The distance from the anterior-most point of the head to the posterior-most point (viewed dorsally), in mm. VNA (Value Not Available) indicates that this value was not measured.

Abdomen length (mm) - The length of the abdomen from its anterior junction with the thorax to its posterior end, in mm. VNA (Value Not Available) indicates that this value was not measured.

Body length (mm) - Distance from the tip of the head to the tip of the abdomen, in mm. VNA (Value Not Available) indicates that this value was not measured.

Sharing/Access information

Not applicable

Code/Software

Excel was used to enter the data and R was used to clean and analyze the data and produce visual graphics.

Packages in R used:
bipartite - to analyze network data
dplyr
tidyverse
SpadeR
MuMin
vegan
ggplot2
nlme
MASS
lme4
lmerTest