Data and R code for: Up high, hot and dry: individual reproductive output in subalpine bees declines with increasing drought severity
Data files
May 27, 2026 version files 3.54 MB
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data_and_scripts_gcb_wong_et_al_2025.zip
3.48 MB
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README.md
62.90 KB
Abstract
Wild bees play indispensable ecological roles in many ecosystems, yet declines in many species have been documented in recent years. These declines have been linked to numerous anthropogenic pressures, including climate change, which can influence bee populations directly (i.e., via physiological mechanisms) and indirectly (e.g. through changes to floral resource quantity and quality). Widespread changes in the distributions and abundances of many bee species have been linked to climate change at large spatial scales; yet the local-scale processes that generate these broad-scale patterns are little known. Specifically, it is unclear how climate change influences the fitness of individual bees, despite the fact that broad-scale patterns of decline must be driven by individual-level processes. Our study examines the individual fitness responses (i.e. reproductive output) of five solitary bee species in the genus Osmia to variation in local climate variables in subalpine habitats. Over nine years, we tracked brood cell production in over 700 individual female bees, conducted repeated surveys of floral abundance (while taking into account the specific floral host taxa used by each bee species), and recorded local precipitation and temperature at seven sites. Our data revealed both direct and indirect (floral resource-mediated) negative effects of drought: the total number of brood cells produced by nesting females decreased significantly in summers characterized by greater drought severity and high temperatures—a relationship driven partly by significant decreases in floral host-plant availability in hotter and drier years. Our study highlights how the negative consequences of climate change for bee populations can manifest at the level of individuals and the role of floral resources in mediating these relationships. Overall, our results suggest that the increasingly warm and dry conditions forecasted for our study area will have net negative effects on the demographic success of these solitary bees.
All data (raw and compiled for analysis) and R codes (for compilation, analysis, and data visualization) associated with this article are contained herein.
Global Change Biology, 2025
Lydia H. Wong, Brian D. Inouye & Jessica R. K. Forrest
Correspondence:
lwong014@uottawa.ca
This README file describes the data package in the folder
"data_and_scripts_gcb_wong_et_al_2025.zip" which accompanies the above
publication. The RStudio Project file "data_and_scripts_gcb_wong_et_al_2025.Rproj" automatically sets the working directory to the folder containing the appropriate folders if using RStudio.
File structure and organization
The folder and associated R project file:
data_and_scripts_wong_and_forrest_ecol_2026 contains two sub-folders:
(1) data and (2) scripts. The data folder contains two
sub-folders (i) raw and (ii) compiled. The work-flow is as
follows:
- The R script
scripts > data_compilation.Rreads in comma-separated
value (CSV) files containing raw data located in thedata > raw
sub-folder. The script performs various procedures to compile the
raw data (e.g., calculate means, combine data across data sets). It
then produces several CSV files containing the compiled data to the
data > compiledsub-folder. - The R scripts in the
scriptsfolder that have the pre-fix
"analysis_" read from the CSV files containing compiled data in
thedata > compiledsub-folder to perform analyses and create
figures
Folder contents
Folder: data > raw
Description: Contains raw data CSV files (data collected from the
field).
Contents:
data_raw_bee_floral_hosts_2013_2022.csvdata_raw_floral_abundance_2013_2022.csvdata_raw_hobo_temperature_2013_2022.csvdata_raw_longterm_climate_1975_2022.csvdata_raw_longterm_floral_abunbdance_1976_2022.csvdata_raw_prism_climate_2013_2022.csvdata_raw_site_coordinates.csvdata_raw_trap_nest_occupancy_2013_2022.csv
Folder: data > compiled
Description: Contains compiled CSV files (e.g. total numbers of brood
cells per individual bee, maximum floral density, average climate
conditions, combined across datasets).
Contents:
compiled_bees_flowers_climate_2013_2022.csvcompiled_flowers_climate_1976_2022.csvcompiled_flowers_climate_2013_2022.csv
Folder: scripts
Description: Contains R scripts that compile the raw data, perform
various analyses, and generate figures
Contents:
data_compilation.R- This script: (1) reads in raw data from
data > raw, performs calculations (e.g., totals, averages), and
combines data across different files, and (2) writes compiled data
in CSVs to thedata > compiledfolder to be used in analysisanalysis_bees_vs_climate_flowers.R- Runs models to test
relationship between bee reproductive output, climate and floral
abundance at the the 7 study sites from 2013 - 2022 using negative
binomial regression models and structural equation models. Generate
figures.analysis_flowers_vs_climate.R- Runs models to test relationship
between floral host abundance of the three floral groups and climate
at the the 7 study sites from 2013 - 2022. Generates figures.analysis_longterm_climate trends.R- Generates descriptive results
to characterize intensity of drought by comparing conditions during
the focal study period (2013-2022) to long-term averages.analysis_longterm_flowers_vs_climate.R- Runs models to test
relationship between floral host abundance of the three floral
groups and climate at the the long-term study site. Generates
figures.
Metadata: raw data files:
File: data > raw > data_raw_bee_floral_hosts_2013_2022.csv
Description: List of plant taxa (floral hosts) found in each floral
group. A floral group contains all the plant taxa each bee species in
the study was observed to provision their nest with during the study.
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| iridis | character | 0 | NA | NA | List of floral host taxa in the plant tribe Fabeae (family: Fabaceae) used by Osmia iridis that are found at the seven study sites |
| asterSpp | character | 0 | NA | NA | List of floral host taxa in the plant family Asteraceae used by Osmia coloradensis, O. montana, and O. subaustralis (aster specialists) that are found at the seven study sites |
| tristella | character | 0 | NA | NA | List of floral host taxa used by Osmia tristella that are found at the seven study sites |
File: data > raw > data_raw_floral_abundance_2013_2022.csv
Description: Floral survey data from the seven study sites from
2013 - 2022.
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| year | numeric | 0 | 2013 to 2022 | YYYY | Year of survey |
| site | character | 0 | BC, FT, MC, RP, VB, KP, KC | BC = Brush Creek, FT = 401 Trail, MC = Mount Crested Butte, RP = Rosy Point, VB = Virginia Basin, KC = Kebler Clearing, KP = Kebler Pass | Site of survey (two-character code for site name) |
| date | Date | 0 | 2013-06-10 to 2022-08-08 | YYYY-MM-DD | Date of survey |
| day.of.year | numeric | 0 | 133 to 237 | NA | Day of year of survey |
| sampling.occasion | numeric | 0 | 1 to 23 | NA | Survey number |
| plant.taxon | character | 0 | various | NA | Plant taxon surveyed (typically individual species or genera, but sometimes groups of related genera with indistinguishable pollen) |
| family | character | 0 | various | NA | Plant family |
| floral.units.counted | character | 0 | various | NA | Floral unit counted; for some taxa, individual flowers were counted (e.g., Lathyrus lanszwertii); for others, the number of capitula with at least 1 open disc floret were counted (e.g. Helianthella quinquenervis) |
| distance.to.first. 100.units.m | numeric | 10915 | 0.1 to 180 | metres | Straight-line distance from the site centre to the 100th floral unit counted; the distance (r) to the 100th flower was measured so that floral density could be calculated as 100/πr^2. Occasionally, observers walked further than a 100 m distance from the site centre. NAs recorded when fewer than 100 flowers were found within a 100 m radius of the site centre |
| number.of.units. counted.if.fewer. than.100 | numeric | 18439 | 1 to 99 | NA | If fewer than 100 flowers of a taxon were encountered within a 100 m radius, its floral density was considered to be 0 (floral density would be near-negligible within a 100 m radius); however, the number of units counted was still recorded. The number of units were not recorded if 100 units were counted before 100 metres reached; NA recorded for these cases. |
| notes | character | 15724 | NA | NA | Field notes; NA if no field notes recorded |
| area.surveyed.m2 | numeric | 12423 | 0.03 to 101787.60 | square metres | Area surveyed (πr^2), where r is the distance to the 100th flower; if fewer than 100 flowers were counted within a 100 m radius of the site centre, the distance was not measured, and the cell was filled in with NA |
| density.no.per.m2 | numeric | 0 | 0 to 3183 | flowers per square metre | Density of floral units within a 100 m radius of the site centre given by 100/πr^2, where r is the distance to the 100th flower |
| flowers.counted.by | character | 13419 | Initials of the individual who counted the floral units (list of names in the supplementary); NA when observer did not initial |
File: data > raw > data_raw_hobo_temperature_2013_2022.csv
Description: Hourly temperature data at each site for the seven
study sites from 2013 - 2022
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| year | numeric | 0 | 2013 to 2022 | YYYY | Year of temperature record |
| site | character | 0 | BC, FT, MC, RP, VB, KP, KC | BC = Brush Creek, FT = 401 Trail, MC = Mount Crested Butte, RP = Rosy Point, VB = Virginia Basin, KC = Kebler Clearing, KP = Kebler Pass | Site of temperature record (two-character code for site name) |
| date | date | 0 | 2013-05-29 to 2022-12-31 | YYYY-MM-DD | Date of temperature record |
| month | numeric | 0 | 1 to 12 | NA | Month of temperature record |
| day | numeric | 0 | 1 to 31 | NA | Day of tempreature record |
| doy | numeric | 0 | 1 to 366 | NA | Day of year of temperature record |
| time | hms | 0 | 00:00 to 23:00 | HH:MM | Time of temperature record |
| temperature.C | numeric | 83071 | -29.756 to 49.225 | °C | Temperature in degrees Celsius. NAs reflect days or hours during which there was no record. These were retained in the file as placeholders for records to be filled using imputed PRISM data. |
File: data > raw > data_raw_longterm_climate_1975_2022.csv
Description: Monthly climate data (temperature and precipitation)
for the Rocky Mountain Biological Laboratory (RMBL) from 1975 - 2022.
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| year | numeric | 0 | 1975 to 2022 | YYYY | Year of observation |
| month | numeric | 0 | 1 to 12 | NA | Month of observation |
| rmbl.precipitation.mm | numeric | 0 | 0 to 307.34 | millimeters | Cumulative precipitation for each month . This column corresponds to the column "precip.mm.cb.bb" from the file RMBL-weather-months-1975-2022.csv compiled by Rebecca Prather in the data paper "Climate data from the Rocky Mountain Biological Laboratory (1975-2022)"; DOI: https://doi.org/10.17605/OSF.IO/8EZKA |
| rmbl.mean.temp.C | numeric | 0 | -17 to 16.3 | °C | Monthly average temperature. This column corresponds to the column "mean.temp.C.cb" from the file RMBL-weather-months-1975-2022.csv compiled by Rebecca Prather in the data paper "Climate data from the Rocky Mountain Biological Laboratory (1975-2022)"; DOI: https://doi.org/10.17605/OSF.IO/8EZKA |
| rmbl.min.temp.C | numeric | 0 | -27.45 to 6.29 | °C | Monthly minimum temperature. This column corresponds to the column "mean.temp.C.cb" from the file RMBL-weather-months-1975-2022.csv compiled by Rebecca Prather in the data paper "Climate data from the Rocky Mountain Biological Laboratory (1975-2022)"; DOI: https://doi.org/10.17605/OSF.IO/8EZKA |
| rmbl.max.temp.C | numeric | 0 | -7.92 to 27.49 | °C | Monthly maximum temperature. This column corresponds to the column "mean.temp.C.cb" from the file RMBL-weather-months-1975-2022.csv compiled by Rebecca Prather in the data paper "Climate data from the Rocky Mountain Biological Laboratory (1975-2022)"; DOI: https://doi.org/10.17605/OSF.IO/8EZKA |
File: data > raw > data_raw_longterm_floral_abundance_1976_2022.csv
Description: Floral survey data from the RMBL from 1976 - 2022.
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| year | numeric | 0 | 1976 to 2022 | YYYY | Year of survey |
| floral.group | character | 0 | fabeae, aster, generalist | NA | Floral group corresponding to floral hosts of focal bee species |
| number.plots.censused | numeric | 0 | 409 to 2142 | NA | Total number of 2 m x 2 m plots censused for the given year. Further details documented in the Public Project "Metadata file for David Inouye’s database on flowering phenology at the Rocky Mountain Biological Laboratory". DOI: https://doi.org/10.17605/OSF.IO/P9VUJ |
| floral.count | numeric | 0 | 28 to 81874 | NA | Number of floral units counted. Further details documented in the Public Project "Metadata file for David Inouye’s database on flowering phenology at the Rocky Mountain Biological Laboratory". DOI: https://doi.org/10.17605/OSF.IO/P9VUJ |
File: data > raw > data_raw_prism_climate_2013_2022.csv
Description: Daily temperature and precipitation data obtained from
the PRISM Group at Oregon State University.
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| year | numeric | 0 | 2011 to 2022 | YYYY | Year of record |
| site | character | 0 | BC, FT, MC, RP, VB, KP, KC | BC = Brush Creek, FT = 401 Trail, MC = Mount Crested Butte, RP = Rosy Point, VB = Virginia Basin, KC = Kebler Clearing, KP = Kebler Pass | Site of record (two-character code for site name) |
| date | date | 0 | 2011-01-01 to 2022-12-31 | YYYY-MM-DD | Date of record |
| month | numeric | 0 | 1 to 12 | NA | Month of record |
| doy | numeric | 0 | 1 to 366 | NA | Day of year of record |
| prism.precipitation.mm | numeric | 0 | 0 to 63.88 | millimeters | Cumulative precipitation for each day |
| prism.mean.temp.C | numeric | 0 | -26.4 to 18.8 | °C | Daily mean temperature |
| prism.min.temp.C | numeric | 0 | -35.3 to 11 | °C | Daily minimum temperature |
| prism.max.temp.C | numeric | 0 | -18.7 to 29.9 | °C | Daily maximum temperature |
File: data > raw > data_raw_site_coordinates.csv
Description: Latitude and longitude of each of the seven study
sites.
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| site | character | 0 | BC, FT, MC, RP, VB, KP, KC | BC = Brush Creek, FT = 401 Trail, MC = Mount Crested Butte, RP = Rosy Point, VB = Virginia Basin, KC = Kebler Clearing, KP = Kebler Pass | Name of site (two-character code for site name) |
| latitude | numeric | 0 | 38.853 to 38.977 | Degrees of latitude | Latitude of site centre |
| longitude | numeric | 0 | -107.101 to -106.92 | Degrees of longitude | Longitude of site centre |
File: data > raw > data_raw_trap_nest_occupancy_2013_2022.csv
Description: Nesting activity (brood cell production) of
cavity-nesting bees at the seven study sites from 2013 - 2022.
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| year | numeric | 0 | 2013 to 2022 | YYYY | Year of observation |
| site | character | 0 | BC, FT, KC, KP, MC, RP, VB | BC = Brush Creek, FT = 401 Trail, MC = Mount Crested Butte, RP = Rosy Point, VB = Virginia Basin, KC = Kebler Clearing, KP = Kebler Pass | Site of observation (two-character code for site name) |
| current.date | character | 0 | 2013-06-09 to 2022-08-08 | YYYY-MM-DD | Date of observation of the nest |
| previous.date | character | 1 | 2013-06-03 to 2022-08-02 | YYYY-MM-DD | Date of last observation of the nest. NA reflects a scenario where nesting was observed on the first day of the field season and there was no previous date. |
| nest.id | character | 0 | NA | NA | Five- to six-character code for the nest cavity consisting of the code for the site name, the trap-nest letter and cavity number. E.g. BC-I3 is a nest at the site BC (Brush Creek), in trap-nest letter "I", in cavity number 3. Each site had 12 to 24 trap-nests which were assigned letter designations. Each trap-nest had 10 cavities. Note that nest identifications are re-used across years; e.g., the nest BC-I3 in 2013 is not the same nest as BC-I3 in 2015 |
| nest.diameter. mm | numeric | 0 | 4.5, 6.1, 8.2 | millimeters | Diameter of the nest cavity. Cavities were of three sizes |
| bee.genus | character | 0 | Osmia | NA | Nest occupant genus (all are Osmia) |
| bee.species | character | 0 | iridis, tristella, montana, coloradensis, subaustralis | NA | Nest occupant species |
| individual.id | character | 0 | NA | NA | Three-part code for the nesting female consisting of the code for the site name, the first three letters of the occupant species, and the colour of the paint mark. Note that individual IDs are re-used across years; e.g., the bee BC-tri-green in 2013 is not the same individual as the individual with the same individual ID in 2015. Osmia iridis individuals are coded as "?ir" in some years. Osmia tristella individuals are coded as "?tri" in some years. |
| cells.completed. since.last.date | numeric | 38 | -4.4 to 11.7 | NA | Number of brood cells completed since the last time the nest was checked estimated to the nearest 0.1 of a brood cell. Observers estimated cell progress based on their perception of the length of a full brood cell. A brood cell was not considered complete until an egg was laid or the cell was sealed with a wall. Negative values denote cases where nests were excavated by usurpers (other ) or predators (birds). NAs reflected cases where a brood cell count was not recorded because the occupant began nesting in a cavity with no straw. |
| mom.seen | character | 1152 | NA, y, n, ?, y (red), y (blue), y (yellow) | y = yes, n = no | Whether or not the nesting female was seen during the site visit. Not always recorded |
| field.notes | character | 1494 | NA | NA | Field notes; NA recorded if none |
| observer.initials | character | 259 | NA | NA | Initials of the observer who checked the nest; NA recorded if observer did not initial |
Metadata: compiled data files:
File: data > compiled > compiled_bees_flowers_climate_2013_2022.csv
Description: Total reproductive output (brood cell production) of
each individual bee, the highest density of their floral hosts observed
and climate conditions characterizing the year and site in which they
were observed
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| year | numeric | 0 | 2013 to 2022 | YYYY | Year of observation |
| site | character | 0 | BC, FT, MC, RP, VB, KC, KP | BC = Brush Creek, FT = 401 Trail, MC = Mount Crested Butte, RP = Rosy Point, VB = Virginia Basin, KC = Kebler Clearing, KP = Kebler Pass | Site of observation; (two-character code for site name) |
| bee.species | character | 0 | iridis, tristella, montana, coloradensis, subaustralis | NA | Nest occupant species |
| individual.id | character | 0 | NA | NA | Three-part code for the nesting female consisting of the code for the site name, the first three letters of the occupant species, and the colour of the paint mark. Note that individual IDs are re-used across years; e.g., the bee BC-tri-green in 2013 is not the same individual as the individual with the same individual ID in 2015. Osmia iridis individuals are coded as "?ir" in some years. Osmia tristella individuals are coded as "?tri" in some years. |
| total.cells | numeric | 0 | 0 to 63 | brood cells | Total number of brood cells constructed by the individual across all cavities they used |
| total.nests | numeric | 0 | 1 to 8 | nests | Total number of cavities used by the individual |
| first.day | numeric | 0 | 140 to 236 | day of year | The earliest survey date on which the individual was observed nesting |
| floral.group | character | 0 | iri, tri, ast | NA | Floral group of the occupant |
| max.floral.density | numeric | 0 | 0.34 to 3200.6 | flowers per metre square | Maximum density of flowers in the floral group of the nesting individual in the year and at the site in which they were nesting |
| wateryear. precipitation.mm | numeric | 0 | 459.92 to 1395.97 | millimeters | Cumulative precipitation for the year and at the site in which the individual was observed nesting. A water-year covers the period between September 1 of the previous year to August 31 of the current year. |
| summer. precipitation.mm | numeric | 0 | 105.06 to 440.71 | millimeters | Cumulative precipitation from May to August in the year and at the site in which the individual was observed nesting |
| summer. temperature.C | numeric | 0 | 7.15 to 14.34 | °C | Average temperature from May to August in the year and at the site in which the individual was observed nesting |
| spei.12mo.aug | numeric | 0 | -1.63 to 1.71 | NA | 12-month Standardized Precipitation-Evapotranspiration Index ending in August for the year and site in which the individual was observed. Values were multiplied by -1 such that higher values indicate hot and dry conditions; lower values indicate cool and wet conditions. |
| spei.4mo.aug | numeric | 0 | -2.03 to 1.78 | NA | 4-month Standardized Precipitation-Evapotranspiration Index ending in August for the year and site in which the individual was observed. Values were multiplied by -1 such that higher values indicate hot and dry conditions; lower values indicate cool and wet conditions. |
File: data > compiled > compiled_flowers_climate_1976_2022.csv
Description: Total floral densities for each floral group and
climate conditions in each year at the long-term study site.
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| year | numeric | 0 | 1976 to 2022 | YYYY | Year of observation |
| floral.group | character | 0 | fabeae, aster, generalist | NA | Floral group |
| number.plots. censused | numeric | 0 | 409 to 2142 | plots | Total number of 2 m x 2 m plots censused for the given year. Further details documented in the Public Project "Metadata file for David Inouye’s database on flowering phenology at the Rocky Mountain Biological Laboratory". DOI: https://doi.org/10.17605/OSF.IO/P9VUJ |
| floral.count | numeric | 0 | 28 to 81874 | number of units | Number of floral units counted. Further details documented in the Public Project "Metadata file for David Inouye’s database on flowering phenology at the Rocky Mountain Biological Laboratory". DOI: https://doi.org/10.17605/OSF.IO/P9VUJ |
| total.floral.density | numeric | 0 | 0 to 9.75 | flowers per metre square | Density of flowers; the total number of floral units counted for each floral group in each year was summed and divided by the area surveyed in that year (i.e. number.plots.censused * 4 m^2) |
| wateryear. precipitation.mm | numeric | 0 | 440.87 to 1247.64 | millimeters | Cumulative precipitation for the given year and site from September 1 of the previous year to August 31 of the current year |
| summer. temperature.C | numeric | 0 | -0.1 to 2.8 | NA | Average temperature from May 1 to August 31 for the given year and site |
| spei.12mo.aug | numeric | 0 | -2.27 to 1.84 | NA | 12-month Standardized Precipitation-Evapotranspiration Index ending in August for the given year and site. Values were multiplied by -1 such that higher values indicate hot and dry conditions; lower values indicate cool and wet conditions. |
File: data > compiled > compiled_flowers_climate_2013_2022.csv
Description: Total floral densities for each floral group and
climate conditions in each year at the seven study sites.
| column | variable type | number of NAs | range or possible values | units, formats, abbreviations | description |
|---|---|---|---|---|---|
| year | numeric | 0 | 2013 to 2022 | YYYY | Year of observation |
| site | character | 0 | BC, FT, MC, RP, VB, KC, KP | BC = Brush Creek, FT = 401 Trail, MC = Mount Crested Butte, RP = Rosy Point, VB = Virginia Basin, KC = Kebler Clearing, KP = Kebler Pass | Site of survey (two-character code for site name) |
| floral.group | character | 0 | iri, ast, tri | Floral group | |
| max.floral.density | numeric | 0 | 0.34 to 3200.6 | flowers per metre square | Maximum density of flowers in the floral group of the nesting individual in the year and at the site in which they were nesting |
| wateryear. precipitation.mm | numeric | 0 | 459.92 to 1395.97 | millimeters | Cumulative precipitation for the given year and site. A water-year covers the period between September 1 of the previous year to August 31 of the current year. |
| summer. temperature.C | numeric | 0 | 7.15 to 14.34 | °C | Average temperature from May 1 to August 31 for the given year and site |
| spei.12mo.aug | numeric | 0 | -1.63 to 1.71 | NA | 12-month Standardized Precipitation-Evapotranspiration Index ending in August for the given year and site. Values were multiplied by -1 such that higher values indicate hot and dry conditions; lower values indicate cool and wet conditions. |